Bioinformatics

Category: Bioinformatics

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.

BioinformaticsAugust 19, 2014 05:16 PM

Daylight was breaking over the central Pacific and coffee brewing aboard the MY Hanse Explorer. Between sips, about a dozen scientists strategized for the day ahead. Some would don wetsuits and slip below the surface to collect water samples around the southern Line Islands' numerous coral reefs. Others would tinker with the whirring gizmos and delicate machinery strewn throughout the 158-foot research vessel. All shared a single goal: Be the first research group to bring a DNA sequencer out into the field to do remote sequencing in real time. Against an ocean of odds, they succeeded.

Few animals can boast of being as tough as the Antarctic midge. Its larvae develop over not one but two Antarctic winters, losing nearly half their body mass each time. It endures high winds, salt, and intense ultraviolet radiation. As an adult, the midge gets by without wings and lives for only a week or so before starting its life cycle all over again.


Benjamin Hause has joined the Kansas State Veterinary Diagnostic Laboratory as a research assistant professor. Hause uses next-generation sequencing and other new methods to rapidly identify pathogens.
He calls himself the bug hunter, but the target of his work consists of viruses that can only be found and identified with special methods and instruments. Benjamin Hause, an assistant research professor at the Kansas State Veterinary Diagnostic Laboratory at Kansas State University, recently published an article about one of his discoveries, porcine enterovirus G, which is an important find in the United States.


Wild tomato species are not edible, but they can be bred with domestic tomatoes to introduce new traits such as flavor and drought resistance. A new genome sequence for wild...
The genome of Solanum pennellii, a wild relative of the domestic tomato, has been published by an international group of researchers including the labs headed by Professors Neelima Sinha and Julin Maloof at the UC Davis Department of Plant Biology. The new genome information may help breeders produce tastier, more stress-tolerant tomatoes.


Prof. Ruedi Fries and Dr. Hubert Pausch monitor sequence data of breeding cattle.
An international collaboration known as the '1000 Bull Genomes Project' aims to accelerate breeding for desired traits in beef and dairy cattle while also improving animal health and welfare. Results of the project's first phase -- based on sequencing the whole genomes of 234 individual bulls whose direct descendants number in the tens of millions -- are reported in the journal Nature Genetics.

The genetic blueprint is an invaluable resource to plant science researchers and breeders. For the first time, they have at their disposal a set of tools enabling them to rapidly locate specific genes on individual wheat chromosomes throughout the genome. Jorge Dubcovsky, Professor at the University of California Davis, USA, says that these results "have been a fantastic resource for our laboratory. The development of genome specific primers, which used to take several weeks of work, can now be done in hours. Mapping of any sequence to the specific chromosome arm can now be done in silico in minutes. In addition to the acceleration of day to day work in wheat genetics, this resource has made possible analyses and discoveries at the genome level that were not possible before."

Researchers have created the first comprehensive library of genetic switches in plants, setting the stage for scientists around the globe to better understand how plants adapt to environmental changes and to design more robust plants for future food security.


For the first time, the genome of the electric eel has been sequenced.
For the first time, the genome of the electric eel has been sequenced. This discovery has revealed the secret of how fishes with electric organs have evolved six times in the history of life to produce electricity outside of their bodies.

Today the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG) announced completion of a fully mapped and openly accessible salmon genome. This reference genome will provide crucial information to fish managers to improve the production and sustainability of aquaculture operations, and address challenges around conservation of wild stocks, preservation of at-risk fish populations and environmental sustainability. This breakthrough was announced at the International Conference on Integrative Salmonid Biology (ICISB) being held in Vancouver this week.

The mitochondrial DNA of the first Near Eastern farmers has been sequenced for the first time. In the research, published in the journal PLOS Genetics, experts analysed samples from three sites located in the birthplace of Neolithic agricultural practices: the Middle Euphrates basin and the oasis of Damascus, located in today's Syria and date at about 8,000 BC.

The paper is signed by Daniel Turbón and Alejandro Pérez Pérez, from the Department of Animal Biology of the University of Barcelona (UB); Eva Fernández, from Liverpool John Moores University; Cristina Gamba, Eduardo Arroyo Pardo and Pedro Cuesta, from Complutense University of Madrid; Eva Prats, from the Spanish National Research Council, and Josep Anfruns and Miquel Molist, from the Universitat Autònoma de Barcelona (UAB). The study is focused on the analysis of mitochondrial DNA --a type of non-Mendelian maternally inherited DNA-- from the first Neolithic farmers, by means of samples obtained by the UAB research group which were first processed by the UB research group.


Grains of rice reveal just a tiny proportion of the variation of traits in the over 40,000 different varieties of rice in the world.
The open-access, open-data journal GigaScience (published by BGI and Biomed Central), announces today the publication of an article on the genome sequencing of 3000 rice strains along with the release of this entire dataset in a citable format in journal's affiliated open-access database, GigaDB. The publication and release of this enormous data set (which quadruples the current amount of publicly available rice sequence data) coincides with World Hunger Day to highlight one of the primary goals of this project— to develop resources that will aid in improving global food security, especially in the poorest areas of the world. This work is the completion of stage one of the 3000 Rice Genomes Project, a collaborative effort made up of the Chinese Academy of Agricultural Sciences (CAAS), the International Rice Research Institute (IRRI), and BGI, and is funded by the Bill and Melinda Gates Foundation and the Chinese Ministry of Science and Technology.

