Jobs

Jobs in Bioinformatics, Genomics and Life Science

Job Alerts in this week (January , 2020)


Update on January 20, 2020


Postdoctoral Fellow in Computational Genomics

The Ye lab at UCSF is seeking a highly motivated and creative postdoctoral fellow to develop and apply cutting-edge statistical and machine learning approaches to the analysis of high dimensional, population scale single cell sequencing datasets. The scientific goals of this research include the discovery of new diagnostic and therapeutic modalities for autoimmunity, revealing the genetic architecture of gene expression in humans, and mapping the transcriptional circuitry that govern immune cell recognition, interaction and functionalization.

Fellows must possess a PhD (or equivalent) in statistical genetics, computational biology, or other relevant quantitative disciplines (computer science, physics and math preferred). Track record of creative and impactful scientific contributions (first author publications) and two or more years of experience analyzing genomic data is required. One or more years of experience in either immunology or molecular biology is preferred.

Qualifications:
▪ PhD in bioinformatics, computer science, computational biology, physics, mathematics, statistical genetics or relevant field.
▪ Demonstrated previous research experiences through at least one first-author publication.
▪ Proficiency in programming (C/C++), scripting (perl/python) and statistical analysis®.
▪ Strong verbal and written communication skills.
▪ Able to work independently and collaboratively as a member of an interdisciplinary team.
▪ Ability to multitask and manage large, complex projects involving multiple collaborators.
▪ 2+ years of experience analyzing genomic datasets.

Please send your CV, a letter of research interest and a list of three references per email to Dr. Jimmie Ye (jimmie.ye@ucsf.edu).

For details click here


Postdoctoral position in clinical proteomics

Given the epidemiological forecast and the failure of clinical treatments, there is a clear need to detect Alzheimer’s disease (AD) in the preclinical phase to prevent or delay its further development. Nowadays, AD diagnosis relies on a combination of biomarkers obtained from imaging and on the levels of tau and Aβ peptides in cerebrospinal fluid. Blood biomarkers as first screening tools are of high interest as these are cost- and time-effective, obtained in a minimally invasive manner and allow for repeated sampling (e.g., to monitor disease evolution).

Candidates should hold a doctoral degree in life sciences and are junior postdoctoral researchers with a proven track record in applying mass spectrometric techniques, preferentially in biomedical/clinical settings. Candidates must have been involved in all aspects of contemporary proteomics, including sample preparation, analysis by means of mass spectrometry and bioinformatics to identify and quantify proteins. Excellent knowledge of the English language is a prerequisite.

Eligible candidates with excellent grades/an excellent CV will be strongly encouraged to apply for their own fellowships once they started to work in the Gevaert lab. Candidates with a track record in using proteomics for the identification of disease biomarkers and/or the study of neurodegenerative diseases are strongly encouraged to apply. Experience with data-independent analyses is an asset, as is your motivation to get involved in teaching master-level students.

For details click here


Posted on January 17, 2020

Bioinformatician (m/f/d) - Proteomics & Metabolomics

The Max Planck Institute for Terrestrial Microbiology (MPIterMic) is a leading institution in microbiological research. The MPIterMic consists of four departments and several department-independent research groups with approximately 280 people from more than 30 nations working at the institute. The daily language in the institute is English. The institute has established state-of-the art proteomics and metabolomics platforms that develop and integrate cutting-edge mass spectrometric (MS) technology. In order to further advance the technological possibilities, we invite applications for a full time Bioinformatician (m/f/d) to fill the data analysis / bioinformatics branch of the MS-Core.

You will become part of a team that drives the development of proteomics, metabolomics and bioinformatics solutions to realize quantitative investigations of (micro)biological systems. As the MS-Core provides a wide range of targeted and untargeted/global quantitative workflows, your main responsibility will be the analysis and visualization of qualitative and quantitative data sets. You will also organize all data analysis/bioinformatic activities within the MS-Core including active participation in educational activities covering supervision of staff members, scientists and students. Further responsibilities are the support, maintenance and development of the IT infrastructure of the two facilities in collaboration with the local IT unit.

Applicants should have a degree (ideally PhD) in a life science or computational discipline. Strong computational and programming skills are essential in addition to advanced theoretical and practical experience in the statistical evaluation of biological data sets. We seek a good communicator who is able to interact with scientists from a variety of backgrounds, is team-oriented and enjoys working in a highly collaborative and fast paced and evolving research environment.

Application deadline is 31st March 2020.

For details click here


Scientist , Computational Biology

Since 2006, 23andMe’s mission has been to help people access, understand, and benefit from the human genome. We are a group of passionate individuals pushing the boundaries of what’s possible to help turn genetic insight into better health and personal understanding. 23andMe's Therapeutics team is committed to discovering and developing new therapies that can offer significant benefits for patients. This dedicated research and development group in South San Francisco identifies novel targets using 23andMe's genetic database and performs preclinical research to advance programs for disease areas with high unmet need.

We are looking for a quantitative scientist with experience and expertise in using AI/ML approaches to model complex data. 23andMe has the world’s largest cohort of phenotypes and genotypes. Your role will be to work with our team of computational biologists and geneticists to help guide the use of AI/ML technologies to support drug discovery. Areas of application involve: predictive models of genetic risk for various diseases and traits, phenotype imputation, highly multivariate regression modeling, application of methods such as Gaussian processes to longitudinal data, as well as high dimensional clustering approaches to assess complex diseases.

For details click here


Postdoc Computational Biology

Human cells perform highly complex tasks but the map of cellular regulation that controls these processes is surprisingly poorly known. In diseases, these processes are disturbed and targeted interference is required to rebalance disease. Such interference can only result in effective disease eradication with minimal side effects when the map of cellular regulation is known in sufficient detail. We will employ Phenosaurus, a large collection of ~130 genome-wide haploid screens and advanced computational inference to reconstruct this map. Phenosaurus is a genotype to phenotype map that contains the strength of association between every gene and 130 quantitative protein readouts in haploid human cells. We envisage charting the regulatory map using two approaches. First, we will identify functional units.

You will research and benchmark the latest algorithms, develop new algorithms and help design validation and follow-up experiments. You will be working closely with fellow computational scientists of the Wessels group (ccb.nki.nl) experimentalists in the Brummelkamp group and scientists of Scenic Biotech BV (scenicbiotech.com) a biotech startup. You will be part of the Netherlands Cancer Institute (NKI), a world-class cancer research institute residing under the same roof as the Antoni van Leeuwenhoek cancer hospital in the vibrant city of Amsterdam.

Your skills and characteristics

 

  • a degree or advanced skills in bioinformatics, or a related discipline
  • a degree or a high level of proficiency in (molecular) biology
  • proficiency in R, Python and data base management
  • experience in interacting with molecular biologists
  • highly motivated

Please send applications by email to Lodewyk Wessels (l.wessels@nki.nl) and use ‘#application #postdoc’ in the subject line. Include a CV, motivation letter and the names and contact information of at least two references in your application.

For details click here


Posted on January 15, 2020

Bioinformatician

The Oklahoma Medical Research Foundation (OMRF) is an independent, not-for-profit, biomedical research institute adjacent to the campus of the University of Oklahoma Health Sciences Center (OUHSC) located in Oklahoma City. OMRF investigators have internationally recognized expertise in Autoimmunity, Immunology, Genetics, Aging, Cardiovascular Disease, and Cancer. Our Autoimmune Disease Institute (ADI) houses Centers of Excellence and specialty research clinics for Rheumatic Diseases (focusing on Lupus, Rheumatoid Arthritis, UCTD, and Sjogren’s) and for Multiple Sclerosis and related diseases. In addition to following over 4,000 patients with these conditions, teams of basic and clinical investigators conduct extensive clinical, translational and mechanistic research using samples obtained from these large clinical programs. Investigators at OMRF enjoy close scientific interactions with OUHSC faculty and participate in OUHSC graduate programs.

Our Translational Informatics group is seeking a bioinformatician to support both our clinical and basic research programs in autoimmune disease. Projects will include quality control, basic and Machine Learning analytic approaches to interpret single cell technology data from a wide range of technologies in the ADI. Technologies include but are not limited to single cell transcriptomics, single cell proteomics, spatial transcriptomics, inclusion of genetic variant information in eQTL analyses and highly multiplexed imaging technologies data including cell-distance and cell-pairing interation analyses. Systems in the division include 10X Genomics (scRNA-Seq, T-B repertoire, snATAC-Seq, Total-Seq, spatial transcriptomics), Fluidigm Helios and Hyperion mass cytometry/mass imaging, Zellkraftwerks ChipCytometry systems.

Ph.D. in Bioinformatics, Math, Statistics, Biostatistics, Computer Science, MIS, or relevant field. Experience with analysis of single cell data analysis pipelines, including single cell transcriptomic/cell-hashing/Total-Seq and CytoBank (Mass Cytometry/Helios CyTOF, multispectral cytometry) and tissue-based analytics (Hyperion/imaging mass cytometry, ChipCytometry a plus. Consultative experience would be beneficial. Programming experience (Python, R) is a plus.

Posting Number 000145

For details click here


Posted on January 13, 2020

Postdoctoral Associate (Bioinformatics)

The Terskikh laboratory has a Postdoctoral Associate opening. This position focuses on the novel approach to study epigenetics at a single cell level. The Postdoc Associate will explore the capability of Microscopic Imaging of Epigenetic Landscape (MIEL) and fluorescence-based reporters enabling live imaging of epigenetic modifications at a single cell level. MIEL combines fluorescence detection of epigenetic marks with automated cell imaging and machine learning to profile and quantify the “epigenetic signatures” of individual cells. They will investigate the epigenetic heterogeneity at the single cell level and the asymmetry during stem cell division in normal neurogenesis and in brain tumors. One of the long-standing question of this project is to determine whether the outcome of stem cell division is stochastic or deterministic and whether such outcome could be predicted based on the epigenetic signature of the mother cell.

Duties and Responsibilities

  • Independently design and perform experiments and procedures with high degree of complexity, demonstrating increasing expertise with a wide range of techniques
  • Demonstrate flexibility in adapting methods and skills according to evolving project priorities
  • Provide independent experimental design and planning
  • Be able to analyze and interpret data from different sources and draw relevant conclusions
  • Demonstrate knowledge in relevant specialized disciplines
  • Be able to present results at internal and external meetings
  • Accurately document experiments
  • Contribute to writing of reports and manuscripts with increasing responsibility over time
  • Work collaboratively across lab functions and train other junior lab staff as needed

Required Experience

  • Ph.D. degree in any discipline of Biological Sciences is required
  • The qualified candidate must have proven experience in one or more of the following areas:  Tissue culture, cell and molecular biology, fluorescent microscopy, and computational biology
  • Experience with transgenic mice model is highly desirable

For details click here


Genomics Scientist

The purpose of this position is to manage ongoing Genomics and bioinformatics research and provide genomics services to internal and external clients in the genomics Core. This position is necessary to provide comprehensive assistance with the design and implementation of experiments, technical assistance with advanced equipment and methods, computational and statistical analysis, and results reporting for SMHS faculty, staff, and students, as well as outside collaborating entities.

 

  • Manage Genomics Core Laboratory Functions
  • Manage, design, execute, and analyze data of genomics and transcriptomics projects on behalf of the Core in consultation with investigators.
  • Perform and analyst single-cell sequencing (scRNA-seq, scATAC-seq, etc.).
  • Keep track of multiple sets of samples or data from multiple customers, organizing work-flow for the Core to optimize turn-around time and quality.
  • Troubleshoot assays or data analyses as required when results prove unsatisfactory.
  • Conduct quality control procedures for Core operations as directed by the Core Director.
  • Execute Next-generation sequencing procedures including quality control of samples provided by investigators pre- and post-sequencing.

Minimum Requirements:

  • B.S. in Biology , Life Sciences, Computer Sciences, Mathematics, Chemistry, agriculture or other related field.
  • 2 or more years of experience in either a dry or wet lab.
  • Evidence of independent research in form of co-authored peer-reviewed publications or experience in working in a core facility environment.
  • Experience with MS Office software (Word, Excel and PowerPoint).
  • Experience with Linux, R, python, or equivalent.
  • Successful completion of Criminal History Background Check.

For details click here


 

Posted on January 10, 2020

Post Doctoral Position in HIV Vaccine Research / Computational Vaccinology

The research group of Prof. Alexandra Trkola is based at the Institute of Medical Virology, University of Zurich, Switzerland. The main focus of the group is on defining processes that lead to broadly neutralizing antibody (bnAb) responses in HIV-1 infection to enable the design of bnAb based vaccines. Investigating bnAb activity alongside viral, immunological and genetic factors in large cohorts of HIV-1 infected individuals, we generate comprehensive data sets that allow unraveling parameters and predictive biomarkers of bnAb induction. Our research is highly translational and feeds on close collaborations with clinicians (group Prof. Huldrych Günthard, University Hospital Zurich) and experts in mathematical modeling and biostatistics (group Prof. Roger Kouyos, University Hospital Zurich).

Your responsibilities :

The candidate will develop, apply and optimize cutting-edge bioinformatics and machine learning methods to further our understanding of HIV-1 bnAb induction. Development of computational methods using deep learning will be used to identify predictive biomarkers and factors directly involved in bnAb induction. A large emphasis of the work will be on deciphering genetic fingerprints of the HIV-1 envelope gene that are linked with bnAb induction to foster the development of effective immunogens.

Your profile :

You should have a strong background in computer science, biostatistics, bioinformatics, computational biology or related disciplines and be versed in biology and genomics. Excellent proficiency in R, data base management and profound experience in analysis of complex data are required. You enjoy working in an inter-disciplinary team. You have excellent presentation and English language skills, and are experienced in writing scientific papers.

Please submit your application by January 20, 2020.

For details click here


Computational Biologist I - Microbiome

The Xavier lab is looking for a Research Scientist in Computational Biology to investigate the mechanisms of host microbiome interactions in health and disease. We are an interdisciplinary group with expertise in computational analysis, microbiology and immunology. The candidate for this project will be responsible for computational analysis of large multi-‘omic datasets with the goal of identifying microbes, genes or microbial products that are relevant to human health. The ideal candidate should be broadly experienced with analyzing next generation sequencing data and will collaborate closely with other computational postdocs for methods implementation, and with experimental team members for validation of computational results. Prospective applicants should have made significant contributions to their area of study, as evidenced by a strong publication record. We are seeking creative and highly motivated individuals who want to work in a dynamic, multi-disciplinary research environment.

