Jobs in Bioinformatics, Genomics and Life Science
Job Alerts in this week (February , 2020)
Update on February 19, 2020
Postdoctoral position in bioinformatics to explore novel perspectives of 3D epigenome
Karolinska Institutet is one of the world's leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 per cent of the medical academic research conducted in Sweden and offers the country's broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine.
Division We are seeking a highly motivated postdoctoral researcher in bioinformatics to join a consortium of two research teams dedicated to understand the function of 3D epigenome folding and its deregulation in human diseases from entirely novel perspectives. The candidate is expected to drive a postdoctoral project and participate in collaborative efforts to uncover hitherto unknown therapeutic targets in complex diseases, such as cancer. The work will be carried out at the department of Oncology and Pathology in the labs of Drs Anita Göndör and Rolf Ohlsson. We have innovated state-of-the-art techniques enabling the analysis of 3D chromatin structures and chromatin fibre networks in single cells and small cell populations to provide unique opportunities for novel discoveries.
Duties The successful applicant will employ state-of-the-art bioinformatic techniques adapted to the analyses of single cells, and join a lab currently consisting of 4 PhD students, 7 postdocs and four affiliated professors.
In addition, it's advantageous if the successful candidate has:
- Experience in the analysis of NGS data, in particular: RNA-seq, single cell RNA-seq, ChIP-seq, 3C-based chromatin interactome datasets
- Experience in network analysis
- Excellent knowledge in biostatistics
- Extensive experience in using R/BioConductor, Unix/Linux environment (prior scripting language experience e.g. Python/Perl is a plus)
- Experience in data visualization
- Experience in meta-analysis
- Experience in SNP calling from NGS data is a plus
- Proficiency in written and spoken English
- Good understanding of biological concepts and/or willingness to learn
- Experience in working with wet lab scientists
Reference number: 2-844/2020
Last application date: 01.Mar.2020
Postdoctoral Position in Bioinformatics
We are interested in understanding the intersection of genetics, genomics and human disease, with a focus on cancer. By leveraging large datasets and utilizing different computational methods we are better able to investigate the biology underlying cancer and other diseases.
- A PhD degree in Computational Biology or Bioinformatics, or other relevant field (e.g. statistics, computer science, or quantitative biology)
- Experience in algorithm development
- Experience in the application and development of statistical methods or machine learning algorithms
- Experience analyzing microarray and/or next generation sequencing data
- Demonstrable expertise in R/Matlab/Perl/Python and other computational skills
- Knowledge of basic molecular biology
Please send your CV with current publications and contact information for three references to Chao Cheng, Ph.D.
Posted on February 17, 2020
Postdoctoral position in Bioinformatics
The Human Genetic division is seeking a Postdoctoral Fellow to join the Deciphering Developmental Disorders in Africa (DDD-Africa) project. Developmental disorders are severe, chronic disabilities attributable to mental and/or physical impairment, which occur during childhood and are likely to continue indefinitely. The genetic aetiology of developmental disorders is complex and therefore traditional diagnostic tests have a low success yield. Our aim is to assess the utility of new genomic sequencing technologies as potential diagnostic tools for developmental disorders. The fellow will have the opportunity to work with a dynamic, multidisciplinary group of researchers based in the Wits/NHLS Division of Human Genetics, Johannesburg. They will be expected to lead bioinformatics analyses and oversee data storage for the DDD-Africa project. They will work closely with core project members and students to refine analytical approaches. A good understanding of human genetics is beneficial.
The successful candidate will be expected to assist in the design, implementation, and execution of standard and custom pipelines for routine genomic sequencing data analyses. Perform robust data quality control and validation. Work closely with bench scientists to understand and help accomplish their research goals. Contribute to the writing and submission of journal manuscripts. Solve problems collaboratively as well as independently. Work well within a team. Be able to prioritize and shift focus to other tasks when required. Have excellent communication and interpersonal skills. Have good time management skills, and the ability to work to deadlines The position will be based at the National Health Laboratory Services (NHLS), Braamfontein.
PhD in bioinformatics or a related field.
Experience in the analysis of next-generation sequencing data.
Proficiency in common scripting languages and analysis packages (e.g. Python, R).
Strong written and oral communication skills.
Active publication record, published in peer-reviewed journals
The closing date for all applications is 25 February 2020
Research scientist in the field of Bioinformatics and Data Management
The Institute of Bio- and Geosciences, Plant Sciences Division (IBG-2), develops integrated concepts for the intensification and sustainability of plant production for the bioeconomy on the basis of molecular, physiological and ecological expertise. The aim is to improve yield, adapt quality to different forms of use (food, feed, raw materials, bioenergy), close nutrient cycles - generally adapt both production and product use to future climate and production conditions. IBG-2 is a world leader in plant phenotyping, with excellent knowledge of the dynamic interaction between plants and the environment, combined with technology development, engineering and bioinformatics. The department develops and operates relevant next-generation infrastructure platforms and technologies and makes them available to external users.
