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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.

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...

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...

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...

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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.

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)...

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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.

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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.

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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."

This is an early draft of the title page for what would become On the Origin of Species.  Darwin Manuscripts Project

Digitizing Darwin’s Writings: Over 12,000 Pages Released Online

December 9, 2014 1:53 pm | by American Museum of Natural History | News | Comments

Tracing the evolution of Charles Darwin’s thoughts about evolution is becoming an increasingly accessible project, thanks to a growing cache of publicly available digitized Darwin manuscripts on the American Museum of Natural History’s Web site. By June 2015, the Museum will host more than 30,000 digitized documents written by Darwin between 1835 and 1882.

Left to right: Ron Weiss, professor of biological engineering; Domitilla Del Vecchio, associate professor of mechanical engineering; and Deepak Mishra, MIT graduate student in biological engineering. Courtesy of Brian Teague

New Device Could Make Large Biological Circuits Practical

November 26, 2014 1:49 pm | by David L. Chandler, MIT | News | Comments

Researchers have made great progress in recent years in the design and creation of biological circuits — systems that, like electronic circuits, can take a number of different inputs and deliver a particular kind of output. But, while individual components of such biological circuits can have precise and predictable responses, those outcomes become less predictable as more such elements are combined.

IBM is investing in Pathway to position both companies on the cutting edge of offering truly personalized wellness information.

Evidence-based Medicine: Bringing Big Data to Healthcare Consumers

November 26, 2014 9:31 am | by Kalorama Information | News | Comments

The IBM Watson Group's investment in Pathway Genomics is a model for the types of partnerships that are bringing Big Data to the healthcare consumer marketplace. IBM hopes to use Watson, their cognitive technology, and Big Data — enormous medical datasets — to transform the quality and speed of care delivered to individuals through individualized, evidence-based medicine.

Moleculomics’s core business is focused on developing new computational tools (known as pipelines) that take genetic information (in the form of DNA sequences) and automatically convert this into detailed three-dimensional models of all of the proteins wi

High Performance Computing for All (Yes, You Too…)

November 19, 2014 1:34 pm | by Gilad Shainer, HPC Advisory Council | Blogs | Comments

High-performance computing can help a business to become more efficient and more productive. And, for a small business, HPC can be a game changer, helping it leapfrog ahead of the competition by reducing its costs and dramatically improving its time to market.

John Wass is a statistician based in Chicago, IL.

Exploration and Analysis of DNA Microarray and Other High-Dimensional Data

November 18, 2014 3:10 pm | by John A. Wass, Ph.D. | Articles | Comments

The introduction of newer sequencing methodologies, DNA microarrays and high-throughput technology has resulted in a deluge of large data sets that require new strategies to clean, normalize and analyze the data. All of these and more are covered in approximately 300 pages with extraordinary clarity and minimal mathematics.

The Center for Pediatric Genomic Medicine at Children’s Mercy was the first genome center in the world inside children’s hospital and one of the first to focus on genome sequencing and analysis for inherited childhood diseases.

HPC Innovation Excellence Award: The Center for Pediatric Genomic Medicine

November 17, 2014 6:40 pm | Award Winners

The Center for Pediatric Genomic Medicine at Children's Mercy Hospitals Kansas City was the first genome center in the world to be created inside a children's hospital and one of the first to focus on genome sequencing and analysis for inherited childhood diseases. 

IBM and Pathway Genomics are aiming to revolutionize the health and wellness industry by leveraging the natural language processing and cognitive capabilities of Watson. For the first time consumers will be able to ask the Pathway Panorama app questions t

IBM Watson Group Invests in Pathway Genomics

November 13, 2014 2:28 pm | by IBM | News | Comments

Cognitive apps are in market today and continue to change the way professionals and consumers make decisions. To help accelerate this transformation, the IBM Watson Group announced an investment in Pathway Genomics, a clinical laboratory that offers genetic testing services globally, to help deliver the first-ever cognitive consumer-facing app based on genetics from a user’s personal makeup.

Vintana during the age of the dinosaurs. Courtesy of Lucille Betti-Nash

Paleontologists Find Ancient, Bizarre Groundhog-like Mammal

November 5, 2014 4:37 pm | by Stony Brook University | News | Comments

A newly discovered 66 to 70 million-year-old groundhog-like creature, massive in size compared to other mammals of its era, provides new and important insights into early mammalian evolution. Stony Brook University paleontologist David Krause, Ph.D., led the research team that unexpectedly discovered a nearly complete cranium of the mammal, which lived alongside Late Cretaceous dinosaurs in Madagascar.

GeneSpring Pathway Architect Software

GeneSpring Pathway Architect Software

November 3, 2014 11:44 am | Agilent Technologies | Product Releases | Comments

GeneSpring Pathway Architect software is designed to enable faster discovery of complex relationships across multi-omic data. Designed for researchers focused on genomics, proteomics, metabolomics, transcriptomics or any combination of life science disciplines, the package includes GeneSpring GX and Mass Profiler Professional, as well as Pathway Architect.

Researchers are expanding the applicability of biological circuits. Background: Microscopic image of human kidney cells with fluorescent proteins in cell culture.

Constructing Precisely Functioning, Programmable Bio-computers

October 23, 2014 3:40 pm | by Fabio Bergamin, ETH | News | Comments

Bio-engineers are working on the development of biological computers with the aim of designing small circuits made from biological material that can be integrated into cells to change their functions. In the future, such developments could enable cancer cells to be reprogrammed, thereby preventing them from dividing at an uncontrollable rate. Stem cells could likewise be reprogrammed into differentiated organ cells.

Diver collecting microbial samples from Australian seaweeds for Uncovering Genome Mysteries

Crowdsourced Supercomputing Examines Big Genomic Data

October 21, 2014 9:31 am | by IBM | News | Comments

What do the DNA in Australian seaweed, Amazon River water, tropical plants, and forest soil all have in common? Lots, say scientists. And understanding the genetic similarities of disparate life forms could enable researchers to produce compounds for new medicines, eco-friendly materials, more resilient crops, and cleaner air, water and energy.

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