Category: Bioinformatics

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

This image shows a DNA computer simulation.
DNA carries out its activities "diluted" in the cell nucleus. In this state it synthesises proteins and, even though it looks like a messy tangle of thread, in actual fact its structure is governed by precise rules that are important for it to carry out its functions. Biologists have studied DNA by observing it experimentally with a variety of techniques, which have only recently been supplemented by research in silico, that is to say, the study of DNA by means of computer simulations. This is a recent area of study, but it has already given a major contribution to knowledge in this field. Angelo Rosa, a theoretical physicist of the International School for Advanced Studies (SISSA) in Trieste, with the collaboration of Christophe Zimmer, an experimental physicist from the Pasteur Institute in Paris has assessed the state of the art of this novel but powerful approach in a systematic review that has just been published in the journal International Review of Cell and Molecular Biology.

Eurofins Scientific (EUFI.PA), a European leader in Genomics Services, Forensics and Paternity Testing, announces a milestone in genetic and forensic research. A multidisciplinary Eurofins team in the Eurofins flagship Genomics laboratory in Ebersberg, Germany, has successfully completed a research project to genetically discriminate "identical" monozygotic twins.

Predicting adult body height from genetic data is helpful in several areas such as pediatric endocrinology and forensic investigations. However, despite large international efforts to catalogue the genes that influence the stature of humans, knowledge on genetic determinants of adult body height is still incomplete. Now DNA-based prediction of taller-than-average body height is feasible, as reported by researchers from the Netherlands and Sweden in an article published in Springer's journal Human Genetics.

This image shows a great white shark.
The great white shark, a major apex predator made famous by the movie "Jaws," is one of the world's most iconic species capturing an extraordinary amount of public fascination. An intriguing question is what makes a white shark so distinctive? One way to address this is to explore the genetic makeup of this remarkable animal.

A new method to take the DNA fingerprint of individual cancer cells is uncovering the true extent of cancer's genetic diversity, new research reveals.

What does it mean to be human? According to scientists the key lies, ultimately, in the billions of lines of genetic code that comprise the human genome. The problem, however, has been deciphering that code. But now, researchers at the Gladstone Institutes have discovered how the activation of specific stretches of DNA control the development of uniquely human characteristics—and tell an intriguing story about the evolution of our species.

Software that can recognize patterns in data is commonly used by scientists and economics. Now, researchers in the US have applied similar algorithms to help them more accurately diagnose breast cancer. The researchers outline details in the International Journal of Medical Engineering and Informatics.

A collaborative team of researchers has used next generation sequencing to identify clinically relevant genetic variants associated with a rare pediatric speech disorder. The findings are published in the September 16, 2013 issue of the Journal of Neurodevelopmental Disorders

By any measure, tuberculosis (TB) is a wildly successful pathogen. It infects as many as two billion people in every corner of the world, with a new infection of a human host estimated to occur every second.

The genome sequencing started with the Chinese hamster (picture).
Genome researchers from Bielefeld University's Center for Biotechnology (CeBiTec) headed by Professor Dr. Alfred Pühler have succeeded in sequencing the genome of the Chinese hamster. The Chinese hamster supplies the cell cultures used by the pharmaceutical industry to produce biopharmaceutical products such as antibodies used in medicine. This costly project was only possible thanks to a cooperation between Bielefeld University and its international project partners. The researchers have now published their results in the internationally renowned scientific journal 'Nature Biotechnology'.

Recent technological developments in genomics have revealed a large number of genetic influences on common complex diseases, such as diabetes, asthma, cancer or schizophrenia. However, discovering a genetic variant predisposing to a disease is only a first step. To apply this knowledge towards prevention or cure, including tailoring treatment to the patient's genetic profile –also known as personalized medicine – we need to know how this genetic variant affects health.

Scientists at the Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg have developed a model that makes predictions from which differentiated cells – for instance skin cells – can be very efficiently changed into completely different cell types – such as nerve cells, for example. This can be done entirely without stem cells. These computer-based instructions for reprogramming cells are of huge significance for regenerative medicine. The LCSB researchers present their results today in the prestigious scientific journal Stem Cells.

The strain of cholera that has sickened thousands in Haiti came from a single source and was not repeatedly introduced to the island over the past three years as some have thought, according to a new study published in mBio®, the online open-access journal of the American Society for Microbiology.

Researchers can now compare not only the genomes, but all the genes expressed, by domestic and wild tomatoes.
You say tomato, I say comparative transcriptomics. Researchers in the U.S., Europe and Japan have produced the first comparison of both the DNA sequences and which genes are active, or being transcribed, between the domestic tomato and its wild cousins.

It is nothing short of a world record in DNA research that scientists at the Centre for GeoGenetics at the Natural History Museum of Denmark (University of Copenhagen) have hit. They have sequenced the so far oldest genome from a prehistoric creature. They have done so by sequencing and analyzing short pieces of DNA molecules preserved in bone-remnants from a horse that had been kept frozen for the last 700.000 years in the permafrost of Yukon, Canada. By tracking the genomic changes that transformed prehistoric wild horses into domestic breeds, the researchers have revealed the genetic make-up of modern horses with unprecedented details. The spectacular results are now published in the international scientific journal Nature.

Camels are divided into two species, the one-humped dromedary and the two-humped Bactrian camel. Whether equipped with one or two humps, camels are precious in desert regions throughout the world. Their ability to carry heavy loads over long distances makes them ideally suited for transportation. In addition, camels are able to survive for weeks in hostile environments without food and water. Despite the extremely arid conditions, camels still provide enough milk for human consumption and also have an important role as a source of meat. Camels are specialists when it comes to adapting to the environment and have been characterized as sustainable food producers.

Children born with rare, inherited conditions known as Congenital Disorders of Glycosylation, or CDG, have mutations in one of the many enzymes the body uses to decorate its proteins and cells with sugars. Properly diagnosing a child with CDG and pinpointing the exact sugar gene that's mutated can be a huge relief for parents—they better understand what they're dealing with and doctors can sometimes use that information to develop a therapeutic approach. Whole-exome sequencing, an abbreviated form of whole-genome sequencing, is increasingly used as a diagnostic for CDG.

When Woods Hole Oceanographic Institution (WHOI) marine paleoecologist Marco Coolen was mining through vast amounts of genetic data from the Black Sea sediment record, he was amazed about the variety of past plankton species that left behind their genetic makeup (i.e., the plankton paleome).

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