You will be responsible for managing and operating interdisciplinary research projects in the framework of EPPN 2020, EMPHASIS and EOSC-Life aiming at enabling interoperability of plant data in the European scientific community. The concrete data management challenges of this position include: (i) structuring and standardizing data as basis for interoperability; (ii) preparing metadata in accordance with the FAIR principles; (iii) developing software capable of handling large volumes of scientific data, adapting itself to evolving data models, and enabling useful access in the form of a standard application programming interface (API) and a graphical user interface (GUI); (IV) developing strategies and data policies supporting the technical aspects of data interoperability.
- A university degree in computer science or a natural scientific discipline with relevant and proven experience in the field of activity
- Sound knowledge of and experience in bioinformatics and data management, especially in the design, development, and implementation of requirement-oriented, complex web applications, database applications, and storage technologies
- Sound experience in the management of research projects, preferably in an international context.
- Knowledge of and experience in distributed computing and/or the parallelization of applications (e.g. workload managers, Pachyderm framework)
- Experience in programming languages and platforms (e.g. Node.js, R, Scala, Python, C/C++, Fortran)
- Experience in Linux administration, Shell, and particularly Docker
Posted on February 14, 2020
Postdoc in Bioinformatics
The Novo Nordisk Foundation Center for Basic Metabolic Research’s vision is to strengthen interdisciplinary research that transforms our basic understanding of the mechanisms that underlie metabolic health and disease, and to accelerate this knowledge toward new prevention and treatment strategies.
The position available is in the Translational Cell Metabolism Group headed by Associate Professor Camilla Schéele. The research group studies human adipose tissue. A major focus is how secreted factors affect metabolism by mediating crosstalk at a cellular or tissue-level. The group has a strong international network and several active collaborations in the field. We are also highly collaborative and supportive within the group, and strive for diversity in gender, age and nationalities.
The ideal candidate combines:
- A PhD degree in Bioinformatics/Systems biology, Biology, Biochemistry, Molecular Biology, Molecular Biomedicine, biomedical or natural sciences
- Excellent scientific track record in relation to career stage
- Expertise in scripting in R or Python
- Advanced skills in establishing of omics analysis pipelines and interpretation of the results.
- Solid statistical knowledge and advanced level of using R Bioconductor packages and developing Shiny applications.
- Capability in integrative network and systems biology analysis
- Familiarity with basic Machine learning techniques (preferable)
- An interest in interacting with experimental biologists and explaining basic bioinformatic approaches
- Excellent English communication skills, both written and oral
Application Deadline: March 22, 2020, 23.59pm CET
Postdoc position in Bioinformatics / Computational Genomics
The Animal Genomics group within the Institute of Agricultural Sciences at ETH Zurich investigates animal genomes. The group applies bioinformatics and statistical methods to detect and characterize trait-associated sequence variation. We are looking for a motivated and talented Postdoc that is eager to work on cutting-edge research projects within our young and international team.
Our research focuses on the genomic characterization of cattle and pig populations. We have established a comprehensive a database of whole-genome sequencing variants that segregate in various pig and cattle breeds. We have access to whole-genome genotyping and sequencing data of >40'000 (partially) progeny-tested animals with excellent phenotypic records. This data enables powerful genome-wide association studies. Other ongoing projects include the development of graph-based reference genomes, the characterization of individual cattle genomes using long sequencing reads (PacBio and ONT), and the de-novo assembly of mammalian genomes. Moreover, our group is involved in international endeavours that aim at characterizing animal genomes such as the 1000 Bull Genomes Project and the EU H2020 project BovReg.
The successful candidate should have a strong research interest in bioinformatics, statistical genomics, computational biology or animal genetics. Experience with a programming/scripting language (e.g., python, R) is required as well as a certain level of proficiency in high-performance computing. Applicants should hold a PhD (or should be close to the completion of the PhD thesis) in disciplines that are related to the PhD position (e.g., genomics, computational biology, bioinformatics, genetics, agricultural sciences, animal sciences). Affinity to computational genomics, bioinformatics and statistics is required. The writing of scientific papers and participation in international conferences requires good knowledge of English.
The application review will begin on April 1, 2020, and continue until the position is filled (and this advertisement is online).
Posted on February 12, 2020
Postdoctoral and Research Assistant Positions in Computational Biology
Postdoctoral and Research Assistant Positions are available in the laboratory of Dr. Benjamin Kidder at Wayne State University in the Barbara Ann Karmanos Cancer Institute, an NCI-designated Comprehensive Cancer Center. Our lab focuses on epigenetic mechanisms of stem cell fate, genome stability, and reprogramming/transdifferentiation, using experimental, genomics, and bioinformatics approaches. We integrate functional studies and computational analysis of epigenomic and transcriptomic data.
