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A mathematical will give researchers an opportunity to discover the earliest words and languages spoken to date, with the potential to go back thousands of years. Courtesy of woodleywonderworks

Statistical Technique Traces Languages Back to Oldest Spoken Words

February 24, 2015 12:42 pm | by Current Biology | News | Comments

Researchers have developed a statistical technique that sorts out when changes to words’ pronunciations most likely occurred in the evolutionary history of related languages. Their model gives researchers a renewed opportunity to trace words and languages back to their earliest common ancestor or ancestors — potentially thousands of years further into prehistory than previous techniques.

Seven Myths about Scientists Debunked

February 19, 2015 2:07 pm | by Jeffrey Craig and Marguerite Evans-Galea, Murdoch Childrens Research Institute | Articles | Comments

As scientific researchers, we are often surprised by some of the assumptions made about us by...

Data Storage for Eternity: Encapsulated DNA-encoded Information Expected to Survive a Million Years

February 13, 2015 3:36 pm | by Angelika Jacobs, ETH Zurich | News | Comments

How can we preserve our knowledge today for the next millennia? Researchers have found a way to...

Modern DNA Sequencing Requires a Modern Day Approach

February 13, 2015 2:27 pm | by Tim Cutts, Wellcome Trust Sanger Institute | Blogs | Comments

The sequencing machines that run today produce data several orders of magnitude faster than the...

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Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source

Helping to Save Lives of Critically Ill Children

February 12, 2015 10:17 am | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Articles | Comments

For those on the front lines of treating cancer, speed and precision are key to patients’ survival. Pediatric cancer researchers have been making incredible strides in accelerating delivery of new diagnostic and treatment options. Supercomputer-powered genetic diagnosis is being used to harness the power of high throughput genomic and proteomic methods and is playing a key role in improving the outcome for children with genetic diseases.

Supported through crowdfunding, researchers have concluded a successful experiment to identify a novel genetic mutation as the source of a specific rare disease.

Crowdfunding Helps Solve Rare Disease Mystery

February 11, 2015 1:47 pm | by Tel Aviv University | News | Comments

Rare diseases — those that affect fewer than one in 200,000 people — are often identified early in life. Some 30 percent of children afflicted by these "orphan diseases" do not live to see their fifth birthday. While the US Orphan Drug Act of 1983 was written into law to promote research on the topic, the cost of identifying the source and progression of these diseases remains prohibitive for many families.

Researchers found that the link between having a faster-running biological clock and early death held true even after accounting for other factors such as smoking, diabetes and cardiovascular disease. Courtesy of Elliott Brown

DNA Clock Helps Predict Individual Lifespans

February 5, 2015 4:14 pm | by University of Edinburgh | News | Comments

Scientists have identified a biological clock that provides vital clues about how long a person is likely to live. Researchers studied chemical changes to DNA that take place over a lifetime, and can help them predict an individual's age. By comparing individuals’ actual ages with their predicted biological clock age, scientists saw a pattern emerging.

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Microscopic image of senile plaques seen in the cerebral cortex of a person with Alzheimer's disease of presenile onset. Courtesy of KGH

Blue Waters Project helps Uncover Alzheimer's Complex Genetic Networks

February 5, 2015 4:06 pm | by NSF | News | Comments

The release of the film, Still Alice, in September 2014 placed a much-needed light on Alzheimer's disease, a debilitating neurological disease that affects a growing number of Americans each year. More than 5.2 million people in the U.S. are currently living with Alzheimer's. One out of nine Americans over 65 has Alzheimer's, and one out of three over 85 has the disease. For those over 65, it is the fifth leading cause of death.

In the United States, big data environments are utilizing advanced computing systems to map phenotype to underlying process and to compare those who develop disease with those who don’t. To accomplish this, the researchers are assembling publically availa

Reversing the Global Diabesity Epidemic

February 5, 2015 2:38 pm | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Blogs | Comments

Diabesity has been identified as a major global health problem by researchers and healthcare professionals world-wide, including England’s National Health Service, Brigham and Women’s Hospital and Harvard Medical School, Ain Shams University Hospital in Cairo, Egypt, and a research consortium of the European Union.