Qualified candidates should have:

  • Ph.D. in Computational Biology, Bioinformatics, or a related field
  • 1-2 years postdoctoral experience in computational biology preferred
  • Proficiency in one or more statistical or scripting languages appropriate for scalable data analysis
  • Familiarity with functional genetic and/or genomic data, as indicated by publication record
  • Ability to clearly communicate scientific material and work collaboratively

For details click here


Posted on January 08, 2020

Post-doctoral Computational Biology (Research)

Cold Spring Harbor Laboratory invites applications to fill multiple computational post-doctoral positions in the laboratory of Dr. Jesse Gillis and colleagues. The successful candidates will join a team at CSHL working to understand the molecular and functional basis of cellular properties in diverse systems, including mammalian brains. This is a largescale project involving a number of complementary positions, ranging from bioinformatics, to neuroscience, to molecular genetics. While the position is solely computational, all projects involve substantial collaboration with wet-lab researchers generating unique data. This interdisciplinary work offers opportunities to address important questions in computational biology and molecular genetic with first access to large novel data sets from single-cell RNA-seq. The expected duration of the position is approximately 3-5 years with renewal at the end of each year.

This research sits at the intersection of Computational biology and molecular genetics. A strong candidate would have expertise in one of these areas and an interest in learning about the other. While a broad range of backgrounds are suitable for this position, a PhD in bioinformatics or computational biology is desirable. A particular focus of our methodological research is replicability and meta-analysis and an interest in these areas is helpful. Experience with either Matlab or R is a plus. Exceptional applicants without a formal computational background will also be considered, particularly if they are familiar with standard bioinformatics tools.

Please include a letter of interest outlining your research accomplishments and include the contact information of three references. Applications can be sent directly to JGillis@cshl.edu.


Postdoc in Computational Biology/Bioinformatics

KTH Royal Institute of Technology in Stockholm has grown to become one of Europe’s leading technical and engineering universities, as well as a key centre of intellectual talent and innovation. We are Sweden’s largest technical research and learning institution and home to students, researchers and faculty from around the world. Our research and education covers a wide area including natural sciences and all branches of engineering, as well as architecture, industrial management, urban planning, history and philosophy.

These projects are concerned with applications of computational methods to cancer omics data. Some of the cancer data has a single-cell resolution and some carries spatial information. The bacterial data consist of an extensive collection of NGS genomes. We are collaborating with groups developing new experimental methods as well as generating biomedical data.

Qualifications

Requirements

A doctoral degree or an equivalent foreign degree, obtained within the last three years prior to the application deadline.

You need a very strong background in bioinformatics analysis of biological data. Excellent programming skills are a requirement. A good understanding of Biology is clear merit, but a basic knowledge and a desire to contribute to biology is a prerequisite.

Reference number J-2019-3134

Last application date 31.Jan.2020 11:59 PM CET

For details click here


Posted on January 06, 2020

Postdoctoral Associate in Bioinformatics

The O’Donnell-Luria lab is a new research team based within the Division and Genetics and Genomics at Boston Children’s Hospital and closely affiliated with the Program in Medical and Population Genetics at the Broad Institute of MIT and Harvard and the Analytic and Translational Genetics Unit (ATGU) at Massachusetts General Hospital. The successful candidate will become a part of the Broad Institute and Harvard Medical School communities. You will work with clinical geneticists, computational biologists, software engineers, genomic analysts and others in a unique and collaborative intellectual environment, and have access to new informatic and experimental technologies being developed in the world’s leading center for human genomics.

We are looking for talented and motivated individuals for additional training in a postdoctoral associate position to develop projects to improve rare disease diagnosis and gene discovery. Possible areas of future projects include new methods for variant detection and interpretation, evaluating the impact of unannotated (novel) human genes or DNA methylation in Mendelian diagnosis.

Qualifications

  • PhD in Computer Science, Bioinformatics, Mathematics, Statistics, Genetics or another relevant field or MD with residency in human genetics

  • Comfortable applying relevant statistical methods

  • Demonstrated attention to detail and analytical skills

  • Strong publication record and outstanding written and oral English communication skills

  • Independent, creative, highly-motivated, highly collaborative, and flexible team member

  • Familiarity with genomic data, tools and databases and experience analyzing rare disease datasets and variant interpretation advantageous

  • Programming experience in Python, R, Unix and/or cloud computing are strongly advantageous

For details click here


Postdoctoral Associate in Bioinformatics

Howard Hughes Medical Institute (HHMI) is an independent, ever-evolving philanthropy that supports basic biomedical scientists and educators with the potential for transformative impact. We make long-term investments in people, not just projects, because we believe in the power of individuals to make breakthroughs over time. HHMI scientists have radically advanced the understanding of cells, the brain, the immune system, the development of organs, and how to treat many diseases. Founded in 1953 by aviator and industrialist Howard R. Hughes, HHMI is headquartered in Chevy Chase, Maryland, and employs more than 2,500 people across the U.S.

We are currently seeking a self-motived and enthusiastic Postdoctoral Associate within the lab of Dr. Evgeny Nudler at NYU School of Medicine in New York, NY. Working in both prokaryotic and eukaryotic species, the lab investigates cellular stress responses with a special emphasis on damage sensing and repair. To learn more about the science of the lab, visit our website: http://nudlerlab.info/lab/ We are looking for ambitious, creative and hard-working candidates with a can-do spirit. Our lab especially encourages applications from candidates who enjoy performing both bench-work and analysis of large data-sets. We welcome applicants with expertisie in one or more of the following areas: molecular biology, bacterial genetics, synthetic biology, bioinformatics, biochemistry, and structural biology.

The candidate is expected to work both independently and as part of a collaborative team within the lab.  Academic development is a central feature of this role, and we will actively support the fellow’s professional growth through individual development plans, one-on-one mentoring, and professional skill development through workshops offered by our lab on NGS, proteomics, and data analysis – as well as by NYU’s postdoctoral training program.

Required Qualifications

  • PhD in molecular biology, Microbiology, Biochemistry, Bioinformatics, structural biology, or a related field
  • Basic coding and data analysis skills are a strong plus
  • Strong publication record is highly preferred

Tracking Code: 1145-908

For details click here


Posted on January 03, 2020

Postdoctoral Scientists and Staff Scientist (Computational Biology & Neurogenomics)

The Reitz Lab and Human Genetics Core at the Taub Institute for Research on the Aging Brain are recruiting multiple Postdoctoral Research Scientists and senior research scientists. The Reitz Lab generates and analyzes high-throughput multi-dimensional -omics data to study neurodegeneration and diseases of the central nervous system with emphasis on Alzheimer’s disease and related dementias. The ultimate goal is to understand the biology of these diseases, to define novel biomarkers, and to identify novel therapeutical targets. The Taub Institute for Research on the Aging Brain at Columbia University is a world-leader in research of neurodegenerative diseases and the nucleus of a dynamic, translational, multidisciplinary endeavor bringing together Columbia University researchers and clinicians to uncover the causes of Alzheimer’s, Parkinson’s and other age-related brain diseases.

We are seeking highly motivated researchers with strong analytical skills at both the PostDoc and staff scientist level to join our effort and generate novel insights of neurodegeneration using these unique datasets, while working in a highly dynamic multidisciplinary and collaborative environment. Dr. Reitz is well funded with several grants from the National Institute of Ageing.

Current research projects include the analyses of:

- GWAS, whole-exome and whole genome sequencing data of Neurodegenerative (ND) Disorders including blood, cerebrospinal fluid (CSF) and neuroimaging biomarkers

- Identification of rare genetic variants in large family-based and population-based whole-exome and whole-genome sequencing studies

- Brain transcriptomic analysis (RNA-seq)

- Plasma, CSF and Brain Proteomic analysis using Mendelian Randomization

- Identification of shared genetic architecture among neurodegenerative and other traits (Alzheimer’s, Parkinson and FTD)

Requirements

The successful applicant will hold, or shortly expects to obtain, a PhD qualification in Genetics, Bioinformatics, Computer science, Data science, Statistical Genomics or a related discipline involving the interrogation of ‘omics’ datasets. Hands-on experience with large-scale human genomic or other omics datasets is expected. The candidate would have solid skills in at least one programming language (R, python or perl) and experience working in Linux and/or high-performance cluster environments.

Interested candidates should send their cover letter and CV to Dr. Reitz (cr2101@cumc.columbia.edu).


Postdoctoral Research Fellow in Bioinformatics/Computational Biology

Overview

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

Responsibilities

Dr. Heng Li’s research group at Dana-Farber Cancer Institute (DFCI) and Harvard Medical School invites applicants for a bioinformatics/computation biology postdoctoral position. The general research theme is to tackle biological problems with advanced computational and statistical methods. The laboratory developed algorithms fundamental to the application of high-throughput sequence data, including sequence alignment (e.g. bwa and minimap2), sequence assembly (e.g. fermi, miniasm and wtdbg2), variant calling (e.g. samtools) and data query (e.g. tabix and bgt). The laboratory also studies species and human evolution (Mallick et al, Nature 2016 on SGDP), and analyzes single-cell sequencing data to investigate mutagenesis (e.g. Chen et al, Science 2017 on the LIANTI protocol), the 3D conformation of genomes (Tan et al, Science 2018 on dip-C) and the mosaicism between cells.

Qualifications

An ideal applicant should have:

  • A PhD in a quantitative field such as bioinformatics, computational biology, computer science, mathematics, physics or a related discipline.
  • Strong programming skills. Demonstrated experience in developing high-performance algorithms is beneficial.
  • Familiarity with analysis of large-scale genomic sequence data.
  • A strong track record of scientific publications.
  • Good oral and written communication skills in English.

Job ID 2020-17500

For details click here


Posted on January 01, 2020

Postdoctoral fellow in computational protein design

Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has 40 000 students and 7 600 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the human condition. The Faculty of Science conducts research and education within Biology, Astronomy, Physics, Geosciences, Chemistry, Mathematics and Environmental Sciences. The Faculty is organized into nine departments, gathered in the northern campus area. The Faculty has approximately 1500 students, 330 PhD students and 700 employees.

Workduties

The researcher should work on developing computational methods to design higher order protein assemblies such as protein capsids. The position is within an ERC project where the goal is to develop computational and experimental methods for de novo design of large protein assemblies using a geometric shape-based protein design paradigm. This is an opportunity to work with and learn state of the art computational protein design. The researcher will be tasked in computational method development for structure-based computational protein design. Custom-made programs will be developed for adapting geometric shape matching approaches to protein design and design algorithms will be developed in the Rosetta macromolecular modeling suite. The researcher will also work with the experimental members of the team that will be involved in experimental testing of computationally designed proteins. This may involve some assistance with supervision of PhD and master students.

Qualifications

  • Interest in protein design
  • PhD in computer science, bioinformatics, structural biology, biochemistry, biophysics, physical chemistry or similar not older than 3 years at the application deadline. Under special circumstances, the doctoral degree can have been completed earlier.
  • Experience of development of computation methods in molecular science backed up by scientific publications and/or publicly available code
  • Skilled programmer
  • Solid understanding of protein structure and interactions
  • Good collaborative skills, drive and independence
  • Publications in high-quality peer-reviewed scientific journals
  • Good written and oral skills in English.

For details click here


Two  Postdoctoral Researchers in bioinformatics

This is a unique collaborative project between the groups of Claudia Kutter (Karolinska Institute, KI) and Erik Sonnhammer (Stockholm University, SU) both located at SciLifeLab in Stockholm, Sweden. SciLifeLab is Sweden’s national center for large-scale (big data) life science research and one of the largest sequencing cluster in Europe. The applicant benefits from knowledge and expertise in both labs as well as professional training at SciLifeLab. The Kutter lab has a research focus on functional genomics, transcriptomics (including RNA binding proteins (RBPs) and their bound RNAs). The Sonnhammer group has extensive experience in inferring gene regulatory networks (GRNs) and has developed several new algorithms to improve the reliability of the GRNs inferred from perturbations.

The successful candidate should be highly motivated and have a Ph.D. in bioinformatics or related field, and good knowledge of molecular biology. Applicants who have not completed a doctorate at the end of the application period may also apply, providing that all requirements for a completed degree are met before the agreed date of employment. This must be substantiated by the applicant's main supervisor, director or equivalent. Alternatively, applicants with a Ph.D. in molecular biology or related fields who have 2 years of postdoctoral experience in bioinformatics and programming, documented by scientific publications are also encouraged to apply. Demonstrable familiarity with sequence and gene expression data analysis techniques is essential. Excellent skills in computer programming (primarily Matlab, Python, R) and UNIX are necessary merits.

Reference number 2-6505/2019

Last application date 31.Jan.2020 11:59 PM CET

For details click here


Posted on December 30, 2019

Bioinformatics Analyst

NYU School of Medicine is one of the nation’s top-ranked medical schools. For 175 years, NYU School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral part of NYU Langone Health, the School of Medicine at its core is committed to improving the human condition through medical education, scientific research, and direct patient care.

NYU Langone Health Medical Center, a world-class, patient-centered, integrated, academic medical center, and one of the nations premier centers for excellence in clinical care, biomedical research and medical education, is seeking highly motivated, enthusiastic individual to join the Applied Bioinformatics Laboratories (ABL). The successful candidate will be responsible for first tier genomics data analysis generated in ABL and supporting innovative cutting-edge research conducted by principal investigators at the NYU School of Medicine.

Job Responsibilities:

  • Assist in preparing concise presentations of computational results.
  • Work with bioinformatics team to integrate different types of genomics.
  • Adapt genomic data analysis pipelines in a rapidly evolving research environment.
  • Assist in the design, implementation and execution of customized pipelines for collaborative research projects.
  • Assist in the design, implementation, and execution standard pipelines for routine genomics data analyses.
  • Perform robust data quality control and validation.
  • Develop expertise in various types of sequencing data analysis (e.g. RNA-seq, scRNS-seq, ChlP-seq, sequencing of long reads).
  • Work closely with bench scientists to understand and help accomplish their research goals.
  • Other duties as assigned.

Minimum Qualifications:

To qualify you must have a B.S. in mathematics, biological sciences, computer science or related disciplines.

Experience in Unix/Linux systems including HPC environments.

Scripting languages: Python or Perl.

Statistical packages: R (preferred) or MATLAB

For details click here


Post Doctoral Researcher--Biomedical Engineering (Bioinformatics)

The Biomedical Engineering Department at USD (University of South Dakota) is seeking a strong candidate for a postdoctoral position to work on the Data Analysis with Predictive Modeling for bioscience and biomedical engineering. The candidate will work with the BiCBE (Bioinformatics and Computational Bioengineering) research group to develop new data mining and machine learning model for biomaterial and medical device discovery. The candidate will have ongoing projects in leveraging big data mining tools for the development and implementation of data analysis algorithms and workflows for bioengineering knowledge discovery, with application on animal and plant. The candidate will seek grant opportunities in the areas of Big Data analytics, bioinformatics, and medical applications, publish high quality research papers in peer-reviewed journals, as well as explore collaboration possibilities at USD and beyond.