Qualified bioinformaticians or computational biologists should have a (1) Ph.D. or master’s degree in Bioinformatics, Genomics, Computer Science, Statistics, or a related field, (2) computer programming skills in at least one language (python, perl, C/C++, R), (3) experience with analyzing next-generation datasets, (4) first or co-first publications, (5) excellent communication skills (oral and written).
Interested applicants should email a cover letter with a description of research interests, curriculum vitae, and contact information for three references with subject “Postdoctoral Position” to Dr. Benjamin Kidder at: Benjamin.firstname.lastname@example.org
Postdoc position in Bioinformatics/Computational Biology
Applications are invited for a postdoctoral research position at the Institute of Biology of the Ecole Normale Superieure in Paris, France. We are seeking an enthusiastic postdoc to work on computational developments for functional interpretation of human genetic variation. This project is part of a nation-wide collaborative effort to analyse and interpret genetic variation in an extensively phenotyped sample of the French population. The postdoc will explore machine-learning and statistical approaches to (i) integrate functional and population genomics data in order to identify non-coding genetic variants with an impact on gene expression, (ii) infer tissue-specific outcomes of allelic variation in humans, and (iii) interpret molecular impacts of allelic variants associated with well-characterized phenotypes studied by collaborators.
Applicants must have a PhD degree or equivalent, or have submitted their thesis at the time of application. The ideal applicant will have experience with computational analysis of genomics data, methodological developments for genomics, machine-learning for biological applications, biostatistics and/or population genetics ; however, we will also consider applicants coming from computer science, physics and mathematics with relevant experience with machine-learning or big data problems and a strong interest for biology. Programming skills in a relevant bioinformatics language (Python, R, etc) are a requisite. Candidates will also be expected to write manuscripts, deliver research presentations and be involved in the daily life and management of the laboratory.
Application deadline : February 28th 2020
Posted on February 10, 2020
Postdoctoral position in bioinformatics & analysis of single cell genomics data sets
The lab of biomedical microfluidics (LBMM) is looking for a bioinformatician analyzing single-cell RNAseq datasets. Our overall aim is the development of novel therapeutics (e.g. antibodies) against a variety of diseases, including cancer. The lab has a very translational focus and runs a tech development lab on the EPFL campus, a translational lab in the AGORA cancer research center (with direct access to patient material) and a startup company making the results of our research widely available. The successful candidate will closely interact with other bioinformaticians at the European Molecular Biology Laboratory (EMBL) in Heidelberg, at Heidelberg University and at the University of Lausanne.
Main duties and responsibilities include :
- Analysis of single-cell RNAseq data sets.
- Analysis of barcoded DNA sequences.
- Outlier analysis.
- Preparation of data plots such as t-SNE, PCA.
- Help in the design of wet lab experiments.
Your profile :
- Hands on experience in the analysis of genomics data sets. Solid expertise in R, Python, etc.
- Knowledge of single-cell RNAseq workflows such as 10X genomics, DropSeq, Fluidigm.
- PhD in bioinformatics.
- Good communication skills.
- Highly motivated and keen to work in an interdisciplinary environment.
Postdoc in bioinformatics with focus on integrative data analysis
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.
The group of Integrative Omics and Precision Medicine is headed by Professor Mathias Uhlén and is located at SciLifeLab Stockholm. The main project of this group is the Swedish SCAPIS SciLifeLab Wellness Profiling (S3WP) program, which was started to define the wellness profiles in a healthy population based on a combination of classical clinical chemistry, advanced medical imaging and extensive omics profiling and is now focusing on disease cohorts.The group is also involved in data integration within the Human Protein Atlas project, where a combination of genomics, transcriptomics, proteomics and antibody-based profiling is used to study the global protein expression patterns in human cells, tissues and organs.
The candidate must have a strong background in bioinformatics, computer science, computational biology or equivalent with a profound knowledge about biology and biostatistics. Furthermore, the applicant must have:
- A doctoral degree in bioinformatics, biostatistics, biotechnology, computational biology, or a related field (or an equivalent foreign degree), obtained within the last three years prior to the application deadline.
- Excellent skills in English, both written and spoken.
- Documented experience in management, visualization, analysis and integration of large scale biological data sets.
Reference number C-2020-0303
Last application date 27.Feb.2020
Posted on February 07, 2020
Computational Biologist-Postdoctoral Scientist (Immuno-oncology)
The team of Prof. Abhishek D Garg (Department of Cellular & Molecular Medicine, KU Leuven), working in close collaboration with the clinical team of Prof. Sabine Tejpar (Department of Oncology, KU Leuven) is seeking, in this collaborative context, a suitable postdoctoral candidate with specialization in computational biology approaches. Prof. Garg’s team aims to apply advanced computational biology approaches in the context of immuno-oncology, to tumour transcriptomics data generated in close collaboration with Prof. Tejpar, who is involved in conducting several cancer immunotherapy relevant clinical trials.
