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Bioinformatics

Category: Bioinformatics


The researchers found DNA 'fossils' of parasitic nematodes in seven groups of birds (clockwise): trogons, mesites, parrots, hummingbirds, hornbills, manakins, tinamous.
In rare instances, DNA is known to have jumped from one species to another. If a parasite's DNA jumps to its host's genome, it could leave evidence of that parasitic interaction that could be found millions of years later -- a DNA 'fossil' of sorts. An international research team led from Uppsala University has discovered a new type of so-called transposable element that occurred in the genomes of certain birds and nematodes.

Researchers at The University of Texas MD Anderson Cancer Center have announced a new method for detecting DNA mutations in a single cancer cell versus current technology that analyzes millions of cells which they believe could have important applications for cancer diagnosis and treatment. The results are published in the April 18 online issue of Nature Methods.


Queen and worker ants develop from the same sets of genes, but end up being structurally, behaviourally, and functionally different.
Queen and worker ants develop from the same sets of genes, but perform completely different ecological roles. How the same genes result in two types of individuals is an ongoing mystery. In the past, scientists have only studied a small number of ant species at a time to try to understand the nature of queen-worker differences. However, a team from the Okinawa Institute of Science and Technology Graduate University (OIST) in tandem with the University of Helsinki and other collaborators from around the world, recently looked at a large data set with 16 species that provides insight into the differences between queen and worker ants.


Female orphan chimpanzee are cared for at the Sanaga-Yong Chimpanzee Rescue Center.
Understanding the origins of emerging diseases - as well as more established disease agents -- is critical to gauge future human infection risks and find new treatment and prevention approaches. This holds true for malaria, which kills more than 500,000 people a year. Symptoms, including severe anemia, pregnancy-associated malaria, and cerebral malaria, have been linked to the parasite's ability to cause infected red blood cells to bind to the inner lining of blood vessels.


This image shows Yucca Brevifolia Tikaboo, June 2014.
Scientists at the Donald Danforth Plant Science Center have teamed up with researchers at Willamette University, a liberal arts college in Salem Oregon, to develop genetic tools that could save the Joshua tree from extinction. Together with scientists from The University of Georgia and the University of British Columbia, and with the support of several Mojave Desert conservation organizations, researchers are inviting members of the public to help get the project off the ground by making donations at the crowdfunding site Experiment.com. In the past two weeks, more than 100 backers have donated more than $4,000 to The Joshua Tree Genome Project. The project aims to raise $8,500 by March 24th.


The same metabolic pathway can produce different results in different bodily tissues. A Rice University algorithm is designed to find those differences.
Rice University bioengineers have introduced a fast computational method to model tissue-specific metabolic pathways. Their algorithm may help researchers find new therapeutic targets for cancer and other diseases.

Led by Drs John Postlethwait and Ingo Braasch from the Institute of Neuroscience, University of Oregon, US, in collaboration with the Broad Institute, the study of the Spotted Gar (Lepisosteus oculatus) genome reveals that it is small and manageable. Furthermore, it lacks much shuffling and duplication that occurred in the 'main' fish ancestral line; it conserved its genome.

BioinformaticsFebruary 16, 2016 05:20 PM


These bloodsuckers originally parasitized bats.
The bed bug (Cimex lectularius) has been a familiar human parasite for more than 3,000 years. After a significant decrease in its population density in the middle of the last century, we have seen a dramatic increase again around the world over the past 20 years. In Australia, for instance, there is an increase of 4,500%.


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.

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