The candidate should have data analytical skills with strong programming background in languages, including but not limited to Python, R and Java. The candidate should demonstrate good communication skills and an interest in working collaboratively across disciplines. USD Biomedical Engineering offers a competitive salary and an initial appointment of 12 to 24 months, starting as soon as possible. Extension of the postdoctoral position for up to 5 years is possible. Once employed, the postdoc researcher will participate in a number of workshops and receive proper career and scientific mentoring on grantsmanship, pedagogy, time management, research group management, science communications, and commercialization. The successful candidate will be expected to pursue research in the areas described above, with activities including interacting with experimental collaborators, setting up models, data analysis workflows, and other computational procedures, writing up and publishing results in peer-reviewed journals, presenting results at conferences and helping with developing new projects.

Candidates should have earned a Ph.D. in Bioinformatics/Computer Science/Computational Systems Biology or any related field, be highly motivated and have extensive knowledge and experience with Systems Biology modeling and simulation or Bioinformatics Data Mining. Applicants must apply online at https://yourfuture.sdbor.edu. Application must include the following: CV, letter describing your interest in the position, statement of teaching philosophy, statement of research interests, and names, addresses, telephone numbers, and email addresses for at least three professional references.

For details click here


Posted on December 27, 2019

Bioinformatician

The St. Anna Children´s Cancer Research Institute (CCRI) is further expanding its (epi)genomic research program to decipher the origin and molecular heterogeneity of childhood cancer, and to use systematic genome-scale analyses to derive knowledge for personalized treatment options as part of a recently initiated Pediatric Precision Oncology program, in partnership with the closely connected St. Anna Children’s Hospital (StA). We are thus extending our bioinformatics team and are seeking for an enthusiastic bioinformatician (postdoc level) who would like to build and advance her/his career in translational cancer genomics.

You will conduct analyses of genomics data from childhood cancers and cancer predisposition syndromes in close collaboration with molecular biologists, geneticists, pediatric oncologists and other bioinformaticians. Current projects include genomic, transcriptomic and epigenomic analyses of pediatric leukemia and solid tumors on primary tumors and liquid biopsies), and the analysis of experimental model systems (e.g. Sheffield et al Nature Medicine 2017; Serwas et al Nature Communications 2019; Halbritter et al Cancer Discovery 2019). The CCRI is also involved into several large-scaled national and international research collaborations.

Your Qualification

  • Degree or extensive track record in bioinformatics, computational biology or data analysis
  • Strong experience in applied NGS data analysis, including RNA-seq (required), WGS, WES or ChIP-seq
  • Good programming and/or scripting skills (e.g., R, Java, Python, C++), proficiency with Linux/Unix
  • Solid Statistics background
  • Ability to work independently, self-motivated and creatively
  • Excellent communication skills (both written and oral) with the ability to communicate effectively at different levels of technical knowledge
  • Ability to assess new developments in the field and apply them efficiently
  • Strong publication record

For details click here


Postdoc Opening in Machine Learning in Healthcare

The University of Zurich together with the University Hospital of Zurich are embarking on a concerted effort to develop informatics programs to advance biomedical research and healthcare using cutting edge computational approaches. As part of these efforts, the newly created Chair of Medical Informatics will establish a research group that will investigate topics in clinical data science and translational bioinformatics, such as knowledge discovery from Big Data sources (Electronic Medical Record), development of Natural Language processing, information retrieval and extraction routines, as well as the analysis of human Omics data. One key goal is the building of predictive algorithms for guiding patient therapy across all disease stages. The group is headed by Prof. Michael Krauthammer who is joining the University of Zurich after having led a research group in biomedical informatics at Yale University.

Your responsibilitiesFor this position, we are looking for a motivated PostDoc candidate who is interested in applying his/her computational skills to real world medical problems.
Your profile

  • PhD degree in computer science (focused on machine learning), optimization, statistics, applied math or closely related discipline
  • Strong publication record with at least one first-author paper in top-tier conferences (such as NeurIPS, ICML, ACL, CVPR, AISTATS, AAAI, ICLR, etc.)
  • Proficient in Python and the scientific computing stack (SciPy, Numpy, Scikit-learn)
  • Proficient in one of the deep learning frameworks (PyTorch, Tensorflow)
For details  click here


Posted on December 23, 2019

Postdoc position at the Biotech Research & Innovation Centre (BRIC), University of Copenhagen

We aim to further our understanding of the genome by integrating large-scale genomic datasets. We develop computational methods to exploit multi-dimensional genomic/epigenomic/transcriptomic landscapes to understand cell-type specific or spatio-temporal gene regulation. Using computational integrative approaches, we also study transcriptional mechanisms controlling cell differentiation and cell identify. Our areas of research include studying gene regulations in adipocyte, liver, cancer cells and stem cell differentiation.

For this, we develop computational algorithms for various genome scale datasets including DNA methylation, single cell RNAseq, ChIP-exo, GROseq and HiC.

Qualifications
We expect you to be a highly motivated and highly ambitious scientist with the following qualifications:

  • A PhD in Math, Computer Science, Engineering.
  • Strong programming skills (Python, C, etc.).
  • Knowledge of next generation sequencing data and/or data mining.
  • Excellent English skills written and spoken.

Application deadline: 2 February 2020, 23:59 p.m. CET.

For details click here


Postdoctoral Research Associate - Functional Annotation of Animal Genomes (FAANG)

The Functional Annotation of Animal Genomes (FAANG) project at Iowa State University is seeking a Postdoctoral Research Associate to contribute to the FAANG project in swine through developing and testing of pipelines for the analysis of high-throughput genomics data. Primary responsibilities include analyzing high-throughput genomics data generated for the FAANG project in swine, and contributing to publishing results.

PhD in bioinformatics, or a related field obtained prior to appointment date. At least 2 years of experience with Next Generation Sequencing data analysis. Knowledge of current best practices in epigenetic and transcriptomic data analysis. Proficient in UNIX command line and high performance computing. Computer programming skills with at least one language (R, Python or Perl). Documented excellence in verbal and written communication in English.

Preferred Qualifications:

Expertise in R language and application to high-dimensional data analysis.

Experience with deploying web applications on a server.

Experience collaborating with other members of a research team.

Professional experience showing strong independent problem solving skills.

Posting Close Date: January 28, 2020

Job Requisition Number: R1400

For details click here


Posted on December 20, 2019

Computational PostDoc Position - Cleveland Clinic

We are seeking a motivated Computational PostDoc with expertise in human NGS data analytics and interest in single-cell analyses and/or methods development to join the Lal research group at the Cleveland Clinic, Ohio. The Lal Research Group focuses on the discovery, evaluation, and translation of biomarkers into clinical care. Specifically, the group develops computational methods that integrate large genetic, clinical, and biological data sets to improve the prediction of patient outcomes – paving the way for personalized medicine. The group’s long-term research interests involve the development of a comprehensive understanding of how alterations in the genome contribute to brain disorders.

Key responsibilities:

  • Develop and optimize computational pipelines to analyze human brain tissue single cell sequencing data
  • Visualize, summarize, and communicate findings to project teams and other key stakeholders
  • Follow relevant cutting-edge advancements in the fast-paced field of genomics, bringing developments in-house or building upon them as appropriate
  • Partner with team members to improve or expand computational methods and develop best-practice, easy-to-use analytical workflows to answer common genomics questions

Minimum Qualifications:

  • PhD with experience in computational biology, statistical genetics, population genetics, bioinformatics, bioengineering, machine learning or a related field
  • Required: Coding proficiency with R, Python, or a related high-performance language.
  • A proven track record in the analysis, visualization, and interpretation of genomic and next-generation sequencing (NGS) data
  • Demonstrated ability to work closely with project teams and/or experimental collaborators to design studies and develop analyses to answer scientific questions
  • Familiarity with applying computational methods and bioinformatics tools to large- scale data including proficiency with Linux/Unix systems and high-performance computing environments

Interested applicants please submit a curriculum vitae, brief description of research interests and career goals, and contact information for three references who are familiar with the candidate’s work to Dr. Dennis Lal via email at: lald@ccf.org

For details click here


Bioinformatics research scientist

The Princess Máxima Center for Pediatric Oncology is a fast-growing research hospital for children with cancer. The institute houses an increasing number of research groups, which aim to develop cures with minimal long-term side effects for all children with cancer. In May 2018, the new building for the Princess Máxima Center opened its doors with the aim to centralize all pediatric cancer treatment and research in the Netherlands. The Molenaar Group is a large translational research groups in the Princess Máxima Center with 5 postdocs, 1 bioinfo postdoc, 6 PhDs and 5 technicians.

The primary tasks of the candidate are

  • To perform processing and integrative analysis of all high-throughput data with the ultimate goal to identify biomarkers and guide patient treatment.
  • To generate reusable analytic tools for the above purposes that fit in our current bioinformatics platforms. This should be done in close collaboration with the bioinformatics research groups from Patrick Kemmeren (our institute) and Jan Koster (Amsterdam UMC).
  • To generate analytic methodologies and tools for compound sensitivity analysis.
  • To report the relevant outcomes of all these analyses in our precision medicine program.

Education and skills

For the offered position, we are looking for a highly enthusiastic and motivated bioinformatics research scientist with a great interest in omics-based cancer research and data integration. You have programming experience with R, Perl, Python, Java and/or C. You are familiar with the development of algorithms for the analysis of high-throughput genomics data. You like to collaborate and support other researchers and you are keen on clear communication with colleagues about research methods and results.

You can apply for this position until January 15th by pressing the apply button on this screen.

For details click here


Posted on December 18, 2019

Bioinformatics Engineer

The Department of Medicine, Division of Cardiovascular Medicine is looking for a Bioinformatics Engineer / Data Scientist to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC) tasked with building a molecular map of physical activity (MoTrPAC - https://commonfund.nih.gov/moleculartransducers/overview). The Bioinformatics Core is supervised by co-PIs Dr. Euan Ashley and Dr. Matthew Wheeler in the Division of Cardiovascular Medicine at Stanford University. Dr. Ashley’s research focuses on leveraging emerging technologies such as genomics and wearable sensors to provide insights into precision medicine (https://ashleylab.stanford.edu/). Dr. Wheeler’s research focuses on genomics, rare myocardial and skeletal muscle disease, and undiagnosed diseases (https://undiagnosed.stanford.edu).

DESIRED QUALIFICATIONS:

  • Graduate degrees that emphasize engineering, computer science, and statistics are preferred
  • Experience with mass spectrometry-based data analysis
  • Experience with cloud computing environment
  • Exposure to container systems such as setting up virtual machines and Docker instances
  • Experience on a bioinformatics and/or software development team-based project
  • Familiarity with build/release/deploy and continuous integration frameworks
  • Familiarity with the R programming language
  • Biological domain knowledge
  • Experience in exercise science and/or untargeted metabolomics-based / proteomics projects
  • An understanding of data modeling including ontologies and database design
  • Experience with experimental design protocols

EDUCATION & EXPERIENCE (REQUIRED):

  • Bachelor's degree and three years of relevant experience or combination of education and relevant experience. Experience in a quantitative discipline such as economics, finance, statistics or engineering.

For details click here


Postdoctoral Fellow in Computational Epigenetics

The Zhou lab at The Children's Hospital of Philadelphia (CHOP) and The University of Pennsylvania is looking for a collegial and motivated post-doctoral researcher to work on the topics of Computational Epigenetics, Big Data, and Machine Intelligence for Genomics. The lab is based in the new Center for Computational and Genomic Medicine at CHOP. The position will be inside the laboratory of Wanding Zhou, a new investigator trained and working in the field of Computational Epigenetics for human cancer (Nature Genetics 2018, PNAS 2016), organismal development (PNAS 2018) and informatics for analyzing high-throughput -omics data (Nature Methods 2015, Bioinformatics 2014, Nucleic Acids Res 2017 and 2018). The planned projects aim at developing computational methods to uncover the dynamics of epigenetics and the biology of gene regulation. The recruit will use a wide range of big data analytics to tackle human medical problems, particularly pediatric oncology.

Qualified candidates should be proficient in computer programming (e.g., via R, Bash etc) and should have experience in the interpretation and execution of computational analysis of genomics data. He or she should hold or expect at the time of hire, a Ph.D. or D.Sc. degree in a related field (e.g., Genomics, Bioinformatics, Computer Science, Computational Biology, Bioengineering, etc.). Knowledge of Genetics and Epigenetics is a plus.

Please send your application to Dr. Wanding Zhou at zhouw3@email.chop.edu.

For details click here


Posted on December 16, 2019

Single Cell Data Analyst

The Technology Watch Team at VIB is continually analyzing the potential of emerging and disruptive technologies that can be used to advance research within the institute. Where appropriate, we mediate privileged access to these platforms by forming partnerships and negotiating purchasing licenses. In addition, the Technology Innovation Lab, a subunit of Tech Watch, evaluates, optimizes and implements prototype instruments and early-stage technologies in the labs across all Life Science fields, in collaboration with the VIB scientists and core facilities.

VIB Tech Watch is looking to hire a motivated Single Cell Data Analyst to work on the SCA program. In this role, you will ensure the organization, integration, reporting and analysis of the single cell sequencing data generated in the SCA collaboration with industry. In addition, novel developed processing pipelines will be implemented, in collaboration with other teams at VIB.

Your profile

  • Ph.D. in Bioinformatics or Life Sciences, preferably with (single cell) sequencing background
  • Experience in data curation
  • Experience in sequencing data analysis (Python, R, Linux, Seurat, Scanpy, CellRanger, etc)
  • Experience in analyzing large data sets
  • Experience in technologies related to Single Cell analysis / Sequencing is considered a plus (Drop-Seq, SMART-seq2, 10x Genomics, etc)
  • Excellent organizational, communication, writing skills
  • Excellent IT-knowledge
  • Strong and broad interest in the interplay of science and technology
  • Strong capability to work independently as well as in team

For details click here


Bioinformatician- Proteomics data pipelines

We are seeking an enthusiastic Bioinformatician to join the Proteomics Team at the European Bioinformatics Institute (EMBL-EBI) The team is responsible of the maintenance and further development of the PRIDE (PRoteomics IDEntifications) database and related tools and resources. PRIDE is a world-leading international proteomics database, a founding member of the ProteomeXchange Consortium that is capturing large-scale mass spectrometry (MS)-based proteomics data from the scientific community and currently managing hundreds of TBs of data. In addition, the team aims to re-use and integrate proteomics data in other EMBL-EBI added-value resources such as UniProt, Ensembl and Expression Atlas.

You have

You must have a degree in computer science or bioinformatics and be able to demonstrate a minimum of 3 years’ experience in software development and/or bioinformatics data analysis, ideally with some knowledge of cloud technologies.