The aim of Prof. Garg’s team, in collaboration with Prof. Tejpar, is to capitalize on multi-dimensional cancer patient datasets (tumour/lymph node/polyp bulk or single-cell RNAseq, TCR sequencing, microbiome 16S RNA or meta-transcriptome and others) and apply highly relevant computational biology/immunology and systems biology approaches to shed light on various clinically relevant immuno-oncology areas like effector functions or exhaustion of tumour-infiltrating lymphocytes, polarization of tumour-associated myeloid cells (DCs or macrophages), cross-talk between normal or tumorigenic tissue and last but not least, immunological cross-talk with environmental factors like gut microbiome.
We are looking for a computational biologist/bioinformatician who is highly motivated, well organized and dynamic with a high level of independence and creative thinking but a flexible research approach: You need to have a PhD with a topic in one of the following areas: Bioinformatics, computational biology, systems biology or similar.
You can apply for this job no later than April 30, 2020
The CoLabs are a collection of integrated laboratories specializing in infrastructure or technologies. It seeks to revitalize the model for core resources by capitalizing on critical personnel and cutting-edge technologies, and driving collaboration across disciplines. The model will house all CoLabs teams in a contiguous space and create a set of common pipelines and workflows in one centralized locale. It will recruit and retain world-class staff through project engagement, backstopped “tenure,” and annual operational funds. It will develop and invest in transformative methods and technologies.
The Genomics CoLab serves as an innovative hub of molecular biologists, genomicists and bioinformaticians engaging in collaborative research across UCSF campuses. At the Genomics CoLab, we emphasize in the development of novel genomic approaches and providing advanced genomic and bioinformatic resources for investigators who wish to integrate modern genomic approaches into biological research. These approaches include bulk- and single-cell RNA-seq, small RNA-Seq, ChIP-Seq, ATAC-seq and whole exome/genome sequencing. We are also actively working on integrating novel genomic methods such as combinatorial genomic methods, special transcriptomics, and new epigenomic approaches such as CUT&TAG.
• Bachelor's degree in biological science, computational/programming, or related area, and/or equivalent experience/training
• Basic knowledge of bioinformatics methods and data structures
• Basic project management skills
• Basic knowledge of modern biology and applicable field of research
• Basic understanding of molecular genetic principles
• Basic knowledge in Python and/or R
• Ability to communicate technical information in a clear and concise manner
• Self motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills
• Basic consultation and strong communication skills
• Strong organizational and interpersonal skills for working in a multi-discipline and collaborative team
• Basic knowledge of applications programming and web development
• Basic knowledge of databases
• Basic knowledge of application and data security concepts
• Working knowledge of next generation sequencing (NGS) methodologies and applications
• Previous exposure to Linux/Unix systems
• Interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization
Job ID: 54649BR
Posted on February 05, 2020
System Biologist & Data Scientist positions
Centaura is an ambitious and industry-defining project aimed at fighting aging. Instead of targeting one single reason why humans grow old, Centaura applies a multi-factor approach to understand the forces driving aging, identify the connections between aging and the onset of chronic health conditions, and develop novel interventions that extend human health and longevity. Centaura is headquartered in Switzerland, with ongoing projects in the UK, USA, Russia, and Singapore.
We are looking for Data Scientists and System Biologists to join our ‘Aging Profiles’ project. The primary goal of the project is to differentiate multi-omically determined clinical markers and age parameters that correspond to aging in different organ systems across individuals in order to define “age profiles.” In other words, map the trajectories of functional decline in specific organ systems. To achieve this, we will combine various omics profiles with medical records. By applying machine learning analyses, we will determine which mutations are the primary drivers of a degenerative process in an organ. This approach will allow us to generate novel predictors, which can then be used as benchmarks for clinical intervention. We envision that data generated from our research will be used in proactive medicine.
Required experience & skills
- MSc/PhD candidates with a strong background in Systems/Computational Biology, Bioinformatics or related areas. Experience in Aging research is a plus.
- Strong programming skills
- Strong background in statistical methods
- Experience in the analysis of large-scale omics data
- Full English language proficiency
To apply for this position please send a CV and a brief letter describing your research experience and interests to email@example.com.
The Department of Bioinformatics at the University of Texas Southwestern Medical Center is looking to hire a faculty position at the level of an Instructor. Candidates must posses a Ph.D.
Job duties as Instructor include:
- Organize our weekly “rapid fire” paper review in lab meeting where we select the articles we read and present in the weekly journal club.
