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.
Extracting meaningful information out of clinical datasets can mean the difference between a...
In case you missed it, here's another chance to catch this week's biggest hits. Writing like a...
The list of authors for an article on comparative genomics of a fruit fly chromosome runs three...
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.
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.
Computer Science, Statistical Methods Combine to Analyze Stunningly Diverse Genomic Big Data CollectionsApril 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.
Cray XC40 will be First Supercomputer in Berkeley Lab’s New Computational Research and Theory FacilityApril 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.
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 order to realize the promise of this field, there needs to be an increased focus on creating robust clinical databases.
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.
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.
Efficient, Time Sensitive Execution of Next-gen Sequencing Pipelines Critical for Translational MedicineApril 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.
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.
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.
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...
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.
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.
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.
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.
University of Pittsburgh, Carnegie Mellon University, UPMC Form Alliance to Transform Healthcare through Big DataMarch 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.
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.
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.
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.
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.
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.
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.
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.
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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