You must be able to demonstrate at least 3 years’ working experience in a suitable programming language such as Java, C++ or Python. Working experience in bioinformatics and computational proteomics is essential. In addition:

  • Good understanding of code versioning tools, such as Git.
  • Good understanding of technologies such as JSON, XML and relational databases.

Applicants will work in a highly international, team-oriented environment and collaborate closely with external partners. Excellent communication skills are essential. The ability to work independently, under time pressure, and the dedication to communicate openly are necessary skills.

Reference Number: EBI01574
Closing Date: 13 January 2020

Posted on December 13, 2019

Postdoctoral Fellow in Computer Science / Bioinformatics/ Epigenomics

The Waterland laboratory at Baylor College of Medicine (BCM) has an immediate opening for a highly motivated individual with expertise in genomic and epigenomic informatics. This position is supported by grants from NIH/NIDDK and CPRIT (Waterland and Coarfa, Co-PIs).  The fellow will lead the design and implementation of data analysis projects aimed at understanding the epigenetic etiology of disease. Specifically, projects focus on the role of epigenetic dysregulation in cancer and obesity in humans, and mouse models of developmental epigenetics in the brain, related to energy balance and obesity.

Recent PhDs in computer science, bioinformatics, computational biology, and related fields will be considered. A strong background in statistics, and programming experience in a UNIX/Linux environment using programming languages such as Python, R, and/or Perl are required. Experience in high-throughput analysis of next-generation sequencing data and familiarity with cluster computing and widely-used genomic databases and software are advantageous.

The candidate must have excellent verbal and written communication skills (in English) and be capable of working within a team of biologists and programmers. No biological background is required, but the ideal candidate will have some familiarity with genetics and genomics. This position presents an outstanding training experience for someone with a solid computer science background who wishes to break into bioinformatics. Alternatively, this could be a great opportunity for someone with a strong background in molecular biology/genetics who seeks formal training in computer science/bioinformatics.

To apply, submit a single PDF containing your CV, statement of research interests, and names and contact information of three references to: Robert A. Waterland, PhD, Departments of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, 1100 Bates St., Houston, TX 77030; E-mail: waterland@bcm.edu.


Bioinformatics Developer

The University of Colorado Comprehensive Cancer Center (UCCC) is seeking a software developer to produce bioinformatics analysis tools that make large-scale datasets accessible and usable by basic and clinical research scientists. Our mission is to develop and provide novel, user-friendly, and interactive tools to encourage and empower researchers to explore their own data. This position will collaborate with analysts and faculty in the Biostatistics and Bioinformatics Shared Resource (BBSR), as well as basic and clinical researchers across the Anschutz Medical Campus, to identify bottlenecks in data analysis workflows. Under the guidance of the BBSR, the developer will design, build, and deploy software solutions to these areas. The candidate should have a proven track record in software development, particularly in R and/or python, and have current knowledge of or interest in biomedical research to fully understand the needs and bottlenecks of data analysis.

Examples of Work Performed

  • Collaborate with a team to understand researcher goals in a specific bioinformatics experiment and analysis
  • Understand and work with the data generated in a bioinformatics analysis pipeline
  • Adapt an analysis workflow to design and build effective and generalizable software
  • Identify and develop creative alternative analysis of the data
  • Implement visualization approaches to make data more accessible to researchers
  • Iterate over the software to continue to meet the demands of researchers
Minimum Qualifications for PRA
  • A Bachelor’s degree in Bioinformatics, Computational Biology, Computer Science, Biostatistics, Biology, or related field
  • A demonstrated history of at least 1 year of developing software or programming tools
  • Advanced knowledge of the R programming language

Minimum Qualifications for Sr. PRA

  • A Master’s  degree in Bioinformatics, Computational Biology, Computer Science, Biostatistics, Biology, or related field
  • A demonstrated history of at least 1 year of developing software or programming tools
  • Advanced knowledge of the R programming language

Position Number: 00692724

For details click here


Posted on December 11, 2019

Postdoc in Computational Biology/Bioinformatics

KTH Royal Institute of Technology in Stockholm has grown to become one of Europe’s leading technical and engineering universities, as well as a key centre of intellectual talent and innovation. We are Sweden’s largest technical research and learning institution and home to students, researchers and faculty from around the world. Our research and education covers a wide area including natural sciences and all branches of engineering, as well as architecture, industrial management, urban planning, history and philosophy.

These projects are concerned with applications of computational methods to cancer omics data. Some of the cancer data has a single-cell resolution and some carries spatial information. The bacterial data consist of an extensive collection of NGS genomes. We are collaborating with groups developing new experimental methods as well as generating biomedical data.

Qualifications

Requirements

A doctoral degree or an equivalent foreign degree, obtained within the last three years prior to the application deadline.

You need a very strong background in bioinformatics analysis of biological data. Excellent programming skills are a requirement. A good understanding of Biology is clear merit, but a basic knowledge and a desire to contribute to biology is a prerequisite

Great emphasis will be placed on personal competence and suitability.

Reference number J-2019-3134

Last application date 31.Jan.2020

For details click here


Postdoctoral Research Fellow and Bioinformatics Analyst

Dr. Hee Woong Lim’s laboratory in the Division of Biomedical Informatics has multiple positions available to work at the cutting edge of bioinformatics & computational biology research in the Division of Biomedical Informatics (BMI), Cincinnati Children’s Hospital Medical Center (CCHMC). The lab is interested in regulatory genomics to understand the fundamental mechanisms of gene expression regulation. We primarily focus on enhancer regulation and aiming at systems level understanding of enhancer architectures and functions in various contexts. To this end, we develop computational methods integrating various types of high-throughput multi-omics data such as ChIP-seq, ChIP-exo, CUT&RUN, GRO-seq, RNA-seq, ATAC-seq, and Hi-C as well as single-cell data.

Qualification

Postdoctoral Research Fellow: The ideal candidate will have a Ph.D. in a quantitative science such as computer science, bioinformatics, physics, or a related interdisciplinary field, be a highly motivated problem solver, and have strong communication skills. Experience with next-generation sequencing data and bioinformatics tool development is preferred. Candidates with a biology background with quantitative training are also encouraged to apply.

Bioinformatics Analyst: The ideal candidate will have MS or BS degree in a related quantitative science field. Must have strong programming skills and be familiar with the Linux environment enough to setup, execute, and develop bioinformatics pipelines. Previous experience of bioinformatics software development and analysis is preferred; decent background knowledge of genomics/molecular biology is plus.

Interested applicants should send an email to Dr. Hee Woong Lim (HeeWoong.Lim@cchmc.org) including CV and cover letter.

For details click here


Posted on December 09, 2019

Ad Astra Fellows, UCD School of Biomolecular and Biomedical Science

In support of the 2024 University College Dublin Strategic Plan ‘Rising to the Future’, UCD has begun an ambitious plan to increase our faculty numbers by 500 over five years. With an initial 5-year contract, research support for these 5 years and the opportunity for an on-going contract subject to performance, there has never been a better time to join the faculty at Ireland’s Global University and to live in one of Europe’s most vibrant, friendly and connected capital cities.

The School of Biomolecular and Biomedical Science is a vibrant teaching- and research-intensive School. The School has strength, critical mass and competes at an international level in the following areas of research excellence: Infection Biology, Genomic Analysis & Bioinformatics, Drug Discovery & Development, Diagnostics & Personalised Medicine, Mechanisms of Disease, Model Organisms for Biomedical Research and Biotechnology & Synthetic Biology. These research areas are underpinned by our fundamental disciplines of Biochemistry & Molecular Biology, Genetics, Microbiology, Neuroscience and Pharmacology.

Closing date: 17.00hrs (Local Irish Time) on 24th January 2020

For details click here


Project Scientist in Proteomics/Metabolomics to join the Superti-Furga Lab at CeMM

With the RESOLUTE consortium (www.re-solute.eu), we are trying to de-orphanize human transporters at a large scale and “unlock” them as potential pharmacological targets. We are currently pushing towards a paradigm-shift in the science of human cellular transporters by creating a massive, historical advance in knowledge on hundreds of individual transporters and the way they act together. These are very exciting times and research and the consortium is reaching full speed and thriving on synergies to turn this large effort into exploitable and practical knowledge.

We are searching for a highly motivated Project Scientist who wants to seize this opportunity and contribute to cutting-edge biomedical research in a highly dynamic public-private partnership. The RESOLUTE consortium is supported by the Innovative Medicines Initiative (IMI, www.imi.europa.eu) with 13 partners from academia and the pharmaceutical industry and is coordinated by the Superti-Furga laboratory at CeMM.

Your main mission is to plan, conduct and supervise de-orphanization studies -mainly proteomics and metabolomics - as part of the RESOLUTE team at CeMM in the Superti-Furga laboratory and in collaboration with the Proteomics/Metabolomics Facility at CeMM and RESOLUTE consortium partners. You are a creative scientist able to seize the opportunity to create, navigate, integrate, visualize and interpret original data in innovative ways.

Requirements and desired qualifications

  • PhD in cell biology, biochemistry, biotechnology or similar
  • Experience in mammalian cell culture (immortalized cell line models)
  • Excellent background in MS-based analytical techniques (LC-MS/MS) and corresponding data analysis methods
  • Experience with interaction (AP-MS) and proximity (BioID/APEX) proteomics is a plus
  • Need to be meticulous, highly-organized and must have the ability to work on a team towards well-defined goals and deliverables
  • Very good written and oral communication skills in English and excellent social skills are absolutely required

Closing date for applications: 06 January 2020

For details click here


Posted on December 06, 2019

5 Postdoctoral Research Associates in Bioinformatics and Data Science

The Cluster of Excellence on Plant Sciences is a joint unit of Heinrich Heine University Düsseldorf, University of Cologne, Max Planck Institute for Plant Breeding Research Cologne and Forschungszentrum Jülich. CEPLAS is developing innovative science-based strategies for sustainable plant production. Our aim is to mechanistically understand complex plant traits of agronomic relevance that impact on yield and adaptation to limited resources.

CEPLAS creates an international, interdisciplinary research environment. We offer a comprehensive training program for early career researchers tailored to your respective career level. Program components are (scientific) training, mentoring, coaching and networking with industry.

Within the field Bioinformatics and Data Science

Project 1: Comprehensive and efficient identification of genomic differences from whole-genome alignments
Qualifications needed: good algorithmic background, programming skills, basic knowledge in bioinformatics, Plus: experience with genomic data and/or plant genomics
Project leaders: Gunnar Klau, Korbinian Schneeberger

Project 2: GeneCOMPLETE
Qualifications needed: programming skills. Understanding of plants and background in machine learning are a plus.
Project leader: Björn Usadel

Within the field Plant Development and Metabolism

Project 3: Meristematic regulatory networks controlling floral transition
Qualifications needed: Molecular biology, confocal imaging, computational capability

Project leader: George Coupland

Project 4: Control of shoot meristem development in barley
Qualifications needed: molecular plant biology, grass genetics, plant development, imaging
Project leaders: Maria von Korff-Schmising, Rüdiger Simon

Project 5: Physiological and metabolic consequences of diversification of leaf margin complexity
Qualifications needed: Plant Physiology skills particularly on gas exchange or hydraulics, Plant Molecular/Developmental Genetics (especially in Arabidopsis), NGS data analysis Project leader: Miltos Tsiantis.

For details click here


Associate Research Scientist - Computational Biology

Associate Research Scientist – Computational Biology available in Sidi Chen Laboratory at Yale University (https://sidichenlab.org). This individual carries out computational research and development activities as directed by the PI.

#Minimal Required Education and Experience: 

PhD Degree in the area of computer science, computational biology, bioinformatics, data science, biostatistics, physics, or relevant scientific disciplines and strong skill sets of computing.

Preferred specific skills or experience:

1.     Linux / Unix operating systems, server operation, Awk or similar languages

2.     Custom scripting with Perl, Python, and/or C++

3.     Data analysis and graphics using R or similar

4.     Analysis of large datasets such as genomics, transcriptomics/RNA-seq, ATAC-seq, single cell sequencing, Mass-spec/proteomics/metabolomics, genetic screening

5.     Processing of large complex datasets such as high-content imaging, clinical data

6.     Machine learning, artificial intelligence

7.     Software development, API

8.     Fluent English communications

For details click here


Posted on December 04, 2019

Post-doctoral Fellow in Statistical Genetics

The University of Hong Kong Post-doctoral Fellow in Statistical Genetics in the Department of Statistics and Actuarial Science (Ref.: 499157) Applications are invited for appointment as Post-doctoral Fellow in Statistical Genetics in the Department of Statistics and Actuarial Science (Ref.: 499157), to commence as soon as possible for one year, with the possibility of renewal.

Applicants should possess a Ph.D. degree in a quantitative field including, but not limited to, statistics, biostatistics, computer science, bioinformatics, and computational biology. They should have experience and interest in human genetics. The appointee will conduct research in the group of Dr. Yan (Dora) Zhang. Current topics of the group include statistical genetics, bioinformatics, risk prediction, and large-scale biomedical data analysis.

Review of applications will commence as soon as possible and continue until May 31, 2020, or until the post is filled, whichever is earlier.

For details click here


Bioinformatician

Ranked among the "50 Smartest Companies" in the world according to the MIT Technology Review, SOPHiA GENETICS is a fast-paced growing health-tech company. Combining deep expertise in life sciences, medical disciplines and mathematical modeling, we bring to market data analytics solutions to support healthcare professionals in better diagnosing and treating patients. Today SOPHiA’s technologies are being adopted and trusted by over 980 leading hospitals worldwide, all connected to each other and motivated to provide equal benefits to all patients.

We are primarily looking for passionate people. Seize the opportunity to contribute to a great cause, improving the diagnosis and treatment of serious illnesses, from Cancer to Genetic Diseases, within an outstanding company! In our journey to impact patients' lives, we currently have two open positions in the Tertiary Analysis Operations team, based at our headquarters in Bidart, France. The team is transversal working across the two business lines of : Genomics and Clinical Trials. On numerous projects central to the company such as: Alamut, SOPHiA DDM™ and SOPHiA Trial Match™.

Requirements:

·      PhD in a scientific field would be advantageous or a Masters with several years of experience

·      Competence in a widely used bioinformatics programming language, Python, R and Snakemake workflows would be an advantage

·      Database experience in mysql and or postgres

·      Linux bash scripting experience

·      Knowledge of Genetics and Molecular Biology. Experience in a clinical setting would be an advantage

·      Knowledge of variant annotation software and or concepts would be advantageous

·      Excellent communication skills, including experience in communicating complex scientific principles in simple terms

·      English (the business language) is mandatory, French is a plus

For details click here


Posted on December 02, 2019

Postdoctoral Scientist Bioinformatics in Multiple Sclerosis

The Laboratory for Neuroimmunology focusses on translational research on multiple sclerosis (MS). This means that we start from important clinical questions, and investigate these in the laboratory. The aim is to translate the results back to improved health care for MS patients. To reach this goal, the Laboratory for Neuroimmunology has a translational structure with a clear research and clinical pillar. These two pillars build on the complementary expertise of Prof. An Goris and Prof. Bénédicte Dubois. Our research lines include identification of genetic risk factors for susceptibility of MS, genetic risk factors for heterogeneity in MS and functional follow-up of genetic risk factors. More information and examples of recent work can be found on our website (http://gbiomed.kuleuven.be/lni). Our research group also contributes to leading large-scale international communities, such as the International Multiple Sclerosis Genetic Consortium and the MultipleMS project.