- In the wet-lab part of our group, train technicians, graduate students and postdoc in molecular cell biology. This includes instructions in current and novel protocols and techniques and help them setting up new assays and validate them.
- In our bi-weekly subgroup meeting on cell and molecular biology run tutorials on novel technologies in the field of molecular biology, biochemistry and in particular all flavors of genome engineering and screening technologies.
- Occasionally, organize seminars with field scientist who support our wet-lab equipment. This helps us keeping up to date with new technology development and helps train our students and postdocs on these instruments.
- As outlined in my development plan, I have one more project to finish and plan to hit the job market after the reviews from the first submission are back.
- All the above
- Help one or our late stage graduate student getting his manuscript ready for submission and potentially work on revisions that will be required for re-submissions later this summer. This includes hands on molecular and cell biology support, but also guidance in the preparation of the figures and manuscript writing.
Posted on February 03, 2020
Postdoctoral Researcher in Integrated Multi-Omics Analyses of Human Atherosclerosis
The prospective postdoctoral researcher will be integrated in the Vascular Surgery research group, MMK, KI. The Vascular Surgery group lead by Prof Ulf Hedin, MD, PhD is dedicated to translational and clinical research on vascular diseases and pathological vascular conditions. The Group is situated at the new BioClinicum building and consists of ~20 members including 5 PIs, researchers, clinicians, PhD students and technical staff. For more information about the Group and research activities, please visit: https://ki.se/en/mmk/vascular-surgery Within the Vascular Surgery research group, the Team Vascular Molecular Medicine led by PI Ass Prof Ljubica Matic, MSc, PhD is specialized in molecular mechanisms underlying atherosclerosis and vascular injury. This Team gathers 5 PhD students and 1 postdoc and more information can be found at: https://www.cmm.ki.se/ljubica-matic-team.
The suitable candidate should have a bioinformatic background, programming skills and interest in the complex pathophysiology of vascular diseases. We are looking for a highly motivated person that should be dedicated to full time research, have the potential to work both independently and within a translational team, and manage the close collaboration between academia and industry. The postdoc will be in a position to manage different collaborations and contact with core facilities for omics analyses. The daily presence at work will be required despite the computational nature of analyses. Advanced experience in several different types of omics bioinformatic analyses and programming will be assessed as highly meritorious. The appointed person will be expected to plan, perform, analyze and interpret results independently and within the Team, present at congresses, and participate in national/international collaboration networks. Willingness to work flexibly in order to achieve project demands and targets as agreed within a Team is necessary.
Reference number 2-495/2020
Last application date 28.Feb.2020 11:59 PM CET
Bioinformatics Scientist, Translational Genomics
We are seeking a highly motivated Bioinformatics Scientist to join our Translational Genomics group supporting computational efforts across the Research organization. Our Translational Genomics efforts span the interface of human genetics, functional genomics, molecular biology, disease model engineering, and advanced computational methodology. This group works closely with our disease area scientists to identify new therapeutic hypotheses and advance transformative medicines.
As a member of the Genentech Bioinformatics & Computational Biology department, he/she will work both independently and as a member of interdisciplinary teams, carry out data analysis and integration across various domains, and apply best-in-class algorithms — or develop new algorithms — that directly address motivating biological questions. Regular publication of both scientific and methodological results is strongly encouraged. Finally, the successful candidate will be able to effectively present complex results in a clear and concise manner that is accessible to a diverse audience of quantitative, experimental scientists.
- PhD in bioinformatics, computational biology or similar, with a strong publication record. Alternately, a PhD in molecular biology with a very strong record of high-throughput data analysis, supported by publication in this area.
- A solid understanding of algorithmic approaches to analyze genomic data as well as tools and genome databases. Candidates with working knowledge of genome editing and gene expression/function will be prioritized.
- Experience and interest in analyzing and interpreting data generated by next-generation sequencing technologies such as long read sequencing and a variety of single-cell sequencing applications.
- An understanding of the statistical principles, machine learning methods and current best practices in high-throughput molecular data analysis.
- Strong experience in the use of a high-level programming language such as R or Python for complex data analysis, familiar working in Linux and HPC compute environment.
Job ID: 201904-110911
Posted on January 31, 2020
Are you a skilled microbiome bioinformatician? Would you like to be part of a dynamic team to help SNIPR BIOME develop new medicines? If yes, you have the opportunity to join SNIPR BIOME in the capital of Denmark, Copenhagen. Our main goal is to engineer microbiomes using CRISPR technology, to treat a number of serious and life-threatening diseases, such as diabetes, infectious diseases and cancer. The working environment is fun, fast-paced, collaborative, and outcome focused.