A team of international researchers has sequenced the genome of the Nevada dampwood termite, providing an inside look into the biology of the social insect and uncovering new genetic targets for pest control.

Decades after the genomics revolution, half of known eukaryote lineages still remain unstudied at the genomic level--with the field displaying a research bias against 'less popular', but potentially genetically rich, single-cell organisms.


This is a golden eagle.
Purdue and West Virginia University researchers are the first to sequence the genome of the golden eagle, providing a bird's-eye view of eagle features that could lead to more effective conservation strategies.

A new study from investigators with the Autism Genome Project, the world's largest research project on identifying genes associated with risk for autism, has found that the comprehensive use of copy number variant (CNV) genetic testing offers an important tool in individualized diagnosis and treatment of autism.


This is an image of tsetse fly.
An international team of researchers led by the Yale School of Public Health has successfully sequenced the genetic code of the tsetse fly, opening the door to scientific breakthroughs that could reduce or end the scourge of African sleeping sickness in sub-Saharan Africa. The study is published in the journal Science.

Using fish bred at Washington State University, an international team of researchers has mapped the genetic profile of the rainbow trout, a versatile salmonid whose relatively recent genetic history opens a window into how vertebrates evolve.


Mice are nocturnal. When both wild type and Chrono knockout mice are kept in an environment with 12 hours of light (blue) and 12 hours of dark (white).They align their...
Over the last few decades researchers have characterized a set of clock genes that drive daily rhythms of physiology and behavior in all types of species, from flies to humans. Over 15 mammalian clock proteins have been identified, but researchers surmise there are more. A team from the Perelman School of Medicine at the University of Pennsylvania wondered if big-data approaches could find them.


Splicing variants (red) of autism genes were cloned from the brain and screened for interactions. The image on the right represents the network of interactions.
A team of researchers from the University of California, San Diego School of Medicine and the Center for Cancer Systems Biology (CCSB) at the Dana-Farber Cancer Institute has uncovered a new aspect of autism, revealing that proteins involved in autism interact with many more partners than previously known. These interactions had not been detected earlier because they involve alternatively spliced forms of autism genes found in the brain.

A group of scientists from Children's Hospital Oakland Research Institute and UC Berkeley report the first mapping of genome methylation in the fruit-fly Drosophila melanogaster in their paper "Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity," published this month in Genome Research.


Conifers are the predominant members of the 300 million year old Gymnosperm clade. Conifers are also distinguished by their leviathan genomes.
The massive genome of the loblolly pine—around seven times bigger than the human genome—is the largest genome sequenced to date and the most complete conifer genome sequence ever published. This achievement marks the first big test of a new analysis method that can speed up genome assembly by compressing the raw sequence data 100-fold.

Although genome-wide association studies have linked DNA variants in the gene SCN10A with increased risk for cardiac arrhythmia, efforts to determine the gene's direct influence on the heart's electrical activity have been unproductive. Now, scientists from the University of Chicago have discovered that these SCN10A variants regulate the function of a different gene, SCN5A, which appears to be the primary gene responsible for cardiac arrhythmia risk. The SCN10A gene itself plays only a minimal role in the heart, according to the study, published in the Journal of Clinical Investigation on March 18.

A study by Curtin University researchers and colleagues from Denmark and New Zealand strengthens the case for human involvement in the disappearance of New Zealand's iconic megaherbivore, the moa - a distant relative of the Australian Emu.


This photo shows Nematostella vectensis.
The team led by evolutionary and developmental biologist Ulrich Technau at the University of Vienna discovered that sea anemones display a genomic landscape with a complexity of regulatory elements similar to that of fruit flies or other animal model systems. This suggests, that this principle of gene regulation is already 600 million years old and dates back to the common ancestor of human, fly and sea anemone. On the other hand, sea anemones are more similar to plants rather to vertebrates or insects in their regulation of gene expression by short regulatory RNAs called microRNAs. These surprising evolutionary findings are published in two articles in the journal Genome Research.


MSU scientists have identified how a single gene in honey bees separates the queens from the workers.
Scientists have identified how a single gene in honey bees separates the queens from the workers.

A landmark study across many cancer types reveals that the universe of cancer mutations is much bigger than previously thought. By analyzing the genomes of thousands of patients' tumors, a Broad Institute-led research team has discovered many new cancer genes — expanding the list of known genes tied to these cancers by 25 percent. Moreover, the study shows that many key cancer genes still remain to be discovered. The team's work, which lays a critical foundation for future cancer drug development, also shows that creating a comprehensive catalog of cancer genes for scores of cancer types is feasible with as few as 100,000 patient samples.

Through DNA analysis, Illinois researchers have disproved decades of rumors and hearsay surrounding the ancient Battle of Raphia, the only known battle between Asian and African elephants.


The immune system of the elephant shark is simpler than many other vertebrates studied so far. The present studies also explain, why cartilaginous fishes do not generate human-like bones.
An international team of researchers, including scientists of the Max Planck Institute of Immunobiology and Epigenetics, has sequenced and analyzed the genome of the elephant shark. Comparison of the elephant shark genome with human and other vertebrate genomes has revealed why the skeleton of sharks is made up largely of cartilage and not bone like the human skeleton and that the immune system of the shark is much simpler than that of humans. The findings of Byrappa Venkatesh and his coworkers are published in the latest issue of the scientific journal, Nature

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