A code hidden in the arrangement of the genetic information of single-stranded RNA viruses tells the virus how to pack itself within its outer shell of proteins.

Molecular Warfare: Researchers Discover Viral "Enigma Machine"

February 4, 2015 2:21 pm | by University of Leeds | News | Comments

Researchers have cracked a code that governs infections by a major group of viruses, including the common cold and polio. The unnoticed code had been hidden in plain sight in the sequence of the ribonucleic acid (RNA) that makes up this type of viral genome. But researchers have unlocked its meaning and demonstrated that jamming the code can disrupt virus assembly. Stopping a virus assembling can stop it functioning.

Customized Treatment: "Charting the versions of the genes that are only found in cancer cells may help tailor the treatment offered to each patient," says Rolf Skotheim. Courtesy of Yngve Vogt

Supercomputing Reveals Genetic Code of Cancer

February 2, 2015 12:46 pm | by Yngve Vogt, University of Oslo | News | Comments

Cancer researchers must use one of the world's fastest computers to detect which versions of genes are only found in cancer cells. Every form of cancer, even every tumor, has its own distinct variants. A research group is working to identify the genes that cause bowel and prostate cancer, which are both common diseases. There are 4,000 new cases of bowel cancer in Norway every year. Only six out of 10 patients survive the first five years.

Arabidopsis thaliana, a model flowering plant studied by biologists, has climate-sensitive genes whose expression was found to evolve. Courtesy of Penn State

Needle in a Haystack: Finding the Right Genes in Tens of Thousands

January 28, 2015 2:45 pm | by TACC | News | Comments

Scientists using supercomputers found genes sensitive to cold and drought in a plant help it survive climate change. The computational challenges were daunting, involving thousands of individual strains of the plant with hundreds of thousands of markers across the genome and testing for a dozen environmental variables. Their findings increase basic understanding of plant adaptation and can be applied to improve crops.

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The Biosurveillance Gateway site offers a variety of Los Alamos-developed biosurveillance tools that can be used for decision support in disease surveillance.

Biosurveillance Gateway Supports Centralized Global Disease Response

January 28, 2015 2:21 pm | by Los Alamos National Laboratory | News | Comments

A new online resource, called the Biosurveillance Gateway, is in place at Los Alamos National Laboratory, providing a centralized portal for all news, information, resources and research related to biosurveillance at the laboratory. The goal of the site is to support global disease surveillance, providing useful tools for professionals around the world to reference from a single location.

The researchers determined the networks of the active genes and — like a dragnet — looked for the "main perpetrators" using a computer model. Courtesy of Atramos

Computer Model Creates Dragnet for Epilepsy Genes

January 26, 2015 3:07 pm | by University of Bonn | News | Comments

Scientists have taken a new path in the research into causes of epilepsy: They determined the networks of the active genes and — like a dragnet — looked for the "main perpetrators" using a computer model. In doing so, they discovered the molecule sestrin-3 as a central switch. In animal models, the scientists were able to demonstrate that inhibition of sestrin-3 leads to a reduction in seizures.

Clemson University associate professor of genetics and biochemistry Alex Feltus is co-principal investigator on the Tripal Gateway project award.

Researchers get $1.4 Million to Advance Big Data for Genomic Research

January 22, 2015 2:04 pm | by Brian M. Mullen, Clemson University | News | Comments

A team of scientists has received a $1.4 million grant from the National Science Foundation to help meet the growing needs of the data-driven genomic science community. The Tripal Gateway project will build on existing cyberinfrastructure to enhance the capacity of genomic databases to manage, exchange and process “big data.”

Partek Flow 4.0 for NGS Analysis

Partek Flow 4.0 for NGS Analysis

January 22, 2015 1:51 pm | Partek Incorporated | Product Releases | Comments

Partek Flow 4.0 is designed specifically for the analysis needs of next-generation sequencing applications including RNA, small RNA and DNA sequencing. With the ability to either build custom analysis pipelines or download pre-built pipelines, users can perform alignment, quantification, quality control, statistics and visualization.