Responsibilities

You will play a key role in local projects as well as in international collaborative projects, such as the EU Horizon2020 research program “MultipleMS” (www.multiplems.eu). In particular, for the “MultipleMS” project you will analyze large datasets integrating biological (genetic, immune phenotype, biomarker, …) and clinical (disease course, imaging, …) data of a unique prospective cohort of newly diagnosed patients with multiple sclerosis. You will manage these projects, and report and communicate on progress in meetings and telephone conferences.

Essential knowledge, skills, and experience required:

  • MSc in a relevant field such as Biomedical Sciences, Bio-engineering, Bioinformatics or Life Sciences with a PhD in a relevant topic
  • A computational mindset and a strong interest in computational biology
  • Expertise and proven track record in biological data analysis in health sciences such as analysis of genomics, transcriptomics, immunological or clinical data
  • Proficiency in UNIX/Linux and in R programming language
  • High sense of accuracy

You can apply for this job no later than January 03, 2020.

For details click here


Computational Biologists

The University of Cologne offers a wide range of scientific disciplines and internationally leading profile areas organized in six faculties. At the Faculty of Medicine 1.800 scientists are engaged in research, ranging from basic sciences to clinical application, as well as teaching and health care. Together with the University Hospital Cologne the faculty maintains 58 clinics, research institutes and centres. 3.400 students study in this dynamic and innovative environment. The Faculty of Medicine and the University Hospital Cologne are embedded in the scientifically highly active Rhine region. They have strong contacts to and alliances with the surrounding universities and non-university research institutions guaranteeing scientific excellence in research and teaching.

Your responsibilities will include:
•Development, implementation and application of workflows for data processing and statistical analysis of large scale ‘omics’ datasets
•Development and application of bioinformatics tools for data visualization, biological network modeling and pathway mapping
•Development and maintenance of a web-based portal for sample submission, project and data management
•Collaboration with users of the facilities and support in the interpretation of analysis results
•Maintenance of the facilities’ computer equipment

Qualifications:
•Diploma, master or doctorate degree (PhD) in Bioinformatics, Biostatistics, or closely related area
•1-3 years of working experience with analytics of RNA-seq, ChIP-seq and/or mass spectrometry-based data
•Strong experience with various statistical methods
•Solid knowledge in programming languages (e.g. R, Python, C++, Perl)
•Proactive and service-oriented team player with excellent communication and writing skills

We prefer online applications, but you also have the opportunity to apply via regular mail by 31. December 2019.

For details click here


Posted on November 29, 2019

Postdoctoral researcher/Researcher in machine learning/ Bioinformatics

Örebro University seeks to appoint a researcher with established expertise in Machine Learning. This position is jointly offered by three research groups at Örebro University: AASS, MTM/EnForce, and Functional Bioinformatics. AASS is one of the nationally leading research groups in robotics, AI and applied Machine Learning. The MTM/EnForce Centre at Örebro University focuses on environmental toxicant discovery and hazard assessment using advanced analytical methods, bioassay technologies and effect-directed analysis. The Functional Bioinformatics group conducts research in applying and further developing machine learning approaches for pattern discovery in biomedicine (biosignatures for diagnosis, prediction, and prognosis) as well as for systems for biological applications (network biology and network medicine).

Duties and responsibilities

The candidate will work closely together with AASS, MTM/EnForce and Functional Bioinformatics and bring in their Machine Learning (ML) expertise in the respective projects. The selected candidate will represent and apply this expertise and take responsibility for the technical infrastructure. It is possible but *not* required to acquire external funding or to teach. The position thus leaves room to keep in touch with current ML developments and admits further development of specialist skills. While the selected candidate will be included in all publications that result from the collaboration with other researchers at Örebro University, it is optional to pro-actively drive research or to develop a research portfolio at once own beyond their core expertise.

Eligibility

Eligible for the appointment as postdoctoral researcher are applicants holding a doctoral degree. A PostDoc position is offered if the successful applicant’s doctoral degree has been awarded no more than three years prior to the application deadline. Candidates who have obtained their doctoral degree prior to that are also invited to apply, the successful applicant will in that case be offered a researcher position.

The application deadline is 11 December 2019. We look forward to receiving your application.

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Postdoctoral fellow in Bioinformatics

The Bioinformatics Team within the Center for Data-Driven Discovery in Biomedicine (D3b - d3b.center) at the Children’s Hospital of Philadelphia (CHOP) is seeking a talented postdoctoral fellow to carry out a mentored, bioinformatics (computational) research project within the field of oncology, focused on discovery of novel oncogenic mechanisms of pediatric brain tumors. The postdoc experience will serve to extend, refine, and enhance skills necessary for professional and career development, and will enable the individual to broaden his/her scientific background by acquiring new research capabilities.

Responsibilities:

It is expected that this individual will conduct independent scholarly research, and will contribute directly to the overall research goals of the project and the research group. Postdocs will be expected to participate in project planning, recording, and interpretation/evaluation of data, and communication of results. Postdocs will also be expected to acquire technical, lab management, and manuscript/grant writing skills; and participate in seminars, lectures, poster sessions and presentations at national meetings. Postdoctoral fellows also may be required to supervise junior team members, develop new bioinformatics methods for research, and assist with the development of other research projects in the center.

Qualifications:

  • Ph.D., M.D., or D.V.M. in biological or computational discipline;
  • Experience in applied bioinformatics, genomics, and computational work;
  • Experience with management and analysis of complex data types;
  • Experience with genomic and/or proteomic data analysis methods;
  • Doctorate Degree in biological or computational discipline (preferred);
  • Four (4) years of research experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation (preferred);
  • Fluency in two or more of: R, Python, Perl, bash, high-performance cluster computing, and/or cloud computing (preferred);
  • Experience with pipeline or workflow development frameworks (preferred);
  • Experience or knowledge of array/sequencing technologies commonly used in biological labs, such as RNA-Seq, WGS, WES, miRNA-Seq, SNP arrays, single cell sequencing, proteomics (preferred).

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Posted on November 27, 2019

Research Associate - Computational Biology, Bioinformatics

A research associate position in Computational Biology, Bioinformatics is currently available. The qualified candidate will be working on projects related to viral/cancer immunity and evolution. The overall aims of the projects are to develop and apply multi-omic approaches to mine and deconvolute complex datasets including genomic, transcriptomic, and proteomic data from viruses, hosts, and tumors to: a) discover population-specific virus-host interaction mechanisms and identify underlying genetic and evolutionary sources; b) delineate gene expression profiles in cancer and investigate their association with germline/somatic mutations, viral status, and other clinical data. Texas Biomed provides unique research and training opportunities including access to exceptional resources such as BSL4, SNPRC (Southwest National Primate Research Center), a vigorous infectious disease program on HIV, malaria, schistosomiasis, Ebola, Zika, hepatitis C and TB, career development workshops on grant writing, starting a new lab, and skill management, and outstanding imaging, computational, and sequencing facilities. Texas Biomed faculty have adjunct appointments at two universities in San Antonio (UTSA and UTHSCSA), which provide a wide range of additional training and career development opportunities for Texas Biomed employees.

EDUCATION/EXPERIENCE/SKILLS:

Required
A minimum Master degree or equivalent in bioinformatics, computer science, mathematics, statistics, physics, or engineering.
Skills in working with large datasets and developing tools and algorithms for parallel data analysis.
Coding in one or more platforms, e.g. Python, R, Matlab.

Desired
Official training in computational biology, bioinformatics
Experience in analyzing RNAseq, GWAS, Hi-C and other large biological datasets
Familiarity with databases such as UCSC Genome Browser, 1000Genomes, TCGA, and ICGC.
Experience in using standard bioinformatics packages such as Samtools, Cufflinks, Tophat, …
Knowledge of statistics
Knowledge of evolutionary biology, and viral/cancer immunity

For details click here


Bioinformatician

The Oklahoma Medical Research Foundation (OMRF) is an independent, not-for-profit, biomedical research institute adjacent to the campus of the University of Oklahoma Health Sciences Center (OUHSC) located in Oklahoma City. OMRF investigators have internationally recognized expertise in Autoimmunity, Immunology, Genetics, Aging, Cardiovascular Disease, and Cancer. Our Autoimmune Disease Institute (ADI) houses Centers of Excellence and specialty research clinics for Rheumatic Diseases (focusing on Lupus, Rheumatoid Arthritis, UCTD, and Sjogren’s) and for Multiple Sclerosis and related diseases. In addition to following over 4,000 patients with these conditions, teams of basic and clinical investigators conduct extensive clinical, translational and mechanistic research using samples obtained from these large clinical programs. Investigators at OMRF enjoy close scientific interactions with OUHSC faculty and participate in OUHSC graduate programs.

Our Translational Informatics group is seeking a bioinformatician to support both our clinical and basic research programs in autoimmune disease. Projects will include quality control, basic and Machine Learning analytic approaches to interpret single cell technology data from a wide range of technologies in the ADI. Technologies include but are not limited to single cell transcriptomics, single cell proteomics, spatial transcriptomics, inclusion of genetic variant information in eQTL analyses and highly multiplexed imaging technologies data including cell-distance and cell-pairing interation analyses. Systems in the division include 10X Genomics (scRNA-Seq, T-B repertoire, snATAC-Seq, Total-Seq, spatial transcriptomics), Fluidigm Helios and Hyperion mass cytometry/mass imaging, Zellkraftwerks ChipCytometry systems. Rich datasets already exist for immediate application of precision medicine and molecular phenotype classification of subjects using machine learning approaches, systems biology approaches, high content data analysis, data visualization and reporting for publications and grants, bioinformatics analyses of results from various transcriptomic/genomic assays. This position involves working both independently and as part of the translational informatics team.

Master’s degree or Ph.D. in Bioinformatics, Math, Statistics, Biostatistics, Computer Science, MIS, or relevant field and 2 years relevant experience or a combination of relevant experience and education. Strong project management, organizational, attention to detail, analytical, customer service, and verbal and written communication skills required.

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Posted on November 25, 2019

Two Postdoctoral Positions in Machine Learning for Alzheimer's Disease

The Machine Learning and Computational Biology Laboratory at the Department of Biosystems Science and Engineering (D-BSSE) is seeking two postdoctoral researchers to work on Machine Learning for Alzheimer's Disease. The postdocs will be joining a highly interdisciplinary research team and will be supervised by Dr. Catherine Jutzeler/Dr. Bastian Rieck and Prof. Karsten Borgwardt. The positions should start no later than February 15, 2020.

The positions are funded by Dr. Catherine Jutzeler's and Dr. Bastian Rieck's recently awarded SNSF Spark Grants on Machine Learning for Alzheimer's Disease. Alzheimer’s Disease (AD) is the sixth-leading cause of death for Americans ages 65 years and older. It is an irreversible, progressive brain disorder that slowly destroys memory and, eventually, an individual’s ability to perform even the simplest tasks, such as bathing, feeding, and dressing. Beyond the immediate health consequences, the societal costs are of epidemic proportion, thus making AD a pressing public health and medical problem. With disease-modifying treatment trials still unsuccessful at the present time and only medications to treat symptoms available, an emerging research initiative is to identify approaches to intervene before the damage begins, making it potentially possible to prevent AD.

Applicants should be highly motivated and creative, show an exceptional track record, and hold a doctoral degree in Computer Science, Bioinformatics, Engineering, Mathematics, Statistics, or related fields, and be interested in working in an interdisciplinary environment at the interface of Machine Learning and Personalized Medicine. Experience in developing algorithms for large-scale data analysis problems in biology and medicine is an asset. Academic excellence, a professional work attitude, and a proactive and self-driven work ethic are expected. The positions offer the opportunity to gain leadership and supervision experience in joint projects with younger scientists.

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Postdoctoral Scholar Imaging Data Science Radiation Oncology

The Division of Medical Physics within the Department of Radiation Oncology at University of Washington School of Medicine in Seattle, WA is currently recruiting a postdoctoral scholar in imaging data science under the supervision and mentorship of Dr. Stephen R. Bowen, Associate Professor of Radiation Oncology and Radiology (joint). We are seeking highly motivated individuals with strong track records of research in computational image analysis, computer vision, or machine learning. The successful candidate will participate in NIH-funded research projects on multimodality molecular and functional imaging for biomarker response-adaptive radiation therapy and immunotherapy within precision oncology. Specific applications include multiscale and spatially variant imaging-based treatment response prediction and (deep) machine learning of radiomic data for clinical outcome modeling. Imaging datasets will be collected, curated, and analyzed within the operational framework of several ongoing clinical trials.

Preferred

  • Experience with imaging data science analytics, including radiomics, machine learning, and deep learning approaches.
  • Mastery in one or more of the following scientific computing languages: Python, R, MATLAB, or related visual / object-oriented programming.
  • Familiarity with clinical oncology research and clinical trials.
  • Publication of peer-reviewed scientific journal articles on novel imaging data science methodologies or applications.

Qualifications

  • Ph.D. in Medical Physics, Physics, Computer Science, Data Science, Bioinformatics, Engineering, or a related field.
  • Proficiency in one of the following scientific computing languages: Python, R, MATLAB, or related visual / object-oriented programming.
  • Excellent oral and written communication skills.
  • Experience with presentation of original research at professional conferences.

For details click here


Posted on November 22, 2019

Post-doctoral researcher “Integrative Network Analysis for Gene Discovery in Wheat”

For a joint project of the VIB Center for Plant Systems Biology and BASF Agricultural Solutions Innovation Center Gent, we are looking for a postdoctoral researcher who will develop and implement computational pipelines to build and compare different biological networks for gene function analysis in cereals. This 3-year project, starting on 1 March 2020, is fully funded by BASF and VLAIO (Flanders Innovation & Entrepreneurship). The successful applicant will be part of the Comparative Network Biology lab led by Klaas Vandepoele in VIB, but will also closely work together with BASF data scientists and program leaders.

