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Category: Bioinformatics

Scientists have mapped out the genes that keep our cells alive, creating a long-awaited foothold for understanding how our genome works and which genes are crucial in disease like cancer.

Wild-type corn snakes typically exhibit, over a light orange background coloration, a pattern of dark orange dorsal saddles and lateral blotches that are outlined with black
Among the 5 000 existing species of mammals, more than 100 have their genome sequenced, whereas the genomes of only 9 species of reptiles (among 10 000 species) are available to the scientific community. This is the reason why a team at the University of Geneva (UNIGE), Switzerland, has produced a large database including, among others, the newly-sequenced genome of the corn snake, a species increasingly used to understand the evolution of reptiles. Within the same laboratory, the researchers have discovered the exact mutation that causes albinism in that species, a result published today in Scientific Reports.

The acorn worm Saccoglossus kowalevskii is common in brackish, shallow water on the Atlantic coast. Its newly sequenced genome is telling biologists about the genes responsible for pharyngeal gills
The newly sequenced genomes of two marine worms are shedding light on the 570 million-year evolution of gills into the pharynx that today gives humans the ability to bite, chew, swallow and speak.

The dinoflagellates aren't happy. In good times, these tiny ocean creatures live free-floating in the ocean or symbiotically with corals, serving up--or as--lunch to a host of mollusks, tiny fish and coral species. Some of them make glowing waves at night because they are bioluminescent. But when conditions are wrong, dinoflagellates poison shellfish beds with red tides and abandon coral reefs to a slow, bleached death.

This is the world's first NGS bioinformatics processor Bio-IT Processor.
TGAC's high performance computing (HPC) infrastructure will benefit from the addition of Edico Genome's DRAGEN™, the world's first processor designed to analyse specific sequencing data tasks. DRAGEN will be used to accelerate TGAC's next-generation sequencing workflows.

700 million year-old DNA sequences from ancient animals have been unearthed by researchers at the Universities of Leicester and Warwick, shedding new light on our earliest animal ancestors and how they influenced modern species - including the sponge.

The predicted profile for the conformational dynamics of the tyrosine kinase family is shown. Regions highlighted in red correspond to important structural elements involved in protein activation.
Researchers from the Structural Biology Computational Group of the Spanish National Cancer Research Centre (CNIO), led by Alfonso Valencia, in collaboration with a group headed by Francesco Gervasio at the University College London (UK), have developed the first computational method based on evolutionary principles to predict protein dynamics, which explains the changes in the shape or dimensional structure that they experience in order to interact with other compounds or speed up chemical reactions. The study constitutes a major step forward in the computational study of protein dynamics (i.e. their movement), which is crucial for the design of drugs and for the research on genetic diseases, such as cancer, resulting in higher levels of complexity than allowed by current methods. The results have been published this week in the journal Proceedings of the National Academy of Sciences (PNAS).

The largest genetic study of atopic dermatitis ever performed permitted a team of international researchers to identify ten previously unknown genetic variations that contribute to the development of the condition.
The largest genetic study of atopic dermatitis ever performed permitted a team of international researchers to identify ten previously unknown genetic variations that contribute to the development of the condition. The researchers also found evidence of genetic overlap between atopic dermatitis and other illnesses, including inflammatory bowel disease. The results was published in Nature Genetics online on Oct. 19.

This is a structure showing EGFR -- a cancer driver -- in it's active dimer conformation. Red indicates mutations that destroy the protein-protein interface
La Jolla, Calif., October 20, 2015 - In a collaborative study led by Sanford Burnham Prebys Medical Discovery Institute (SBP), researchers have combined two publicly available 'omics' databases to create a new catalogue of 'cancer drivers'. Cancer drivers are genes that when altered, are responsible for cancer progression. The researchers used cancer mutation and protein structure databases to identify mutations in patient tumors that alter normal protein-protein interaction (PPI) interfaces. The study, published today in PLoS Computational Biology, identified more than 100 novel cancer driver genes and helps explain how tumors driven by the same gene may lead to different patient outcomes.

