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Category: Bioinformatics

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.

Upland allotetraploid cotton (right) comes from two extant diploid species, closely related to today's G. raimondii (left) and G. arboreum (middle) or G. herbacieum.
A University of Texas at Austin scientist, working with an international research team, has developed the most precise sequence map yet of U.S. cotton and will soon create an even more detailed map for navigating the complex cotton genome. The finding may help lead to an inexpensive version of American cotton that rivals the quality of luxurious Egyptian cotton and helps develop crops that use less water and fewer pesticides for a cotton that is easier on the skin and easier on the land.

A new method for measuring genetic variability within a tumor might one day help doctors identify patients with aggressive cancers that are more likely to resist therapy, according to a study led by researchers now at The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC - James).

Placebos have helped to ease symptoms of illness for centuries and have been a fundamental component of clinical research to test new drug therapies for more than 70 years. But why some people respond to placebos and others do not remains under debate.

The term "single-nucleotide polymorphism" (SNP) refers to a single base change in DNA sequence between two individuals. SNPs are the most common type of genetic variation in plant and animal genomes and are, thus, an important resource to biologists. The ubiquity of these markers and the fact that these polymorphisms show variation at such a fine scale (i.e., at the individual level) makes them ideal markers for many applications, such as population-level genetic diversity studies and genetic mapping in plants.

Many microbes cannot be cultivated in a laboratory setting, hindering attempts to understand Earth's microbial diversity. Since microbes are heavily involved in, and critically important to environmental processes from nutrient recycling, to carbon processing, to the fertility of topsoils, to the health and growth of plants and forests, accurately characterizing them, as a basis for understanding their activities, is a major goal of the Department of Energy (DOE). One approach has been to study collected DNA extracted from the complex microbial community, or the metagenome, in order to describe its DNA-coded "parts" catalog and understand how microbes respond and adapt to environmental changes. Studying a population rather than an individual raises different obstacles on the path to knowledge. The challenges of assembling genes and genomic fragments into meaningful sequence information for an unknown microbe has been likened to putting together a jigsaw puzzle without knowing what the final picture should look like, or even if you have all the pieces.

Coast redwoods are famous for being the tallest trees in the world, but their height is not the only thing that sets them apart. Unlike most conifer trees, coast redwoods can reproduce by sprouting from cut stumps, fallen logs, and roots. Researchers from the University of California, Berkeley, are uncovering important information about patterns of coast redwood clones with a new DNA analysis method that could help forest management and preservation efforts.

Scientists have for the first time used DNA sequencing to trace the fatal spread of multidrug-resistant tuberculosis between patients in the UK.

An extensive database identifying immune traits, such as how immune cell function is regulated at the genetic level in healthy people, is reported by researchers from the National Institutes of Health (NIH) and their collaborators in the journal Cell. While many genetic risk factors have been linked to various diseases, including autoimmune disorders, how a genetic change causes susceptibility to a disease is not always clear. By studying healthy people, researchers from the National Institute of Allergy and Infectious Diseases (NIAID) Vaccine Research Center, part of the NIH, and colleagues from King's College London have created a reference resource for other scientists.

Scientists and breeders working with poultry and livestock species will get a new set of tools from an international project that includes the University of California, Davis.

While genomics is the study of all of the genes in a cell or organism, epigenomics is the study of all the genomic add-ons and changes that influence gene expression but aren't encoded in the DNA sequence. A variety of new epigenomic information is now available in a collection of studies published Feb. 19 in Nature by the National Institutes of Health (NIH) Roadmap Epigenomics Program. This information provides a valuable baseline for future studies of the epigenome's role in human development and disease.

Maloof and Sinha analyzed the effects of various light environments on leaf development for both the wild and cultivated tomato species.
Plant biologist Julin Maloof met fellow researcher Neelima Sinha while beginning his career at the University of California, Davis. Both interested in plant morphology and natural variation, the two first collaborated on a proposal more than six years ago and continue to work together to examine how plants thrive in disparate environments.

Scientists took a computational approach using the Stampede and Lonestar supercomputers to compare lab data with reference genomes of over a thousand strains of Arabidopsis sampled throughout Europe and Asia.
Scientists using supercomputers found genes sensitive to cold and drought in a plant help it survive climate change. These findings increase basic understanding of plant adaptation and can be applied to improve crops.

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