An international team of roughly 300 scientists pooled brain scans and genetic data worldwide to pinpoint genes that enhance or break down key brain regions in people from 33 countries. This is the first high-profile study since the NIH launched its Big D

Global Consortium Cracks Part of Brain’s Genetic Code

January 21, 2015 4:05 pm | by Alison Trinidad, Keck Medicine of USC | News | Comments

In the largest collaborative study of the brain to date, researchers from the Keck School of Medicine of the University of Southern California (USC) led a global consortium of 190 institutions to identify eight common genetic mutations that appear to age the brain an average of three years. The discovery could lead to targeted therapies and interventions for Alzheimer’s disease, autism and other neurological conditions.

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This live panel discussion looks at how big data and data science have fast become the next frontier for innovation, competition and productivity.

Big Data Insights: Accelerating Discovery in Medicine, Research & More

January 20, 2015 11:51 am | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Blogs | Comments

On Wednesday, January 21, Scientific Computing will host a live panel discussion that looks at how big data and data science have fast become the next frontier for innovation, competition and productivity. One of today’s significant advances in data science introduces us to the Next Generation Cyber Capability (NGCC) at Arizona State University (ASU)...

John Wass is a statistician based in Chicago, IL

Qlucore Omics Explorer: Analysis in an Instant

January 8, 2015 4:00 pm | by John A. Wass, Ph.D. | Articles | Comments

Qlucore is a software platform for the analysis of genomics, proteomics and related data. As with most statistical and genomics software, it generates an immediate graphic for most analyses. Its specific areas of use include gene expression, protein arrays, DNA methylation, miRNA, proteomics, and pattern and structure identification in multivariate data.

A leading cause of skin and wound infections once confined largely to hospitals and nursing homes, methicillin-resistant Staphylococcus aureus, or MRSA, is now cropping up in schools, farms and locker rooms, infecting otherwise healthy people. Researchers

Algorithm Predicts Superbugs' Countermoves

January 2, 2015 4:24 pm | by Duke University | News | Comments

With drug-resistant bacteria on the rise, even common infections that were easily controlled for decades — such as pneumonia — are proving trickier to treat with standard antibiotics. New drugs are desperately needed, but so are ways to maximize the effective lifespan of these drugs. Researchers used software they developed to predict a constantly-evolving infectious bacterium's countermoves to one of these new drugs ahead of time...

The expedition broke several records for the deepest living fish either caught or seen on video. Setting the record at 26,872 feet was a completely unknown variety of snailfish, which stunned scientists when it was filmed several times during seafloor exp

New Species Found at Greatest Depths ever Recorded

December 22, 2014 3:04 pm | by Gina Ohnstad, Whitman College | News | Comments

Biologists have returned from the first detailed study of the Mariana Trench aboard Schmidt Ocean Institute's research vessel Falkor. The Mariana Trench has been the focus of high-profile voyages to conquer Challenger Deep, the deepest place on Earth. This recent expedition set many new records, including the deepest rock samples ever collected and the discovery of new fish species at the greatest depths ever recorded.

Molecule and Deep Learning – Frey’s team used computational deep learning techniques to train a system that mimics the process of splicing in the cell (left panel). Features such as motifs, RNA secondary structures and nucleosome positions are computation

Deep Learning Reveals Unexpected Genetic Roots of Cancers, Autism and Other Disorders

December 18, 2014 4:23 pm | by The University of Toronto | News | Comments

In the decade since the genome was sequenced, scientists and doctors have struggled to answer an all-consuming question: Which DNA mutations cause disease? A new computational technique developed at the University of Toronto may now be able to tell us. A team has developed the first method for ‘ranking’ genetic mutations based on how living cells ‘read’ DNA, revealing how likely any given alteration is to cause disease.

The species used in a Rice University genetic study of mice were collected from 15 locations in Europe and Africa. The green region indicates the range of Mus spretus, the Algerian mouse, while the blue region indicates the range of Mus musculus domesticu

Big Data Analysis Reveals Shared Genetic Code between Species

December 18, 2014 11:32 am | by Mike Williams, Rice University | News | Comments

Researchers have detected at least three instances of cross-species mating that likely influenced the evolutionary paths of “old world” mice, two in recent times and one in the distant past. They think these instances of introgressive hybridization are only the first of many needles waiting to be found in a very large genetic haystack. The finding suggests that hybridization in mammals may not be an evolutionary dead end.

