Bioinformatics

Category: Bioinformatics

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: https://www.synapse.org/#!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.

BioinformaticsJanuary 20, 2015 05:56 PM

Positional cloning is a genetic mapping technique used to pinpoint the location of specific traits of interest, such as disease-causing genes or mutations, within the genome. Very simply, this map-based technique involves crossing mutant individuals with wild-type individuals and examining the offspring in order to localize a candidate region in the genome for the mutation. By identifying genetic markers that are linked to the trait, progressively more precise areas on a chromosome are defined until the gene is identified.


A new method helps scientists create a more accurate picture of gene expression in different cell types, and reveals hidden subtypes of cells.
A new method for analysing RNA sequence data allows researchers to identify new subtypes of cells, creating order out of seeming chaos. Published in Nature Biotechnology, the novel technique developed by scientists at The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) represents a major step forward for single-cell genomics.


A scanning electron micrograph of methicillin-resistant Staphylococcus aureus (MRSA) magnified 2381x.
Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of hospital-acquired infections, with the largest burden of infections occurring in under-resourced hospitals. While genome sequencing has previously been applied in well-resourced clinical settings to track the spread of MRSA, transmission dynamics in settings with more limited infection control is unknown. In a study published online today in Genome Research, researchers used genome sequencing to understand the spread of MRSA in a resource-limited hospital with high transmission rates.

Nora Besansky, O'Hara Professor of Biological Sciences at the University of Notre Dame and a member of the University's Eck Institute for Global Health, has led an international team of scientists in sequencing the genomes of 16 Anopheles mosquito species from around the world.

Looking across evolutionary time and the genomic landscapes of humans and mice, an international group of researchers has found powerful clues to why certain processes and systems in the mouse - such as the immune system, metabolism and stress response - are so different from those in people. Building on years of mouse and gene regulation studies, they have developed a resource that can help scientists better understand how similarities and differences between mice and humans are written in their genomes.


Researchers at Washington University School of Medicine in St. Louis led an international team that sequenced and analyzed the cat genome to better understand the animal's domestication.
Cats and humans have shared the same households for at least 9,000 years, but we still know very little about how our feline friends became domesticated. An analysis of the cat genome by researchers at Washington University School of Medicine in St. Louis reveals some surprising clues.

Cell division, the process that ensures equal transmission of genetic information to daughter cells, has been fundamentally conserved for over a billion years of evolution. Considering its ubiquity and essentiality, it is expected that proteins that carry out cell division would also be highly conserved. Challenging this assumption, scientists from Fred Hutchinson Cancer Research Center have found that one of the foundational proteins in cell division, previously shown to be essential in organisms as diverse as yeast, flies and humans, has been surprisingly lost on multiple occasions during insect evolution.

Researchers in Biomedical Informatics at IMIM (Hospital del Mar Medical Research Institute) and at the Universitat Politècnica de Catalunya (UPC) have recently published a study in eLife showing that RNA called non-coding (IncRNA) plays an important role in the evolution of new proteins, some of which could have important cell functions yet to be discovered.

A team of Spanish researchers have obtained the first partial genome sequence of an ancient pig. Extracted from a sixteenth century pig found at the site of the Montsoriu Castle in Girona, the data obtained indicates that this ancient pig is closely related to today's Iberian pig. Researchers also discard the hypothesis that Asian pigs were crossed with modern Iberian pigs.


Lucia Carbone, Ph.D., is an assistant professor of behavioral neuroscience in the OHSU School of Medicine and an assistant scientist at OHSU's Oregon National Primate Research Center.
A team led by an Oregon Health & Science University researcher has sequenced and annotated the genome of the only ape whose DNA had yet to be sequenced — the gibbon, an endangered small ape that inhabits the tropical forests of Southeast Asia.

A big step in understanding the mysteries of the human genome was unveiled today in the form of three analyses that provide the most detailed comparison yet of how the genomes of the fruit fly, roundworm, and human function.


New findings show a surprisingly high level of genetic diversity in honeybees, and indicate that the species most probably originates from Asia, and not from Africa as previously thought.
In a study published in Nature Genetics, researchers from Uppsala University present the first global analysis of genome variation in honeybees. The findings show a surprisingly high level of genetic diversity in honeybees, and indicate that the species most probably originates from Asia, and not from Africa as previously thought.

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