Job description

  • Collect and integrate public and private crop expression datasets
  • Develop computational pipelines to build and compare cross-species gene co-expression and regulatory networks to identify key transcription factors (TF)
  • Perform data analysis of DAP-seq high-thought experiments to identify TF binding sites and build TF regulatory networks
  • Perform/assistant data analysis on Y2H and build protein-protein interaction networks
  • Develop pipelines and methodologies to compare and integrate multiple biological networks
  • Integrative network analysis for gene function prediction and trait-associated gene identification
  • Closely work with both data scientists, biologists and wet-lab scientists in both VIB and BASF
  • Reporting of results through publications in peer-reviewed international journals.
  • Attending and presenting your results at international scientific events.

Profile

  • PhD in Bioinformatics, Computational biology or similar.
  • Good programming (Python, R) and Linux skills are a must
  • Familiar with reporting in Jupyter notebook, bitbucket and git system for code sharing and sustainable data analysis
  • Strong ability and experience in high-throughput biological network and NGS data analysis
  • Knowledge in plant/crop genetics and molecular biology is a plus
  • You are enthusiastic about scientific research, computational biology, and want to learn more about advanced biological concepts.
  • You have good writing and communication skills with both data scientists and biologists
  • You are proficient in English.

Application deadline: 31/12/2019 or until position has been filled.

For details click here


Postdoc in Computational biology and Bioinformatics

Applicants are invited to apply for a post-doctoral (i.e., postdoc) position in Abyzov lab at Mayo Clinic. The choice of project will depend on the applicant's interests and skills, however, the research must be purely computational and focus on one of the following main fields of computational biology: population/personal human omics, cancer omics, single cell and somatic omics, and the analysis of next-generation sequencing data. Specific sub-areas of interest are discovery, annotation, and the functional annotation of human genomic variants, cancer genomics, cancer evolution, somatic mosaicism in normal human cells.

The ideal applicant will have a Ph.D. in computational biology or bioinformatics, experience in one of the aforementioned research areas, demonstrate a record of peer-reviewed publications, and possess motivation for independent research. He or she should have a very strong understanding of biology and be skilled in programming and using computers to solve problems (e.g., experience with C/C++, Java, Python/Perl, R/ROOT, etc.). Oral and written proficiency in English is also a big plus. To apply, please email your CV, including a list of publications and details for three references, to abyzov dot alexej at mayo dot edu. Please include the phrase “PostDoc application” and your full name in the subject of the email.

For details click here


Posted on November 20, 2019

Computer Scientist / Bioinformatician IT and Cloudtechnology de.NBI Cloud

The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research. The Omics IT and Data Management Core Facility is seeking a Computer Scientist / Bioinformatician IT and Cloudtechnology de.NBI Cloud (Ref-No. 2019-0360) The German Cancer Research Center (DKFZ) conducts innovative health research in the fields of computer science, genomics and personalized medicine. In this exciting research environment, highly complex analysis algorithms are developed and applied in big data analytics, artificial intelligence and deep learning in national and international contexts.

As a computer scientist / bioinformatician in the field of cloud computing, you support us in the implementation of data protection and information security measures on the way to certification. This position will be integrated into the cloud team at DFKZ. In close coordination with the de.NBI Cloud, with commercial providers and in particular with the HD-HuB Cloud locations at the DKFZ, at the University of Heidelberg and at the Berlin Institute for Health Research (BIH), concepts for information security, IT security and data protection are developed and implemented in accordance with the General Data Protection Regulation (GDPR).

Your profile:
Computer scientist / bioinformatician (university) or applicant with a comparable degree with knowledge in the administration of complex systems and the development of cloud environments as well as with a strong interest in the development and implementation of concepts within the framework of information security and data protection.

The position is limited to 31.12.2021.

For details click here


Postdoc Position in Evolutionary Genomics

The postdoc will utilize publicly-available genomes of numerous mammals as well as newly-sequenced genomes of several bats to discover the genomic basis of interesting phenotypic differences between these species. The postdoc will apply and further develop our genomics methods, and analyze results by integrating biomedical knowledge and generated functional genomics data. Promising candidate genes will be tested experimentally, either by the Postdoc or in collaboration. Funding is according to the German TVöD scale and available for at least 3 years.

We combine computational biology, comparative genomics and experiments to investigate how nature's fascinating phenotypic diversity evolved and how it is encoded in the genome. On the computational side, we align and annotate genome assemblies [1-3], develop and apply comparative genomic methods to discover key differences in genes and regulatory elements [4-9], and use statistical approaches to associate genomic to phenotypic differences [10,11]. On the experimental side, we use RNA-seq, ATAC-seq, functional assays and CRISPR-Cas9 to reveal the molecular function of genomic regions and to test causality between genomic and phenotypic differences [12,13]. Our group is part of the Bat1K project that aims at generating reference-quality genomes of all bats.

Requirements

Applicants should have a strong publication record and a degree in bioinformatics / computational biology, genomics or a related area. Excellent programming skills in a Linux environment as well as experience with shell scripting and Unix tools are required. Previous experience in large-scale comparative genomic data analysis is an advantage.

For details click here


Posted on  November 18, 2019

Bioinformatician for Single-Cell-Sequencing-Data Analysis

The German Cancer Research Center is the largest biomedical research institution in Germany. With approximately 3,000 employees, we operate an extensive scientific program in the field of cancer research. A joint position as postdoc/bioinformatician for computational single-cell sequencing analytics is available in the Computational Genomics and Systems Genetics group (https://www.dkfz.de/en/bioinformatik-genomik-systemgenetik) together with the Omics IT and Data Management Core Facility (ODCF). This project is connected to the Human Cell Atlas (https://www.humancellatlas.org), to which the Stegle group contributes as a member of the analysis working group. The Omics IT and Data Management Core Facility (ODCF) supports scientists in structuring and analyzing large omics datasets.

We are looking for a (senior)bioinformatician to guide a single-cell core group that is responsible for the coordination, the establishment and harmonization of (clinical) analysis and data management workflows for single-cell sequencing data. The successful candidate will be part of an interdisciplinary research team developing and applying a diverse range of state-of-the-art methodology to improve the analysis and integration of various data types with a focus on single-cell data. He/she will apply bioinformatics and statistical methods to analyze, interpret and integrate high-throughput ‘omics’ data, including whole genome, RNA and different types of single-cell sequencing data. The position can involve both collaborative involvement in research-centric single-cell projects and/or infrastructure research and development.

Your responsibilities:

  • Establishment of clinical omics-data analysis and integration workflows
  • Collaboration, experimental design and analysis of clinical single-cell projects
  • Infrastructure development, data management and/or integrative/interactive data visualization of multiple omics data
  • Development of cloud-based analysis workflows

Requirements:

The successful applicant will hold a Master as well as a doctoral degree or equivalent qualification in computer science, statistics, mathematics, physics, and/or engineering, or a degree in biological science with demonstrated experience in computational biology/bioinformatics.

Application deadline: 06.12.2019

For details click here


Postdoctoral Fellow and Bioinformatic Analyst position

We are looking for creative, energetic, and collaborative researchers to join our interdisciplinary team to understand the function of the genome, to map the cellular states in a body, and to elucidate the transcriptional control mechanisms underlying developmental processes and diseases.

1. Single Cell Analysis. Develop novel methods for analyzing, visualizing, and integrating single-cell resolution imaging data containing spatially resolved transcriptomic, morphological, chromatin, and/or functional information. Integrate sequencing- and imaging-based data types. Develop and maintain robust, efficient, and user-friendly software packages. Collaborate with basic and clinical scientists to solve various biomedical questions using single-cell analyses.

2. Cancer Epigenetics. Develop novel methods/software for analyzing and visualizing high-dimensional, multi-scale epigenomic data. Engage in collaborations with cancer biologists and physicians to investigate mechanisms underlying cancer initiation, progression, and treatment response.

Please send a cover letter and your CV via email to Dr. Guo-Cheng Yuan. If you are applying for either Postdoctoral Fellow or Bioinformatic Analyst position, please also include the contact information for two references.

For details click here


Posted on  November 15, 2019

Postdoctoral Scholar in Genomics and Bioinformatics

The Penn State Animal Diagnostic Laboratory (ADL) at University Park and the Pennsylvania Veterinary Laboratory (PVL) at Harrisburg are collaborating to develop Next-generation Sequencing based innovative diagnostic tests for bacterial and viral pathogens of veterinary and public health importance. Briefly, the project involves application of whole genome sequencing to study genomes, metagenomes to identify and study pathogens in clinical samples with an emphasis on virulence determinants, bacterial serotype determination, identify and catalog antimicrobial resistance genes, and decipher the molecular epidemiology of bacterial and viral pathogens as it relates to disease outbreaks. Computational/bioinformatics approaches and mathematical modelling of infectious diseases are also included in the overall project.

Applications are sought from highly motivated individuals with a strong experience and interest in genomics and bioinformatics of infectious diseases. Specific responsibilities include: Coordinate the genomics and bioinformatics activities of bacteriology and virology sections of ADL and PVL, Develop and validate a metagenomics approach to identify bacterial and viral agents in clinical samples, and Assist in the data analysis of genomics, transcriptomics and proteomics projects. Hands-on laboratory experience including library preparation for next generation sequencing, operating a next generation sequencing machine (experience with Illumia platform preferred) and bioinformatic analysis of genomic data is essential.

Job Number: 91957

For details click here


Postdoc - Big Data Analytics for Metabolomics & Exposomics

A Postdoctoral Fellow (""postdoc"") is a professional apprenticeship designed to provide recent Ph.D. recipients with an opportunity to develop further the research skills acquired in their doctoral programs or to learn new research techniques, in preparation for an academic or research career. In the process of further developing their own research skills, it is expected that Postdoctoral Fellows will also play a significant role in the performance of research at the University and augment the role of graduate faculty in providing research instruction to graduate students.

Postdoc appointments are characterized by all of the following conditions:

  • the appointee was recently (within the last eight years) awarded a Ph.D. or equivalent doctorate (e.g., Sc.D., M.D.);
  • the appointment is temporary;
  • the appointment involves substantially full-time research or scholarship;
  • the appointment is viewed as preparatory for a full-time academic and/or research career;
  • the appointee works under the supervision of a faculty member; and
  • the appointee has the freedom and is expected to publish the results of his or her research or scholarship during the period of appointment.

Other Work/Responsibilities

The primary research responsibilities of the successful candidates are to develop Big Data Analytics capabilities for metabolomics and exposomics and publish the results.
In particular, the successful candidates are to develop computational algorithms and software tools for:
(1) extracting compound information from raw liquid-chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) exposomics and metabolomics data;
(2) annotating and identifying ions based on existing large-scale compound and mass spectral libraries;
(3) predicting possible structures or substructures of compounds using accurate mass, retention time, isotopic distribution, fragmentation spectra and other meta- data

Position Number POST40

For details click here


Posted on  November, 2019

Post-doc position Population Genomics and Demographic History

We are looking for an enthusiastic post-doc interested in the use of genetic and genomic data to reconstruct the demographic history of species. The candidate will work on questions related to endangered species (with a focus on Madagascar), human evolution or domestication. The questions we ask are related to the importance of population structure (connectivity, habitat fragmentation) and genomic diversity: how do ancient climatic events influence the genome of present-day species? Can we differentiate between the genomic signature of population size changes and changes in connectivity? Should we represent recent human evolution as changes in connectivity or changes in population size change? These are some of the questions that we try to ask within the DISPO project (Demographic Inference in Structured Populations).

Our group has been working on the concept of IICR (inverse instantaneous coalescence rate, Mazet et al., 2016 Heredity), which can be used to address these questions. The candidate will thus learn to use the IICR but could or better should bring his/her own experience to make progress in these issues. Enthusiasm and critical mind are crucial.

Interested candidates should contact L. Chikhi for questions: chikhi(at)igc.gulbenkian.pt

The current deadline is 31/10/2019, to be extended to the 31/12/2019.

For details click here


Postdoc Bioinformatician

The Child Health Research Center in the Department of Pediatrics at the University of Virginia is seeking a Bioinformatician to work in the laboratory of Dr. Ariel Gomez to investigate the epigenetic and genetic determinants of cell fate. The candidate will also interact and advise other investigators within the center. The incumbent will collaborate with researchers in designing and implementing research projects, analysis of large data sets, and presentation and publishing of results. The candidate will be involved in the design of research projects and supervise students and post-doctoral fellows and developing innovative approaches for data analysis. Experience in analysis of genome wide analysis resulting from ATAC-seq, Chip-seq and single cell RNA-seq and whole genome sequencing is a must.

Qualified candidates must have a PhD or MD degree by start date with experience in Computational Biology, Biostatistics, Biomedical Sciences, or a related field, and publications in peer-reviewed journals. The candidate must have demonstrated expertise in the field of biology. Excellent written and verbal communication skills are required. Candidates with postdoctoral experience in bioinformatics applied to epigenetics will also be considered competitive.

Job ID: R0011262

For details click here


Postdoctoral position in Computational Biology

A postdoctoral position is available in the research group of Dr. Ivan Ovcharenko at the National Institutes of Health (NIH). Our current research projects include computational studies of epigenetic and sequence-based mechanisms of gene regulation. We are developing computational approaches to decipher the regulatory landscape of the human genome. By combining next generation sequencing data with a large body of experimental enhancer characterization, our computational approaches target transcriptional mechanisms of tissue-specific regulatory signals and cell-type differences in gene regulation.

Candidates with a PhD in Computational Biology, Deep Learning, Population Genetics, Bioinformatics, or a related field and less than 5 years of prior postdoctoral experience are encouraged to apply. Advanced programming and genome data analysis skills are desirable.

This position is supported by the Intramural NIH Research Program and includes stable, multi-year funding, outstanding benefits and compensation. NIH is an Equal Opportunity Employer and encourages applications from women and minorities.

If interested, please email your CV and the names of 3 references to Ivan Ovcharenko at ovcharen@nih.gov.

For details click here


Posted on October 18, 2019

Postdoc in Bioinformatics

We seek a motivated and independent candidate for a 2-year postdoc position in bioinformatics available at the Department of Molecular Medicine (MOMA), Aarhus University. The position is available from January 1st, 2020 or as soon as possible thereafter. The postdoc will work on an exciting project concerning the evolution of germline mutation processes in humans. This can include comparisons with datasets of human somatic mutations or germline mutations from other species. Depending on your interests, focus can be on methods development, large-scale data analysis, or both.

Your competences
We are looking for a highly motivated applicant that have or are about to obtain a PhD in a relevant subject, which could be bioinformatics, population genetics, statistical genetics or a similar subject.

Furthermore you should have:

  • Experience with genomic data analysis.
  • Good programming skills
  • Fluency in spoken and written English

Deadline: 31 October 2019

For details click here


Bioinformatician/data scientist for research support and training

The Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg has created a local representation in the European bioinformatics infrastructure ELIXIR. This Luxembourgish ELIXIR Node, hosted in the LCSB, is dedicated to translational medicine data management and provide infrastructure, training and services. The Bioinformatics Core Facility of the LCSB is expanding its research activities and is seeking a highly motivated a developer/researcher (Position: Research and Development specialist on project).

