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Bioinformatics

Category: Bioinformatics


Researchers sequence the genome of the Lyme-disease-causing tick and find lots of duplicative elements.
Researchers have sequenced the genetic blueprint of one of the most prolific pathogen-transmitting agents on the planet - the Lyme-disease-spreading tick (Ixodes scapularis) that bites humans. The findings could lead to advances in not only disrupting the tick's capacity to spread diseases but also in eradicating the pest.

Database searches for DNA sequences that can take biologists and medical researchers days can now be completed in a matter of minutes, thanks to a new search method developed by computer scientists at Carnegie Mellon University.

A team of scientists from Germany, USA, and Russia, including Dr. Mark Borodovsky, a Chair of the Department of Bioinformatics at MIPT, have proposed an algorithm to automate the process of searching for genes, making it more efficient. The new development combines the advantages of the most advanced tools for working with genomic data. The new method will enable scientists to analyse DNA sequences faster and more accurately and identify the full set of genes in a genome.

In October, an interdisciplinary group of scientists proposed forming a Unified Microbiome Initiative (UMI) to explore the world of microorganisms that are central to life on Earth and yet largely remain a mystery. An article in the journal ACS Nano describes the tools scientists will need to understand how microbes interact with each other and with us.


Excavated near Belfast in 1855, she had lain in a Neolithic tomb chamber for 5,000 years; subsequently curated in Queens University Belfast.
A team of geneticists from Trinity College Dublin and archaeologists from Queen's University Belfast has sequenced the first genomes from ancient Irish humans, and the information buried within is already answering pivotal questions about the origins of Ireland's people and their culture.

Researchers long have known that some portion of the risk of developing cancer is hereditary and that inherited genetic errors are very important in some tumors but much less so in others.

Oncologists are increasingly using information obtained from investigations of the tumor genome in order to find individualized therapies for patients. They specifically search the hereditary information of cancer cells for mutations that drive malignant growth. By now, targeted drugs against many of these cancer-typical cellular alterations have become available.

Scientists have performed the first comprehensive genomic analysis of Ebola virus sequences from Liberia, one of three countries widely affected by the devastating outbreak that began in 2013 in Western Africa. Their work, published today in Cell Host & Microbe, traces the introduction and spread of the virus in Liberia and also sheds light on how the virus moved between the neighboring countries of Guinea and Sierra Leone.


"Would you rather have $20 now, or can I mail you $40 in a few weeks? "
Opting for smaller rewards immediately instead of waiting for bigger payoffs later is associated with problems such as impulsivity and addiction to food, drugs and alcohol. Now, new research indicates that such decision-making tendencies have a genetic link to brain pathways that underlie these disorders.


Six red clover varieties with diverse architectures and traits have recently been selected as parents of the next year generation.
The Genome Analysis Centre (TGAC) in collaboration with IBERS, has sequenced and assembled the DNA of red clover to help breeders improve the beneficial traits of this important forage crop. The genome is published in Scientific Reports, a journal from the Nature publishing group.

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.

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