We are looking for an experienced bioinformatician with fundamental skills in biological data analysis. The ideal candidate must have significant and proven experience handling next-generation sequencing data, working with large datasets and with excellent interpersonal communication skills, fluent in English, meticulous attention to detail, and the ability to quickly adapt to changing circumstances and tasks.
- PhD in bioinformatics, computational biology, biostatistics, human microbiome ecology or similar
- Proven experience handling next-generation sequencing technologies
- Well-versed in either Python, Perl or R
- Experience with version control
- Experience writing helpful documentation and appropriate unit tests
- Experience with bioinformatics tools and working with high-throughput datasets
- Prior experience from a biotech/pharma is an asset, but not a requirement
- Energized by challenging projects at the conceptual forefront of the current state-of-the-art
- Creative thinker with perseverance in problem solving
- A proactive team player and an efficient communicator
- Fluent in English, spoken and written
Please submit your application no later than 23 February 2020 (local time) via the “Apply Online” button on the portal:
Postdoc in Spatial RNA Characterization Cancer Microenvironments
A 2-year postdoctoral position is open from June 1st 2020 or as soon as possible thereafter, in the project MICROGRAD: A new generation of microfluidics-based methods to study genetic and functional effects of complex spatiotemporal gradients in tumor microenvironments.
The tumor microenvironment fundamentally impacts tumor cell behavior, but cannot currently be accurately mimicked in vitro. This project will develop and apply a new generation of microfluidic devices that allow constitution of spatiotemporally precise gradients of acidosis and hypoxia, key properties of the tumor microenvironment. The devices will be validated using fluorescent reporters, and will be used to determine the phenotypic and RNA expression responses of tumor cells to the tumor microenvironment.
The ideal candidate has a background in RNA/molecular biology and/or genomics and strong expertise in methods development in genomics. Expertise in biophysics, microfluidics, bioinformatics and/or cancer biology is an advantage. Other essential requirements are a PhD in a life science field, a documented track record of strong scientific publications, and excellent written and spoken English. The candidate must be able to work autonomously as well as in a team and have a passion for working in a highly interdisciplinary environment.
The deadline for applications is March 25, 2020, 23:59 GMT +1.
Posted on January 29, 2020
Bioinformatics Position (Postdoctoral Fellow) in Desert Agriculture
We are looking for a highly motivated, enthusiastic, and computationally savvy postdoctoral fellow to join the Center for Desert Agriculture at KAUST. The mission of the KAUST Center for Desert Agriculture is to use cutting-edge technology to develop novel types of agro-ecosystems that can produce high-yielding crops with less water, fertilizers, and pesticides, and that can make use of marginal soils and saline water. An important component of the Center activities is the use of AgriGenomics to study wild and semi-domesticated plant species with a high degree of adaptation to a hot, arid and saline environment and to repeat the process of domestication. The postdoctoral fellow will work on the establishment of genomic resources for several wild and semi-domesticated species that serve as potential targets for desert agriculture.
We are seeking an outstanding young scientist who has recently been awarded a PhD degree in bioinformatics, genomics, or similar. Applicants must have a strong and demonstrated background in bioinformatics (genome assembly, genome annotation, and population genomics). Experience in cereal research is preferable.
For questions relating to the position, kindly contact Prof. Simon Krattinger (firstname.lastname@example.org). Applications should include: full CV and publication list, a statement of research interests not exceeding one page, and three academic references. Position start date is May 1st 2020.
Postdoc position in genomic selection for wheat
SLU Department of Plant Breeding performs research and education addressing global challenges affecting our livelihoods and the environment. The Plant breeding division works on putting traits into usable forms by understanding their diversity and genetics with the aid of advanced breeding tools. We apply this knowledge for the genetic betterment of cultivars of economically important crops.
You will mine large genotypic and phenotypic datasets and apply biometric approaches to study genotype by environment interactions for diseases and other agronomic traits in wheat. Develop genomic selection models for the traits and validate the models on the obtained progenies. The project is in a collaboration with the Swedish plant breeding company Lantmännen Lantbruk. The genetic material to be used in the project is obtained both from a genebank and the breeding material from the company. You will thus have the unique opportunity to be involved in a project in close collaboration with the plant breeders and thus gain first-hand experience of benefits and limitations of genomic selection in a real-world case study. You will have the possibility to develop new connections with many researchers and stakeholders through various seminars and events organized by SLU Grogrund.
For this position, you must have received your PhD degree not more than three years prior to the deadline of this application and have a research focus in plant breeding, genetics, quantitative genetics, bioinformatics, biometrics or similar. You should have documented experience in developing genetic markers for breeding. You should have contributed to research through publications in peer reviewed international journals. Prior experience with genomic selection is a merit. You should have the ability to work independently as well as in a team. You should be motivated, highly interested in plant breeding and have excellent English language skills (both oral and written).
We welcome your application no later than 2020-02-29.
