Blogs

November 2018


Top Bioinformatics and Genomics Blogs

Diving into Genetics and Genomics

YOKOFAKUN

 Getting Genetics Done

Gigabase or gigabyte

Genome Spot

 CoreGenomics

The Genome Factory

RajLab

 Omics! Omics!


Altmetric top 100 for 2016

 In the past year, Altmetric has tracked over 17 million mentions of 2.7 million different research outputs. These are the top 100 most-discussed journal articles of 2016.

For detail click here


Nature Chemistry’s Altmetric top 10 for 2016

1. Fast and selective ring-opening polymerizations by alkoxides and thioureas

2. Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy

3. Molecular rectifier composed of DNA with high rectification ratio enabled by intercalation

4. Self-assembling biomolecular catalysts for hydrogen production

5. A highly stretchable autonomous self-healing elastomer

6. The structural and chemical origin of the oxygen redox activity in layered and cation-disordered Li-excess cathode materials

7. Neutral zero-valent s-block complexes with strong multiple bonding

8. A supramolecular ruthenium macrocycle with high catalytic activity for water oxidation that mechanistically mimics photosystem II

9. Force-induced tautomerization in a single molecule

10. Diindeno-fusion of an anthracene as a design strategy for stable organic biradicals

Source Link


Why proteomics is not the new genomics and the future of mass spectrometry in cell biology

Mass spectrometry (MS) is an essential part of the cell biologist’s proteomics toolkit, allowing analyses at molecular and system-wide scales. However, proteomics still lag behind genomics in popularity and ease of use.

We discuss key differences between MS-based -omics and other booming -omics technologies and highlight what we view as the future of MS and its role in our increasingly deep understanding of cell biology.  Reference


BMC Genomics: highlights of 2016

As we look back on 2016, it is clear it has been a highly productive year, where we have had many interesting articles published in BMC Genomics. Here we have selected three highlighted articles to celebrate the year.

Cosmic rays and the brain

Cold tolerance in Arctic bacterium

Canine fear and aggression

Reference


Why humans develop sex cells as embryos — but corals don’t 

Drive to preserve mitochondrial quality might explain why organisms develop sex cells at different stages of development. Animals and plants prepare their cells for sex in very different ways-but no one knows why. A team of UK researchers now thinks that it has worked out the puzzle. Reference Link


Point of view: Five suggestions for substantial NIH reforms

The National Institutes of Health needs to make radical changes to ensure that biomedical research continues to thrive in the United States.

Five specific reforms points:

1. Increase support for bottom-up basic science

2. Move most support for basic science to a single institute

3. Invest more in people and less in projects, but with limits

4. Increase participation by established scientists in NIH Study Sections

5. Revisit financial relationships between universities and the NIH

Reference Link


An easy way to visualize structural biology data

Here at Biology in 3D, we often talk about the aesthetic side of structural biology and the power of structural images to inspire both artists and scientists. In the last Structure issue of 2016, we published a Letter to Editor by Shuguang Yuan, H.C. Stephen Chan, Slawomir Filipek, and Horst Vogel that emphasizes the importance of user-friendly structural biology data visualization strategies.

I invited the authors to say a bit more about what they are trying to accomplish and how they are trying to accomplish it, and to share some examples with us here at CrossTalk. Here, they discuss how they combined the tools PyMOL and Inkscape to create effective visual models. Source Link


US drug approvals plummet in 2016

US drug approvals are on track to drop by more than half in 2016 compared to 2015, according to a 14 December presentation by the US Food and Drug Administration (FDA).

Click Here for detail


The Human Intestinal Microbiome in Health and Disease

Human-associated microbes have primarily been viewed through the lens of a single species and its environment. Advances in culture-independent technologies have shown the enormous diversity, functional capacity, and age-associated dynamics of the human microbiome (see the Glossary). A large number of diverse microbial species reside in the distal gastrointestinal tract, and gut microbiota dysbiosis — imbalances in the composition and function of these intestinal microbes — is associated with diseases ranging from localized gastroenterologic disorders to neurologic, respiratory, metabolic, hepatic, and cardiovascular illnesses. Much effort is currently concentrated on exploring potential causality and related microbiota-mediated disease mechanisms, with the hope that an improved understanding will fuel the conception and realization of novel therapeutic and preventive strategies. Detail


Sex on the brain

On 30 August, the Alzheimer’s Association announced nine recipients of its “Sex and Gender in Alzheimer’s” research grants, which provided a total of $2.2 million in funding. Women make up about two-thirds of the 5 million people in the US with Alzheimer’s disease, and the primary explanation offered for this sexual disparity—longevity—remains controversial. “Some say that it’s because women live longer,” says Heather Snyder, who oversees the Alzheimer’s Association’s International Research Grant Program, “but some scientists say that it’s more.”

The association created its new grant program to explore what else could explain this disparity. As Snyder says, “We know there are differences in the brains of men and women, and we want to understand how those differences contribute to neurodegenerative diseases.” Source link


Challenges and opportunities of evidence-based precision medicine

This era of groundbreaking scientific developments in high-resolution, high-throughput technologies is allowing the cost-effective collection and analysis of huge, disparate datasets on individual health. Proper data mining and translation of the vast datasets into clinically actionable knowledge will require the application of clinical bioinformatics. These developments have triggered multiple national initiatives in precision medicine—a data-driven approach centering on the individual. However, clinical implementation of precision medicine poses numerous challenges. Foremost, precision medicine needs to be contrasted with the powerful and widely used practice of evidence-based medicine, which is informed by meta-analyses or group-centered studies from which mean recommendations are derived. This “one size fits all” approach can provide inadequate solutions for outliers. Such outliers, which are far from an oddity as all of us fall into this category for some traits, can be better managed using precision medicine. Source Link


Best of 2016: Top Picks from Genome Biology

Dominique Morneau of Genome Biology highlights some of the editors’ favorite articles from the past year, including those that were highly accessed, shared, liked and discussed.

Evolutionary Genomics
Epigenomics
Technological Advances
Plant Genomics
Disease Genomics
source Link


Algorithms compete to predict recipe for cancer vaccine

The Parker Institute for Cancer Immunotherapy in San Francisco, California, and the Cancer Research Institute of New York City announced the algorithmic battle on 1 December. It is part of a multimillion-dollar joint project to solve a major puzzle in the nascent field of cancer immunotherapy: which of a patient’s sometimes hundreds of cancer mutations could serve as a call-to-arms for their immune system to attack their tumours.

Link

Ten years of the Genomics of Common Diseases: “The end of the beginning”

The 10th anniversary ‘Genomics of Common Diseases’ meeting was held in Baltimore, September 25-28, 2016. Professor Chris Haley reports from the meeting on progress and challenges in the field.

The first meeting in the Genomics of Common Diseases series was held just after the publication of the first successful genome-wide association analyses (GWAS), when optimism for the genomic dissection of common complex traits and diseases was high. Much progress has been made in the intervening period, so the 10th meeting provided a good opportunity to assess successes so far and the path ahead. Here, I do not attempt to summarise every presentation but rather to draw out some of the important themes as I saw them. Link