Your Profile

  • A Master degree in bioinformatics or related biological disciplines and extensive experience in translational research environments
  • Solid experience in data analysis environments commonly used in bioinformatics and systems biology, strong in either Python, R or Matlab as well as the Unix environments
  • A strong working knowledge of statistical concepts
  • Laboratory experience in omics environments – sequencing, transcriptomics or proteomics is a plus
  • Familiarity with training environments, e.g. as instructor for Carpentry courses, Elixir Train-the-Trainer courses or as teacher in university-level education
  • Interdisciplinary communication and presentation skills
  • Excellent working knowledge of English

We offer

  • Fully funded position at the Bioinformatics Core Facility of the LCSB, headed by Prof. Reinhard Schneider
  • A multi-disciplinary international research environment, connecting institutes in Luxembourg and Europe through Elixir
  • The University of Luxembourg offers competitive salaries and is an equal opportunity employer

Please apply online until 15/11/2019.

For details click here


Posted on October 16, 2019

Bioinformatician in translational genomics

Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has 40 000 students and 7 600 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the human condition. The Faculty of Medicine is a part of Lund University, and is responsible for education and research within medicine and healthcare. Our academic programs are closely linked with the healthcare system and are firmly anchored in the faculty’s strong research tradition. Our research spans a broad field within experimental preclinical research, near-patient clinical research and health sciences research. The Faculty of Medicine, with its 1,800 employees and 2,700 students in Lund and Malmö, is a knowledge-intensive meeting place for students, teachers and researchers from all over the world.

CTG (https://www.ctg.lu.se/) is a prioritized research infrastructure at the Faculty of Medicine at Lund University, co-funded by Lund University, Region Skåne and SciLifeLab. At the center there is great expertise in sequencing and genomics technologies, and from a national and international perspective, the unit is at the forefront of technology with access to very powerful sequencing instruments (eg Illumina's NovaSeq as well as long read instruments, eg Oxford Nanopore GridION) and methods for single cell analysis. For high performance computations, the center uses a dedicated cluster at Lund University's super computer center (LUNARC).

Requirements

The applicant shall have:

  • Doctoral degree (PhD) from appropriate research field (ie with bioinformatics and genomics as a base) or equivalent (at least 4 years) work experience or advanced studies in bioinformatics, from business, healthcare or academia
  • Experience in working with sequencing data (e.g. WGS, WES or RNA-seq)
  • Experience in working with a terminal based in Linux environment and in working with at least one scripting language (eg Python, Perl or R)

Reference number PA2019/3381

Last application date 04.Nov.2019

For details click here


POSTDOCTORAL ASSOCIATE in Structural Bioinformatics

Established in 1930, Duke University School of Medicine is the youngest of the nation’s top medical schools. Ranked tenth among its peers, the School takes pride in being an inclusive community of outstanding learners, investigators, clinicians, and staff where traditional barriers are low, interdisciplinary collaboration is embraced, and great ideas accelerate translation of fundamental scientific discoveries to improve humanhealth locally and around the globe.

The Postd octoral Appointee holds a PhD or equivalent doctorate (e.g.ScD, MD, DVM) . Candidates with non-US degrees may be required to provide proof of de gree equivalency.1. A candidate may also be appointed to a postdoctoral position if the candidate has completed all of the requirements for a de gree but the degree has not been formally conferred: in this case, the c andidate may present evidence of completion of the degree requirements, together with a statement documenting the date on which the degree is to be conferred.If the degree is not conferred by this projected date, the postdoctoral appointment may be terminated.

Needed to enablethis work:

Background in structural bioinformatics or structural biology Potential tocontribute bothto technical enhancements in the Phenixsoftware system and theMolProbity web service, and also to b asic research that coupleslarge-scale analysis of macromolecular conform ations with development of newmodel-validation tools.

1) Proficiency inat least two of our most-used programming languages (primar y: Python and C++;secondary: C, PHP, Java, and Javascript)

2) Experience insolving or analyzing macromolecular 3D structure.

For details click here


Posted on October 14, 2019

Postdoc Position in Computational Cancer Biology

A postdoc position is computational cancer biology is available in the lab of Dr. Ashley Laughney at the Weill Cornell Medical College (WCM) in NYC. The lab integrates powerful systems biology methods – including massively parallel, single cell sequencing and quantitative imaging technologies – with mouse models of metastasis to better understand lineage plasticity and immune recognition across cell states observed in development and cancer progression.

We are eager to add innovative, determined and enthusiastic researchers to our highly inter-disciplinary team and are especially interested in recruiting highly motivated candidates with backgrounds in constructing gene regulatory networks, bioinformatics analysis of single cell transcriptomic and epigenetic data, high content imaging and feature extraction methods, and machine learning. Postdoc applicants should hold a PhD, MD or doctoral level equivalent in the areas listed above or other related fields.

Interested in joining the fun? Email LaughneyLabPositions@gmail.com the following as a single PDF: (1) a cover letter describing your current and future research interests, (2) your CV, and (3) names and contact information for three references and (4) up to two reprints. Additionally, please arrange for three letters of reference to be emailed on your behalf. Postdoctoral applications will not be reviewed until all letters of reference are received. We are open to applicants from a variety of backgrounds, including both theory and experiment.

For details click here


Postdoctoral Fellow, Human Genetics (Bioinformatics)

The Institute for Health Innovation’s Healthy Nevada Project in Reno, NV is searching for Postdoctoral Fellows specializing in Human Genetics to join the research team located at the Desert Research Institute in Reno, Nevada. The Healthy Nevada Project focuses on finding associations between an extensive Electronic Medical Record database and a growing population of sequenced participants using the Helix Exome+ platform. There are two open positions broadly focused on: 1) examining relationships between genotype and phenotype in the Healthy Nevada population; 2) identifying Gene X Environment interactions as part of a newly funded NIH R01 project to examine genetic effects and environmental carcinogens with cancer.

Successful candidates will use and develop statistical genetics tools and develop techniques to examine human genotypes and phenotypes to generate focused hypotheses driving the identification of disease targets. The postdoctoral fellows will collaborate with a team of computational molecular biologists and clinical data scientists, clinicians and physicians to study medical and sequencing data to uncover links to and regulation of diseases relevant to Northern Nevada. This position will be responsible for supporting high-level genomics and phenomics research and publications.

Required Qualifications

  • Ph.D. in bioinformatics, molecular biology, biochemistry, computer science, or related fields from and accredited institution
  • Minimum three years of experience with genomic data or electronic medical data
  • Proven research experience and publication records

Preferred Skills

  • Genetics/genomics data analysis: GWAS, Whole Genome/Exome Studies, WGES, PheWAS
  • Knowledge and experience with gene-collapsing methods
  • Strong R programming skills
  • Well-versed in Unix/Linux environments and shell scripting
  • Experience using bioinformatics tools and databases: PLINK, PSEQ, IMPUTE2, BEAGLE, UCSC Genome Browser, dbSNP, UK Biobank
  • Python and/or Perl experience

Post code: R0118752

For details click here


Posted on October 11, 2019

Postdoctoral Scientist - Bioinformatics & Functional Genomics

Principle Investigator, Dr. Megan Hitchins, is a member of the faculty of Biomedical Sciences at Cedars-Sinai Medical Center and is situated with the Center for Bioinformatics and Functional Genomics (BFG). The BFG brings together teams specializing in bioinformatics and computational biology, functional analysis of the genome and epigenome coupled with next generation sequencing, epigenetic profiling, and genome editing, to provide a complete pipeline for identifying the functional consequences of genetic and epigenetic variation in cancer risk, subtypes, and outcomes. Dr. Hitchins’ group focuses in particular on the role of genetic and epigenetic variants in high-risk cancers, and on DNA methylation markers of cancer, as applied to the detection of circulating tumor DNAs.

As an appointed Postdoc, you will work with Dr. Hitchins on germline genetic variation, RNA expression, and DNA methylation associated with cancer phenotypes. You will be supported by a Research Associate/Laboratory Manager and work within a highly integrated and multi-disciplinary group comprising senior and junior post-doctoral scientists, research technicians, clinical fellows and graduate students. You will be expected to conduct wet-lab research and statistical analyses of data (both directed and independent) under the mentorship of Dr. Megan Hitchins, submit and publish papers and posters, and make oral presentations. This post-holder must be well organized and be able to demonstrate written and oral presentation skills.

Essential job duties and responsibilities:
  • Lead research project(s) in the genomics and epigenomics of cancer that form part of the research program under the mentorship of the Principal Investigator. This will include the undertaking of intellectual, technical (wet-lab), and analytical aspects of the project(s)
  • Draft manuscripts for publication and author or co-author
  • Contribute to the drafting of grant proposals
  • Attend, contribute to, and present at laboratory group meetings and departmental meetings
  • Present research findings at national and international conferences
  • Provide miscellaneous research support (ad hoc data analysis, hypothesis development, programming, troubleshooting, etc.)
  • Lead and train incoming Graduates Students, Research Fellows, lower level Research Associates, and other related support staff and may be requested by Pl to take on specific day-to-day supervisory activities
  • Comply with all safety standards and procedures
  • Assist with the establishment and maintenance of IRB proposals and protocols relating to projects in the laboratory
  • Assist with the maintenance of database and accompanying biorepository

Educational Requirements:

  • Ph.D in a relevant area (Human Genetics/Epigenetics/Cancer Biology/Molecular or Cellular Biology)
Experience:
  • At least 4 years of wet-lab experience, which may include the Ph.D training period
  • Ph.D. in a relevant area (Human Genetics/Epigenetics/Cancer Biology/Molecular or Cellular Biology)
  • At least 4 years of wet-lab experience, which may include the Ph.D training period

Requisition # 19002437

For details click here


Postdoctoral Fellow in Computational Systems Biology

The Luxembourg Centre for Systems Biomedicine (LCSB) was created within the Health Technologies Initiative from the Government of Luxembourg as one of the research priorities of the University of Luxembourg. The LCSB is an Interdisciplinary Centre of the University, independent of the faculties and it combines experimental and computational approaches to analyze complex biological systems and disease processes from a systems biology perspective. The Computational Biology Group (CBG) provides the LCSB with a solid infrastructure in developing theoretical framework for computational modeling on biomedical problems, especially in the area of network biology. The CBG group includes researchers with theoretical, computational and wet lab backgrounds, thereby providing an unusual interdisciplinary environment.

The Computational Biology Group seeks a highly skilled and motivated Postdoctoral fellow to work on an exciting project that aims at developing a computational framework for modeling stem cell-niche interactions to understand the mechanisms of tissue homeostasis and regeneration. In particular, the selected candidate shall develop a cell-cell interaction network-based computational approach, using single-cell transcriptomics data, to model cell populations dynamics and design strategies for cell rejuvenation. Research will be focused on stem cells of skeletal muscle and to design strategies for enhancing regeneration in the aging muscle tissue. In addition, he/she will participate in the project management and planning, including the supervision of one Ph.D. student. This is a collaborative project with the Universitat Pompeu Fabra in Barcelona, where the experimental validation of the computational predictions will be conducted.

Your Profile

  • Ph.D. degree in computer science, engineering, physics or a related discipline
  • Strong computational skills
  • Prior experience in mathematical modelling of biological networks is strongly desired
  • A strong first-author publication record in the fields of Bioinformatics and Computational Biology
  • Excellent working knowledge in English

All applications should be sent in electronic version before December 1st, 2019.

Ref: 50015159

For details click here


Posted on October 09, 2019

Postdoctoral Fellow - Computational and Statistical Cancer Genomics

The Center for Cancer Research (CCR) is working to solve the most pressing problems in the field through basic, translational and clinical cancer research to create the cancer medicines of tomorrow and is dedicated to preparing the next generation of cancer researchers. Read more about CCR, the benefits of working at CCR and hear from our staff on their CCR experiences. ​

Successful candidates will have the advantage of working with a world-leading team in computational cancer biology and collaborate with experts in statistics, machine learning and related algorithms, etc., while at the same time having ready access to clinical cancer samples, including fresh tumor specimens from the operating theater, with which one can address new questions in real time. Our group is evolving to lead a novel and comprehensive multi-omics sequencing platform of patient tumors at the NCI, which will be unprecedented in its extent and unique possibilities.

Qualifications for this position include Doctor of Philosophy (Ph.D.) in computational sciences or related fields. Candidates should be proficient in bioinformatics, data analysis, algorithms, combinatorial optimization, machine learning and computational biology. Candidates with a strong background and track record in big data analysis, especially in the context of cancer genomics as well as other -omics, will be preferentially considered. A new postdoctoral fellow is expected to be highly motivated and productive, work independently as well as collaboratively with other lab members, and have a strong work ethic and intellectual commitment to the cancer research. Proficient communication in both spoken and written English is strictly required, and excellent interpersonal and organizational skills are highly desired.

For details click here


Postdoctoral Fellow - Cancer Genomics and Epigenomics

The Center for Cancer Research (CCR) is working to solve the most pressing problems in the field through basic, translational and clinical cancer research to create the cancer medicines of tomorrow and is dedicated to preparing the next generation of cancer researchers. Read more about CCR, the benefits of working at CCR and hear from our staff on their CCR experiences. ​

The CCR is dedicated to preparing the next generation of cancer researchers and offers a training environment that is second-to-none in quality of science and mentoring by outstanding principal investigators, including nine members of the National Academy of Science and eight members of the National Academy of Medicine. CCR offers fellows access to cutting-edge technologies and cores, a highly collaborative environment, awards and research forums to recognize outstanding post docs, continuous scientific symposia and lectures featuring leading researchers, a strong commitment to translational research, and a vibrant clinical research program housed in the world’s largest dedicated research hospital, the NIH Clinical Center.

Candidates should have a Ph.D. and/or M.D. degree in molecular biology, cancer biology or a related field, received within the last three years or scheduled to receive very soon. Successful candidates should have a deep understanding and experience in various genomic and epigenomic technologies, such as whole-genome sequencing, ChIP-seq and single-cell sequencing. A new postdoctoral fellow is expected to be highly motivated and productive in pursuing his/her research projects, work independently as well as collaboratively with other lab members, and share the lab’s interest and vision for the future of cancer classification and diagnostics. Proficient communication in both spoken and written English is strictly required, and informatic analysis skills of huge datasets will be a plus.

For details click here


Posted on October 07, 2019

Senior Bioinformatics Analyst

Weill Cornell Medicine is a comprehensive academic medical center that's committed to excellence in patient care, scientific discovery, and the education of future physicians in New York City and around the world. Our doctors and scientists-faculty from Weill Cornell Medical College, Weill Cornell Graduate School of Medical Sciences, and the Weill Cornell Physician Organization-are engaged in world-class clinical care and cutting-edge research that connect patients to the latest treatment innovations and prevention strategies.