Ref SLU ua 2020.2.5.1-232
Posted on January 27, 2020
Research Scientist 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.
- Master’s degree or PhD in bioinformatics, computational biology or a related natural science discipline
- Experience in multi-omics data analysis and method development
- Proficiency in working with bioinformatics tools and understanding of common bioinformatics algorithms
- Knowledge of software development methodology (version control, testing, documentation) is a plus
- Excellent interpersonal and communication skills and the ability to work independently in a fast-paced work environment
Quote Reference: REQ-00827
Machine Learning Data Scientist or Bioinformatics Fellow
The Buck AI Platform (BAIP) in collaboration with the Global Consortium for Reproductive Longevity and Equality at the Buck Institute has an opening for a Machine Learning Data Scientist or Bioinformatics fellow. Proposed work is in support of research programs in reproductive longevity, aging and age-related disease. The goal of BAIP is to catalyze data-enabled science and advance current knowledge on interventions and therapeutics to extend healthspan and lifespan.
- Process, integrate and analyze in-house and public domain data from various independent platforms (proteomics, genomics, phenomics, metabolomics, transcriptomics, microbiome, wearables/behavioromics).
- Advance statistical methods for data integration.
- Develop research objectives and proposals for own or joint projects.
- Contribute to writing research grants.
- Disseminate research findings with publication, research seminars, etc.
- Contribute to developing new models, techniques and methods for the use of public sets of biological data and health records.
- Guide and support other Buck staff and students who may require assistance with their research.
- Deep interest for the science of aging with particular focus in the identification of interventions and therapeutics to extend human healthspan and lifespan
- PhD or equivalent experience in Bioinformatics, Physics, Engineering, Mathematics, Statistics or Computer Sciences
- Significant experience with data science, bioinformatics and specifically integration of multi-omics data (desired, not required)
- Proven proficiency with application of machine learning
- Proven experience in SQL databases (e.g. MySQL).
- Proven capability in python and R; database development, maintaining & sharing code repositories (Github, Jupyter, etc.)
Posted on January 24, 2020
Postdoc in Integrative Evolutionary Hologenomics at The GLOBE Institute
We are looking for a highly motivated and dynamic researcher for a 3 year position to work at the interface of population genomic and hologenomic theory at the Centre for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen. The Centre for Evolutionary Hologenomics was recently funded by the Danish Basic Research Foundation to develop and implement state of the art ‘omics and associated computational techniques, to address through experimental and theoretical research, four key themes underscoring life on earth. Specifically these are: What is the relationship between a host’s genome and the functional and taxonomic makeup of its associated microbial metagenome? Does this relationship explain ongoing ecological and evolutionary processes in the host?
We are witnessing a technological revolution that is enabling the generation of different kinds of ‘omics datasets from not only high quality biological materials, but more unusual sources including historic and archaeological remains. A key challenge facing this revolution is how to analyse and integrate such datasets, especially at the population level. In this regard, your position would be working alongside the research groups of Prof Tom Gilbert, Assoc Prof Shyam Gopalakrishnan and Assoc Prof Hannes Schroeder, on the development of new methods in population genomics, statistical genomics, palaeogenomics and metagenomics, with a specific purpose of integrating multiple ‘omics datasets relevant from these areas into an Evolutionary Biological framework.
Essential experience and skills:
- You have a PhD in population genomics, with experience working with both low and high coverage genomic datasets, from both modern and ancient sources of biological materials.
- You are also highly experienced in working with other kinds of ‘omics data, including shotgun metagenomic and proteomic data
- You have an active interest in evolutionary biology and integrative hologenomics, in particular developing and applying bioinformatic tools and pipelines to new questions
Application deadline: 3 February 2020, 23.59pm CET
Postdoctoral Associate (Bioinformatics)
SBP is a preeminent, independent biomedical research institute dedicated to understanding human biology and disease, and advancing scientific discoveries to profoundly impact human health. For over 40 years, our research has produced breakthroughs in cancer, neuroscience, immunology and children’s diseases, and is anchored by our NCI-designated cancer center and advanced drug discovery capabilities.
A postdoctoral associate opening is available in the laboratory of Alexey Terskikh lab at the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. The Terskikh laboratory is thriving is at the intersection of neurogenesis, cancer, and epigenetics. We have established mouse models of adult neurogenesis using conditional ablation of SOX2 and primary cilia (Shh signaling) in radial glia stem cells and developed a novel platform for microscopic imaging of epigenetic landscape (MIEL) in single cells. MIEL uses advanced imaging and machine learning to investigate the change of epigenetic signatures during cell differentiation and upon exposure to the environment, including the high throughput drug screening format.
