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Investigators have applied NetGestalt to data from The Cancer Genome Atlas (TCGA) colorectal cancer cohort, the first tumor dataset with complete molecular measurements at DNA, RNA and protein levels.

User-friendly Data Query, Visualization Tools Enable Omics Data Integration

May 19, 2015 4:21 pm | by Leigh MacMillan, Vanderbilt University | News | Comments

Advances in technology have generated vast amounts of “omics” data: genomic, epigenomic, transcriptomic, proteomic and metabolomic changes for all types of specimens. Bridging the gap between data generation and investigators’ ability to retrieve and interpret data is essential to realize the biological and clinical value of this wealth of information.

Counterintuitive Approach Yields Big Benefits for High-dimensional, Small-sized Problems

May 15, 2015 3:04 pm | by Agency for Science, Technology and Research (A*STAR) | News | Comments

Extracting meaningful information out of clinical datasets can mean the difference between a...

Recap: The Week's Top Stories — May 8-14

May 15, 2015 2:34 pm | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | News | Comments

In case you missed it, here's another chance to catch this week's biggest hits. Writing like a...

Massively Parallel Genomics Students: Publication has 940 Undergraduate Authors

May 11, 2015 12:04 pm | by Washington University in St. Louis | News | Comments

The list of authors for an article on comparative genomics of a fruit fly chromosome runs three...

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The new program builds on IBM Research advancements in analytics and existing Watson collaborations to develop a genome data analysis solution for clinicians. Partners involved in the program will use Watson Genomic Analytics, a new solution specifically

14 Leading Cancer Institutes Collaborate to Advance Personalized Medicine for Cancer Patients

May 6, 2015 12:33 pm | by IBM | News | Comments

IBM Watson is collaborating with more than a dozen leading cancer institutes to accelerate the ability of clinicians to identify and personalize treatment options for their patients. The institutes will apply Watson's advanced cognitive capabilities to reduce from weeks to minutes the ability to translate DNA insights, understand a person's genetic profile and gather relevant information from medical literature to personalize treatment.

DeskGen Gene Editing Platform

DeskGen Gene Editing Platform

April 29, 2015 9:52 am | Desktop Genetics Ltd. | Product Releases | Comments

The DeskGen Platform for gene editing combines elements of AutoClone and gUIDEbook and allows researchers to design genome editing vectors and cloning strategies optimized to their own laboratories and experimental needs. It provides the power to expertly design optimized genome editing experiments, in any cell line and species, right from the desktop.

The functional genetic network shown is just one of the 144 such networks identified for a diverse set of human tissues and cell types. Courtesy of Simons Center for Data Analysis

Computer Science, Statistical Methods Combine to Analyze Stunningly Diverse Genomic Big Data Collections

April 28, 2015 3:36 pm | by Simons Foundation | News | Comments

A multi-year study led by researchers from the Simons Center for Data Analysis and major universities and medical schools has broken substantial new ground, establishing how genes work together within 144 different human tissues and cell types in carrying out those tissues’ functions. The paper also demonstrates how computer science and statistical methods may combine to analyze genomic ‘big-data’ collections.

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The Cori Phase 1 system will be the first supercomputer installed in the new Computational Research and Theory Facility now in the final stages of construction at Lawrence Berkeley National Laboratory.

Cray XC40 will be First Supercomputer in Berkeley Lab’s New Computational Research and Theory Facility

April 23, 2015 3:17 pm | by NERSC and Berkeley Lab | News | Comments

The U.S. Department of Energy’s (DOE) National Energy Research Scientific Computing (NERSC) Center and Cray announced they have finalized a new contract for a Cray XC40 supercomputer that will be the first NERSC system installed in the newly built Computational Research and Theory facility at Lawrence Berkeley National Laboratory.

GenomeStack Big Data Analytics Database

GenomeStack Big Data Analytics Database

April 22, 2015 2:52 pm | by SQream Technologies | Product Releases | Comments

The GenomeStack Big Data Analytics platform has been developed specifically for bioinformatics researchers, data scientists and analysts conducting genome research. The database replaces the traditional file-based, manual process for storing and analyzing genome sequenced data.

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.

A supercomputer that can do 551 trillion calculations per second is housed at Clemson’s Information Technology Center.

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 scientific research, but now they have some hard data showing it’s true. A Clemson University team found that universities with locally available supercomputers were more efficient in producing research in critical fields than universities that lacked supercomputers.

To demonstrate how neuroelectro.org could be used, the researchers compared electrophysiological data from more than 30 neuron types that had been most heavily studied in the literature. The site was able to find many expected similarities between the dif

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 help scientists make sense of this “brain big data,” researchers at Carnegie Mellon University have used data mining to create a publicly available Web site that acts like Wikipedia, indexing physiological information about neurons. The site will help to accelerate the advance of neuroscience research by providing a centralized resource.

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Genomics processing is now moving mainstream to clinical applications, as new approaches to diagnosing and treatment involving genomics are gaining interest.

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. Genomics is now a "must have" tool for researchers in areas of oncology and rare diseases. It is also becoming a requirement in the clinical space for precision medicine, translational medicine and similar "bench to bedside" initiatives.

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...

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.

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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.

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.

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.

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