Urinary tract infections (UTIs) could be treated more quickly and efficiently using a DNA sequencing device the size of a USB stick -- according to research from the University of...
Urinary tract infections (UTIs) could be treated more quickly and efficiently using a DNA sequencing device the size of a USB stick - according to research from the University of East Anglia.

Using extensive genetic data compiled by the UK10K project, an international team of researchers led by Dr. Brent Richards of the Lady Davis Institute at the Jewish General Hospital has identified a genetic variant near the gene EN1 as having the strongest effect on bone mineral density (BMD) and fracture identified to date. The findings are published in the forthcoming issue of the prestigious journal Nature.

A 'gene signature' that could be used to predict the onset of diseases, such as Alzheimer's, years in advance has been developed in research published in the open access journal Genome Biology.

BioJS conference group is shown.
Drawing upon reusable components to visualise and analyse biological data on the web, BioJS data is freely available to users and developers where they can modify, extend and redistribute the software with few restrictions, at no cost. With a vision for 'every online biological dataset in the world should be visualised with BioJS tools', the community hopes to achieve the largest, most comprehensive repository of JavaScript tools to visualise online biological data, available for all.

Barley is one of the world's most important cereal crops.
Barley, a widely grown cereal grain commonly used to make beer and other alcoholic beverages, possesses a large and highly repetitive genome that is difficult to fully sequence. Now a team led by scientists at the University of California, Riverside has reached a new milestone in its work, begun in 2000, on sequencing the barley genome. The researchers have sequenced large portions of the genome that together contain nearly two-thirds of all barley genes.

Researchers from UC Berkeley, the Okinawa Institute of Science and Technology Graduate University and the University of Chicago have sequenced and annotated the first cephalopod genome
An international team of scientists has sequenced the genome of an octopus, bringing researchers closer to discovering the genes involved in the creature's unusual biology, including its ability to change skin color and texture and a distributed brain that allows its eight arms to move independently.

Associate Professor of Anthropology Ripan Malhi was a senior coauthor among an international team of researchers, who clarified the history of early migration to the Americas
The first human inhabitants of the Americas lived in a time thousands of years before the first written records, and the story of their transcontinental migration is the subject of ongoing debate and active research. A study by multi-institutional, international collaboration of researchers, published this week in Science (DOI: 10.1126/science.aab3884) presents strong evidence, gleaned from ancient and modern DNA samples, that the ancestry of all Native Americans can be traced back to a single migration event, with subsequent gene flow between some groups and populations that are currently located in East Asia and Australia.

Researchers at the Babraham Institute and Cambridge Systems Biology Centre, University of Cambridge have shown that yeast can modify their genomes to take advantage of an excess of calories in the environment and attain optimal growth.

The first comprehensive genome analyses of 7 melon varieties was completed by a research team led by Josep Casacuberta, Jordi Garcia-Mas and Sebastian Ramos-Onsins, providing breeders new knowledge important for understanding phenotypic variability and helping increasing plant quality yields by selective breeding. The findings were published in the advanced online edition of Molecular Biology and Evolution.

A new study on the genomic signatures of adaptation in crop plants can help predict how crop varieties respond to stress from their environments.
A new study led by a Kansas State University geneticist has shown that genomic signatures of adaptation in crop plants can help predict how crop varieties respond to stress from their environments.

These are woolly mammoths.
Evolutionary change in a gene resurrected in the lab from the extinct woolly mammoth altered the gene's temperature sensitivity and likely was part of a suite of adaptations that allowed the mammoth to survive in harsh arctic environments, according to new research. In a study published in Cell Reports on July 2, 2015, researchers determined the whole-genome sequence of two woolly mammoths and three modern Asian elephants, predicted the function of genetic changes found only in the mammoths, and then experimentally validated the function of a woolly mammoth gene reconstructed in the lab. The research team includes scientists from Penn State University, Nanyang Technological University in Singapore, and the University of Chicago.