- Ph.D. degree in Bioinformatics or Biological Sciences (such as Computer Science, Bioinformatics, Biostatistics, Life Sciences) is required
- Emphasis on bioinformatics and relevance to human disease is preferred
- The candididates should demonstrate strong ability in bioinformatics, systems biology, sequence analyses, network analyses or genetics including expertise in high-throughput data analyses, such as RNA-Seq, single cell RNA-seq, differential gene expression analyses, gene co-expression analyses (e.g. Cytoscape, IPA, WGCNA, NextBio)
- Strong programming skills (Python, R, Java or C++ ) is required
- Familiarity with algorithms and tools, such as Bowtie, cufflinks, BWA, STAR, RSEM, UCSC Genome Browser, samtools, bedtools, vcf-tools etc.
- Knowledge of machine learning approaches is a plus
Posted on January 22, 2020
Postdoctoral Research Fellow – Spatial Transcriptomics Computational Biology
Our Research Laboratories’ Postdoctoral Research Fellow Program aims to be a best-in-industry program for industrial postdoctoral researchers, designed to provide you with an academic focus in a commercial environment. With the resources, reach, and expertise of a large pharmaceutical company, postdoctoral researchers will be positioned to excel in an institution committed to breakthrough innovation in research and discovery.
We are seeking a passionate computational biologist with expertise in analyzing single cell sequencing and/or spatial transcriptomics data to join the Genome Sciences team within the Department of Genetics & Pharmacogenomics (GpGx) at our site in Boston. Our mission is to develop high-throughput cutting-edge technologies to better understand disease mechanism and to identify and validate new targets and biomarkers. Our group utilizes innovative genetic screening (i.e., CRISPR) and multi-omics single cell approaches such as simultaneous RNA and protein profiling (i.e., REAP-seq), immune repertoire profiling, CROP-seq/Perturb-Seq, and Spatial Transcriptomics to impact all stages of the drug development pipeline from pre-clinical to clinical development. Genome Sciences collaborates closely with the discovery therapeutic areas (i.e., oncology, immunology, and neuroscience) to utilize these technologies to pursue key biological questions.
What You Bring:
- Candidates must currently hold a PhD or receive a PhD by summer 2020 in Bioinformatics, Biostatistics, Computational biology, Computer Science, Immunology, Molecular Biology, Statistics or related field
- Demonstrated experience on the computational analysis and interpretation of single cell RNA-seq or and/or Total-Seq datasets
- Expertise with data integration and interpretation
- Proficiency in at least one programming language, such as R or Python
- Familiarity with data visualization packages, such as R Shiny, ggplot, or plotly
- Strong communication (oral and written) and collaboration, including an ability to effectively communicate experimental design, results and conclusions
- Publications in high impact journal
Postdoc in Computational Metabolomics
Studies of the molecular mechanisms underlying interactions between lifetime exposures (e.g. from foods and gut microbiota) and the host are urgently needed for improved understanding of their role in the development and prevention of non-communicable diseases. Metabolomics is a fundamental tool in this research and gives a snapshot of the molecular phenotype. Large amounts of data are being generated and there is great need to develop and apply high-throughput analysis pipelines and novel bioinformatic tools to analyze and integrate metabolomics data with other data domains, such as other Omics. We are now looking for a PostDoc in Computational Metabolomics to identify metabolomic profiles associated with exposures to environmental exposures (food, lifestyle, air, noise, etc) in large untargeted LC-MS-based metabolomics data sets.
Major responsibilities This PostDoc position will require a high degree of data analytical competence, including LC-MS data preprocessing, multivariate analysis and multiOmics data integration. The applicant is further expected to contribute to the active software development in the research environment and to apply and develop cutting edge tools for multivariate analysis of repeated measures as well as data integration. There will also be opportunities to contribute to development of AI / machine leaning for metabolomics analysis with the aim to put Chalmers at the forefront in health engineering and precision nutrition.
Qualifications: To qualify for the position of postdoc, you must have a doctoral degree in a relevant field; bioinformatics, metabolomics, computational mass spectrometry, chemometrics. The degree should generally not be older than three years. You are expected to be somewhat accustomed to teaching, and to demonstrate good potential within research and education.
Application deadline: 16 February 2020
Posted 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.
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 (email@example.com).
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.
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.
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.
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 (firstname.lastname@example.org) 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.
Posted on January 15, 2020
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
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
- 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
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.
- 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.
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.
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
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.
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
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.
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
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.
- 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
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)
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 (email@example.com).
Postdoctoral Research Fellow in Bioinformatics/Computational Biology
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.
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.
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
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.
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.
- 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.
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
Posted on December 30, 2019
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.
- 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.
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
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.
Posted on December 27, 2019
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.
- 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
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.
- 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)
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.
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.
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.
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
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.
- 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
- 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: firstname.lastname@example.org
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.
Posted on December 18, 2019
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).
- 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.
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 email@example.com.
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.
- 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
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 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.