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Technological advances are enabling scientists to sequence the genomes of cancer tumors, revealing a detailed portrait of genetic mutations that drive these diseases. But genomic studies are only one piece of the puzzle that is precision medicine. In orde

Big Data Key to Precision Medicine's Success

April 15, 2015 4:04 pm | by Weill Cornell Medical College | News | Comments

Technological advances are enabling scientists to sequence the genomes of cancer tumors, revealing a detailed portrait of genetic mutations that drive these diseases. But genomic studies are only one piece of the puzzle that is precision medicine. In order to realize the promise of this field, there needs to be an increased focus on creating robust clinical databases.

Data-enabled Science: Top500 Supercomputers Provide Universities with Competitive Edge

April 7, 2015 5:02 pm | by Paul Alongi, Clemson University | News | Comments

Researchers have long believed that supercomputers give universities a competitive edge in...

Researchers Create Wikipedia for Neurons

April 7, 2015 11:11 am | by Jocelyn Duffy, Carnegie Mellon University | News | Comments

The decades worth of data collected about the billions of neurons in the brain is astounding. To...

Efficient, Time Sensitive Execution of Next-gen Sequencing Pipelines Critical for Translational Medicine

April 6, 2015 3:26 pm | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Blogs | Comments

Demand for genomics processing is rapidly spreading from research labs to the clinical arena....

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Omics Explorer 3.1 for Mac

Omics Explorer 3.1 for Mac

April 1, 2015 11:18 am | Qlucore AB | Product Releases | Comments

Qlucore Omics Explorer 3.1 for Mac is data analysis software designed to maximize the outcome of research by making it easy to analyze experiment data from a biological point-of-view. Examples of this are the inbuilt Gene Ontology (GO) Browser, a Gene Set Enrichment Analysis (GSEA) function, and freedom to explore data using any variable identifier: variable collapse.

Researchers have harnessed bionanotechnology to emit a full range of colors in one pliable pixel layer — as opposed to the several rigid layers that constitute today's screens.

From Genes to Screens: Molecular Backbone of Super-Slim, Bendable Digital Displays Developed

March 31, 2015 11:44 am | by Tel Aviv University | News | Comments

A new study suggests that a novel DNA-peptide structure can be used to produce thin, transparent and flexible screens. The research harnesses bionanotechnology to emit a full range of colors in one pliable pixel layer — as opposed to the several rigid layers that constitute today's screens.

Yin-yang haplotypes arise when a stretch of DNA evolves to present two divergent forms. A group of engineers at Washington University in St. Louis showed a massive yin-yang haplotype pair encompassing the gene gephyrin on human chromosome 14. This image s

Mining Public Big Data yields Genetic Clues in Complex Human Diseases

March 27, 2015 11:35 am | by Beth Miller, Washington University in St. Louis | News | Comments

Big data: It’s a term we read and hear about often, but is hard to grasp. Computer scientists tackled some big data about an important protein and discovered its connection in human history as well as clues about its role in complex neurological diseases. Through a novel method of analyzing these big data, they discovered a region encompassing the gephyrin gene on chromosome 14 that underwent rapid evolution after splitting in two...

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n artist's rendition of a previously unknown species of crocodile-like "super salamander" that roamed the Earth more than 200 million years ago. University of Edinburgh researchers say the species discovered in Portugal was among the Earth's top predators

Car-sized Ancient Salamanders found in Portugal

March 25, 2015 11:45 am | by AP | News | Comments

Fossil remains of a previously unknown species of a crocodile-like "super salamander" that grew as long as a small car and was a top predator more than 200 million years ago have been found in southern Portugal, researchers announced on March 24, 2015. The prehistoric species, which looked like giant salamanders, grew up to six feet in length and lived in lakes and rivers.

Graphic of viruses attempting to "dock" on a microbial mat, using the tips of their tails. Courtesy of Blair Paul

Strange Viruses Discovered in Deep Ocean

March 23, 2015 11:51 am | by NSF | News | Comments

The intraterrestrials, they might be called. Strange creatures live in the deep sea, but few are odder than the viruses that inhabit deep ocean methane seeps and prey on single-celled microorganisms called archaea. The least understood of life's three primary domains, archaea thrive in the most extreme environments: near hot ocean rift vents, in acid mine drainage, in the saltiest of evaporation ponds and in petroleum deposits.

Life reconstruction of Carnufex carolinensis. Copyright Jorge Gonzales

Before Dinosaurs, Carolina Butcher was Top Beast of Prey

March 20, 2015 10:26 am | by North Carolina State University | News | Comments

A newly discovered crocodilian ancestor may have filled one of North America's top predator roles before dinosaurs arrived on the continent. The "Carolina Butcher" was a nine-foot-long, land-dwelling crocodylomorph that walked on its hind legs and likely preyed upon smaller inhabitants of North Carolina ecosystems, such as armored reptiles and early mammal relatives.

Physicist Chien-Shiung Wu in 1963 at Columbia University, where she was a professor. Known as the First Lady of Physics, Wu worked on the Manhattan Project and helped disprove a widely-accepted law of theoretical physics. Later in her life, Wu researched

Paving the Way: 28 Amazing Women, Trailblazing Science

March 18, 2015 12:16 pm | by NSF | News | Comments

Breakthrough science requires pioneers. People who combine brilliance with courage, even in the face of daunting opposition. The women who paved the way for modern scientific exploration exemplify this spirit; grappling not only with fundamental questions of the universe, but with discrimination and societal constraints that often stripped them of scientific credit.

The alliance, funded by UPMC, will see its work carried out by Pitt-led and CMU-led centers, with participation from all three institutions.

University of Pittsburgh, Carnegie Mellon University, UPMC Form Alliance to Transform Healthcare through Big Data

March 17, 2015 2:19 pm | by UPMC | News | Comments

Today’s health care system generates massive amounts of data — electronic health records, diagnostic imaging, prescriptions, genomic profiles, insurance records, even data from wearable devices. Information has always been essential for guiding care, but computer tools now make it possible to use that data to provide deeper insights. Leveraging big data to revolutionize healthcare is the focus of the Pittsburgh Health Data Alliance.

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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.

Another myth is that scientists look like this. U.S. Army RDECOM/Flickr, CC BY-SA

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 those outside our profession. So we put together a list of common myths we and our colleagues have heard anecdotally regarding scientific researchers.

In the search for ways to store data permanently, ETH researchers have been inspired by fossils. Courtesy of Philipp Stössel/ETH Zurich

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 store information in the form of DNA, preserving it for nearly an eternity. As encapsulation in silica is roughly comparable to that in fossilized bones, researchers could draw on prehistoric information about long-term stability and calculate a prognosis: through storage in low temperatures, DNA-encoded information can survive.

Tim Cutts is Head of Scientific Computing at Wellcome Trust Sanger Institute

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 machines used in the Human Genome Project. We at the Wellcome Trust Sanger Institute currently produce more sequences in one hour than we did in our first 10 years of operation. A great deal of computational resource is then needed to process that data.

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.

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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.

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.

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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