Big Data and genetic complexity: HotNet2 helps define the terrain for complex genetic associations involved in cancer. “The next step,” says researcher Ben Raphael, “is translating all of this information from cancer sequencing into clinically actionable

Big Data v. Cancer: Algorithm Identifies Genetic Changes across Cancers

December 15, 2014 4:00 pm | by Brown University | News | Comments

Using a computer algorithm that can sift through mounds of genetic data, researchers from Brown University have identified several networks of genes that, when hit by a mutation, could play a role in the development of multiple types of cancer. The algorithm, called Hotnet2, was used to analyze genetic data from 12 different types of cancer assembled as part of the pan-cancer project of The Cancer Genome Atlas (TCGA).

For the family of bee-eaters (on the photo Merops bullocki), the study revealed a close relationship to oscine birds, parrots, and birds of prey. Courtesy of Peter Houde

Bird Tree of Life Reproduced using Gene Analysis, Supercomputing

December 15, 2014 1:57 pm | by Karlsruhe Institute of Technology | News | Comments

About 95 percent of the more than 10,000 bird species known only evolved upon the extinction of dinosaurs about 66 million years ago. According to computer analyses of the genetic data, today's diversity developed from a few species at a virtually explosive rate after 15 million years. Scientists designed the algorithms for the comprehensive analysis of the evolution of birds; a computing capacity of 300 processor-years was required.

Duke researchers led by associate professor of neurobiology Erich Jarvis, left, did most of the DNA extraction from bird tissue samples used in the Avian Phylogenomics Consortium. (l-r: Carole Parent, Nisarg Dabhi, Jason Howard). Courtesy of Les Todd, Duk

Mapping the "Big Bang" of Bird Evolution

December 12, 2014 6:04 pm | by Kelly Rae Chi, Duke University | News | Comments

The genomes of modern birds tell a story of how they emerged and evolved after the mass extinction that wiped out dinosaurs and almost everything else 66 million years ago. That story is now coming to light, thanks to an ambitious international collaboration that has been underway for four years. The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 28 papers.

Professor Tandy Warnow developed a new statistical method that sorts genetic data to construct better species trees detailing genetic lineage. Courtesy of L. Brian Stauffer

Sophisticated New Statistical Technique helps Map Species' Genetic Heritage

December 12, 2014 5:50 pm | by Liz Ahlberg, University of Illinois | News | Comments

Where did the songbird get its song? What branch of the bird family tree is closer to the flamingo — the heron or the sparrow? These questions seem simple, but are actually difficult for geneticists to answer. A new, sophisticated statistical technique can help researchers construct more accurate species trees detailing the lineage of genes and the relationships between species.

Researchers will track the lives of people with multiple sclerosis (MS) in unprecedented detail in OPTIMISE — a project to improve the evaluation of treatments.

Big Data Project Captures Multiple Sclerosis Patient Experience

December 11, 2014 3:43 pm | by Francesca Davenport, Imperial College London | News | Comments

MS affects more than two million people worldwide. Symptoms are different for everyone but commonly include fatigue, tingling, speech problems and difficulties with walking and balance. To gain a better understanding of MS and its treatments, there is a need for a system to collect comprehensive data that provides an in-depth picture of the experiences of MS patients across a large population.

Watson's Nobel prize for the discovery of the structure of DNA sold at Christie's in a New York auction for $4.7 million, a world auction record for any Nobel.

Tycoon buys Watson's Nobel Prize, Gives it Back

December 10, 2014 2:25 pm | by AP | News | Comments

Russia's richest man says he has bought James D. Watson's Nobel Prize medal at Christie's in order to return it to the scientist. The 1962 Nobel Prize in Physiology or Medicine was awarded jointly to Francis Harry Compton Crick, James Dewey Watson and Maurice Hugh Frederick Wilkins "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material."

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