Job Responsibilities

  • Responsible for biostatistical analysis and data interpretation for large data sets. Performs genomic analyses including mutation analyses, integrates datasets and generates figures summarizing results and key findings.
  • Implements pipelines for detecting and annotating mutations from single patient, whole-exome sequencing datasets.
  • Implements primary processing pipeline and quality control; runs pipeline(s) on all new samples.
  • Implements procedures for disaster recovery and resuming failed jobs.
  • Works closely with bioinformatics team(s) to define specifications for information systems, relational datasets, and sequencing analysis.
  • Develops novel algorithms and tools for high throughput data analysis.
  • Explores new computing platforms, performs benchmarking and implements data sharing.
  • Performs other related duties as assigned.

Education

  • Bachelor's Degree in related field

Experience

B.S. in molecular biology, genetics, bioinformatics, biomedical engineering or computer science desired. MS or PhD in systems biology, bioinformatics or computer biology is highly desired.

Approximately 3 years of related experience.

Bioinformatics analysis expertise as demonstrated by multiple published papers.

Excellent programming expertise in at least one of the following languages: C, C++, Java or Python.

Experience in biology and/or cancer biology is preferred.

Experience working in an academic environment is highly desired.

Previous experience in designing and building bioinformatics workflows preferred.

Previous experience analyzing and summarizing genomic datasets preferred.

Req Number 26581

For details click here


Computational Postdoctoral Associate

About the Center for Microbiome Informatics and Therapeutics (CMIT) was founded in 2014 to deliver therapeutics to patients with non-infectious, chronic, microbiome-associated disease. Incidence of microbiome-associated diseases like inflammatory bowel disease, Type 1 and Type 2 diabetes, autism, allergy, and asthma are on the rise in urban and industrialized populations and there is an urgent need for a new kind of intervention that is not only safe and effective but low-cost. We aim to do this by targeting the microbiome itself to restore health.

Apply your computational and mathematical skills to the analysis of large multimodal datasets to decipher interactions between the human microbiome and the human body, advancing translational microbiome research at the Center for Microbiome Informatics and Therapeutics.

Requirements

  • Ph.D. in Computer Science, Bioinformatics, Mathematics, Statistics or another relevant field

  • Experience with analyzing complex datasets

  • Familiarity with, or strong desire to learn about, next generation sequencing data analysis tools

  • Comfortable applying relevant statistical methods

  • Fluency in Unix, standard bioinformatics tools, and programing languages (primarily Python)

  • Outstanding written and oral English communication abilities

  • Independent, creative, highly-motivated, highly collaborative, and flexible team member

  • Interest in clinical trial design, patient-powered research, and the human microbiome

  • Experience in high-performance and/or cloud computing is helpful

Job ID: 0180

For details click here


Posted on October 04, 2019

Bioinformatician:  Proteomics data pipelines

We are seeking an enthusiastic Bioinformatician to join the Proteomics Team at the European Bioinformatics Institute (EMBL-EBI). The team is responsible of the maintenance and further development of the PRIDE (PRoteomics IDEntifications) database and related tools and resources. PRIDE is a world-leading international proteomics database, a founding member of the ProteomeXchange Consortium that is capturing large-scale mass spectrometry (MS)-based proteomics data from the scientific community and currently managing hundreds of TBs of data. In addition, the team aims to re-use and integrate proteomics data in other EMBL-EBI added-value resources such as UniProt, Ensembl and Expression Atlas.

The post holder will be working in the context of a BBSRC/NSF grant called “PTMExchange” which aims to: (i) analyse public proteomics datasets with the objective of disseminating high-quality PTM (post-translational modification) data from PRIDE into UniProt; and (ii) develop all the related infrastructure, including further developments in PRIDE, ProteomeXchange and the related data pipelines. The post holder is also expected to collaborate closely with the other partners in the grant and potentially other external stakeholders. The post holder may also have to contribute to other tasks related to the maintenance and development of the services and tools offered by the team.

Responsibilities:

  • Further develop and benchmark open proteomics data analysis pipelines, envisioned for the analysis of PTM data.
  • Develop infrastructure for the PTMExchange project, including further developments in PRIDE and ProteomeXchange.
  • Analyse public proteomics datasets.
  • Collaborate with the EMBL-EBI UniProt team to disseminate and integrate proteomics data from PRIDE into UniProt.

You must have a degree in computer science or bioinformatics and be able to demonstrate a minimum of 3 years’ experience in software development and/or bioinformatics data analysis, ideally with some knowledge of cloud technologies.

Closing Date: 29 October 2019

Reference Number: EBI01514

For details click here


Bioinformatician

The Erasmus MC Cancer Computational Biology Center (CCBC) is a bioinformatics and computational biology research facility. CCBC aims to innovate, facilitate and enhance omics-based cancer research, including genomics and proteomics, within the Erasmus Medical Center Cancer Institute. The objective is to develop and maintain a structured, dedicated and robust infrastructure for combining ongoing activities and creating synergy with different cancer research groups.

As a Bioinformatician you will collaborate in a multi-disciplinary team and should contribute significantly to solve general and specific questions within the cancer research field using your bioinformatics expertise. To accomplish this task, new in-house and publicly available Whole Genome Sequencing, RNA-seq, NGS single cell and proteomics data sets will be interrogated using both publicly and in-house developed computational methods. Furthermore you will develop tools to create and support a sustainable bioinformatics environment that strongly contributes to innovative computational cancer research. You will carry out state-of-the-art work on computational cancer biology using your excellent computer science skills. In a inspiring work environment, you will be a crucial member of a team that facilitates ongoing bioinformatics efforts and build robust long-lasting CCBC infrastructure.

Qualifications and skills: You have a BSc or MSc degree in Informatics, Bioinformatics or related field with, at least, two years of experience in (Bio)informatics, Statistics or Computer Science. Furthermore demonstrated excellent programming skills in R, Bash and preferably in Python and/or Java are required, together with proven experience in relational databases management systems, such as MySQL or PostgreSQL and Linux operating systems. Experience in analyzing next-generation sequencing data or mass spectrometry-based proteomics data is also a prerequisite.

For details click here


Posted on October 02, 2019

Postdoctoral studies in bioinformatics to understand T cell biology

The Department of Medicine, Solna, is one of the largest departments at Karolinska Institutet. The department consists of several divisions that are separated into different research groups. The core activities of the department are research, doctoral education and undergraduate education for medical and biomedical students. The research has three main profiles: allergy, cardiovascular medicine and inflammatory diseases.

Duties The postdoc will be collaborating with wet-lab scientists in both labs. The postdoc is expected to plan, execute and interpret bioinformatic analyses of primarily single-cell RNA sequencing data obtained from T cell receptor and mRNA sequences through Illumina sequencing of libraries obtained through the 10x Genomics workflow. In addition, the postdoc is expected to perform bioinformatic analyses of other datasets available in the labs. There will also be possibilities to analyze epigenetic data, primarily obtained using the ATAC-Seq platform. The postdoc is expected to carefully document the analyses, and to communicate the results within and outside of the research group. The postdoc is expected to work both independently, and as a collaborative and helpful team member. The duties furthermore include actively taking part in research meetings, contributing to the well-functioning of the local research environment, and assisting/training/supervising other lab members in minor computational analyses.

We are looking for a highly motivated, ambitious and talented person with excellent theoretical background and practical experience in bioinformatics, and genuine interest in T cell immunology. Prior experience in working with 10x-based sequencing datasets, ideally including feature barcoding will be highly valued. Excellent communication skills that allow for productive interactions with biologists lacking bioinformatics background will be key. This includes the willingness and ability to explain, justify and discuss analyses/model choices with other lab members and supervisors. The position requires dedication to the project, a high level of accuracy and attention to detail, and a strong desire to excel. A personal fit into the team will be of importance. A proactive and problem-solving attitude will be valued highly. Excellent communication skills in both spoken and written English are required.

Reference number 2-4902/2019

Last application date 27.Oct.2019

For details click here


Data Analyst / Bioinformatics Specialist

The Montgomery lab is looking for a Data Analyst / Bioinformatics Specialist to conduct genetic analyses, perform power calculations and statistics, present data and prepare reports, work independently and as a team player and perform other duties as assigned by supervisor. For additional information please visit: http://omrf.org/research-faculty/scientists/montgomery-courtney-gray/ .

Bachelor’s degree in Math, Statistics, MIS, Computer Science, Biostatistics, Epidemiology or related field and one year of relevant statistical and/or analysis experience and 3 – 5 years of relevant experience Applied analysis experience essential. Superb computer skills including experience with R, S-plus or similar statistical package required. Must have excellent communication skills and the ability to deal with diverse personalities and cultures.

Posting Number 000041

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Posted on September  30, 2019

Post-Doc Research Associate - Agricultural Bioinformatics & Data Sharing

The Department of Statistics and the Department of Agronomy and Horticulture at the University of Nebraska-Lincoln are pleased to recruit candidates for a postdoctoral position in agricultural bioinformatics and modern data management and sharing. This position is supported by the Quantitative Life Sciences Initiative, a university-wide program supporting the integration of the data and life sciences. We are seeking candidates with expertise in crop genetics, bioinformatics, and statistics, who have demonstrated a high level of skill in data management, bioinformatics and computational biology, and FAIR data sharing in the plant sciences.

The successful candidate will be expected to teach at least one regular course per academic year in bioinformatics and computational biology. In addition, the successful candidate will participate in program and curriculum development, including graduate seminars and workshops.

Minimum Required Qualifications:

• PhD in Statistics, Bioinformatics, Computational Biology, or closely related field.
• Experience with one or more data types in plant breeding and genetics and FAIR data principles, as demonstrated by refereed papers, presentations, or other completed projects, e.g., PhD thesis.
• Computing and methodological skills appropriate to the sharing and analysis of data types with which the candidate has experience.

Requisition Number:  F_190162

Application Review Date: 10/31/2019

For details click here


Computational Scientist/Bioinformatician

We are seeking a Computational Scientist to work in Professor Karlsson Hedestam’s group at the Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet in Stockholm. The group studies adaptive immunity and immunogenetics. For more information about the research, see http://ki.se/research/karlsson-hedestam

Adaptive immune responses depend on highly polymorphic gene segments that recombine during lymphocyte development to form highly diverse repertoires of antigen receptors. The Karlsson Hedestam group has developed methodology to study these gene segments in healthy populations and patient cohorts using next generation sequencing (NGS) and computational analyses (see www.IgDiscover.se). These projects generate large amounts of NGS data and the group currently needs to expand its bioinformatics support and increase its ability to develop new algorithms to solve bioinformatic problems for several ongoing research projects.

The successful candidate will have a solid background in statistics and computational biology, expertise in statistical and bioinformatics software and an ability to work in a multidisciplinary research environment. The individual should be highly driven and motivated to solve problems, as well as be able to work independently while also being able to communicate effectively with other members of the team. The candidate should have documented research experience over the past two years.A proven track-record of developing software tools that have been published in high-quality journals is valued. Demonstrable expertise implementing algorithms for sequence alignment, sequence clustering, and distance calculations will be preferred, as will experience with phylogenetic inference and NGS analysis. Extensive experience with Python, R or similar programming languages is required.

Assessment criteria

A selection will be made among qualified applicants using the following bases of assessment:

- Knowledge of Python, R and bash as well as experience with Github or related  resources

- Experience of working in a Linux environment

- Documented experience in applying computational analysis to NGS data

Reference number 2-4869/2019

Last application date 17.Oct.2019 11:59 PM CET

For details click here


Posted on September  27, 2019

Bioinformatics, Postdoctoral Research Fellow

Founded in 1957, UNLV is a doctoral-degree-granting institution comprised of approximately 31,000 students and more than 3,900 faculty and staff. To date, UNLV has conferred more than 136,000 degrees, producing more than 120,000 alumni around the world. UNLV is classified by the Carnegie Foundation for the Advancement of Teaching as an R1 research university with very high research activity.

The Postdoctoral Research Fellow will conduct bioinformatics research for the Personalized Medicine COBRE (Center of Biomedical Research Excellence) Genome Analysis and Acquisition Core at the Nevada Personalized Medicine Institute at UNLV. The successful candidate will be experienced in bioinformatics analysis, genetic data analysis, make corresponding tables and figures, and prepare reports for projects. The postdoc will be responsible for analyzing Next Generation Sequencing (NGS) data, data processing and analysis, including building analysis pipelines, databases, and visual/graphic display. Additionally, the postdoc will assist with database and server hardware management; install and test new versions of the database and ensure data is secure. They will contribute to research grants and publications, and assist with writing grant proposals and journal articles.

QUALIFICATIONS

A Doctoral degree (e.g., Ph.D.) received within the last five years in Bioinformatics, Biostatistics, or Computer Sciences is required.   Credentials must be obtained prior to the start of employment. The ideal candidate should also have the following knowledge, skills, and abilities:

  • Proven computational skills, programming skills (Python, C/C++, and R), and experience in performing data analyses of NGS data are required.
  • Practical experience in genomic data management, high-dimension data analysis is required.
  • Knowledge and experience in SAS programming, data analysis and statistical modeling are required.

For details click here


Research Scientist (f/m/d) Bioinformatics

Evotec is a leader in the discovery and development of novel small molecule drugs with operational sites in Europe and the US. The Company has built substantial drug discovery expertise and an industrialized platform that can drive new innovative small molecule compounds into the clinic. In addition, Evotec has built a deep internal knowledge base in the treatment of diseases related to neuroscience, pain, inflammation and metabolic diseases. Leveraging these skills and expertise the Company intends to deliver superior science-driven discovery alliances with pharmaceutical and biotechnology companies.

We are applying advanced methods in Transcriptomics, Proteomics, CRISPR and compound screening to generate large volumes of biological data. In close collaboration with wet-lab and project scientists, the bioinformatics team analyzes these data to generate knowledge about gene function and compound activities in various disease areas. As integral part of the data analysis, we develop our own pan-omics software platform.

Your key responsibilities

  • Develop tools and methods for multi-omics data analysis, e.g. high throughput RNA-Seq, Genomic Sequencing and Proteomics, within our interactive pan-omics platform
  • Apply these methods to large-scale multi-omics data sets within several projects
  • Work with researchers in interdisciplinary project teams in multiple research programs

​Your Qualifications

  • Master’s degree or PhD in bioinformatics, computational biology or a related natural science discipline
  • Experience in multi-omics data analysis and method development
  • Demonstrated strong programming skills in R and at least one additional programming language (e.g. Python, JavaScript)
  • Proficiency in working with bioinformatics tools and understanding of common bioinformatics algorithms

For details click here