The mSet algorithm by Oliver Stegle at EMBL-EBI makes large-scale, complex genome analyses easier.
Researchers at EMBL-EBI have developed a new approach to studying the effect of multiple genetic variations on different traits. The new algorithm, published in Nature Methods, makes it possible to perform genetic analysis of up to 500,000 individuals - and many traits - at the same time.

The new avian family tree based on whole genomes of 48 bird species representing all 30 neoavian orders and two galloanserae orders and two palaeognathae orders.
The Avian Phylogenomics Consortium formally announces the launch of the Bird 10,000 genomes (B10K) project, an initiative to generate representative draft genome sequences from all extant bird species within the next five years. This will be the first attempt to sequence the genomes of all living species of a vertebrate class. The establishment of this project is built on the success of the previous ordinal level project, which provided the first proof of concept for carrying out large-scale sequencing of multiple representative species across a vertebrate class and a window into the types of discoveries that can be made with such genomes (1). The announcement of the B10K project is published online today in Nature.

A team at the Salk Institute mapped comprehensive epigenomes of several organs and tissue types from four different donors, which could help better understand health and disease.
For more than a decade, scientists have had a working map of the human genome, a complete picture of the DNA sequence that encodes human life. But new pages are still being added to that atlas: maps of chemical markers called methyl groups that stud strands of DNA and influence which genes are repressed and when.

Millions of genetic variants have been discovered over the last 25 years, but interpreting the clinical impact of the differences in a person's genome remains a major bottleneck in genomic medicine. In a paper published in The New England Journal of Medicine on May 27, a consortium including investigators from Brigham and Women's Hospital (BWH) and Partners HealthCare present ClinGen, a program to evaluate the clinical relevance of genetic variants for use in precision medicine and research.

Cancer research leaders at the Ontario Institute for Cancer Research, Oregon Health & Science University, Sage Bionetworks, the distributed DREAM (Dialog for Reverse Engineering Assessment and Methods) community and The University of California Santa Cruz published the first findings of the ICGC-TCGA-DREAM Somatic Mutation Calling (SMC) Challenge (The Challenge:!Synapse:syn312572) today in the journal Nature Methods. These results provide an important new benchmark for researchers, helping to define the most accurate methods for identifying somatic mutations in cancer genomes. The results could be the first step in creating a new global standard to determine how well cancer mutations are detected.

Researchers at Columbia University's Mailman School of Public Health and Leiden University in the Netherlands found that children whose mothers were malnourished at famine levels during the first 10 weeks of pregnancy had changes in DNA methylation known to suppress genes involved in growth, development, and metabolism documented at age 59. This is the first study to look at prenatal nutrition and genome-wide DNA patterns in adults exposed to severe under-nutrition at different periods of gestation. Findings are published in the International Journal of Epidemiology.

A color plot showing the expression level during the day in early (larks) and late (owls) strains of Drosophila.

  • Researchers identify fly strains that exhibit morning- and evening-like behaviour.
  • Team identifies nearly 80 genes associated with different types of behaviour
  • Study could pave way to better diagnostics, and ultimately personal medicine, where larks and owls will receive their tailored therapies

Bumblebees are considered peaceful and industrious creatures, and their commercial value has increased in the wake of the decline of honeybees around the world. The bees are therefore now bred on a large scale and used as pollinators for economically valuable crops. Yet, these cute little, buzzing creatures, of which there are around 250 different species worldwide, is doing poorly in some places. The large shadow cast by the honeybee collapse has distracted from the fact that in recent years in the US as well as in other areas some previously common bumblebee species have also become rare or endangered, or disappeared altogether.

Bees play a key role in our ecosystem and in the world's food supply.
Bees play a key role in our ecosystem and in the world's food supply. Thanks to a large collaborative effort, the genomes of two important pollinating bumblebees have been sequenced and compared with those of other bees, laying the foundations for the identification of biological factors essential for their conservation.

This image shows a colony of Trichodesmium.
Scientists have found something they can't quite explain in one of the most barren environments on Earth: a bacterium whose DNA sequence contains elements usually only found in a much higher organism.

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