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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.

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...

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...

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...

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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.

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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.

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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.

The first act of copulation in our distant ancestors, Microbrachius dicki

Planet’s First Sex Act: Ancient Armored Fish did it Sideways

October 20, 2014 12:11 pm | by Flinders University | News | Comments

A profound new discovery reveals how the intimate act of sexual intercourse first evolved in our deep distant ancestors. In one of the biggest discoveries in the evolutionary history of sexual reproduction, Flinders University Professor John Long has found that internal fertilization and copulation was invented by ancient armored fishes, called placoderms, about 385 million years ago in Scotland.

A 500-million-year-old fossil used by Australian researchers to make their discovery about vetulicolians. These marine creatures had a rod through their tail similar to a backbone, which places them as distant cousins of vertebrate animals. Courtesy of Un

Bizarre Ancient Fossils Confirmed as Strange Human Cousins

October 16, 2014 2:50 pm | by University of Adelaide | News | Comments

More than 100 years since they were first discovered, some of the world's most bizarre fossils have been identified as distant relatives of humans. The fossils belong to 500-million-year-old blind water creatures, known to scientists as "vetulicolians" (pronounced: ve-TOO-lee-coal-ee-ans).

Phylogenetic tree constructed with the BEAST software and built on a subset of both contemporary and ancient samples. Courtesy of Oxford University Press

Treasure Trove of Ancient Genomes Helps Recalibrate Human Evolutionary Clock

October 14, 2014 4:18 pm | by Molecular Biology and Evolution, Oxford University Press | News | Comments

To improve the modeling and reading of the branches on the human tree of life, researchers compiled the most comprehensive DNA set to date, a new treasure trove of 146 ancient (including Neanderthal and Denisovian) and modern human full mitochondrial genomes (amongst a set of 320 available worldwide).

“The collective expertise of NeuroLINCS investigators provides a unique opportunity to increase our knowledge of what makes brain cells unique and what happens during neurodegenerative diseases," said UC Irvine's Leslie M. Thompson.

Novel NIH Program will Create Database of Human Brain Cell Activity

October 10, 2014 12:08 pm | by UC Irvine | News | Comments

UC Irvine will receive $8 million from the NIH to establish one of six national centers dedicated to creating a database of human cellular responses that will accelerate efforts to develop new therapies for many diseases. The center will partner with researchers from Cedars-Sinai Medical Center’s Regenerative Medicine Institute, the Gladstone Institute of Neurological Disease, UC San Francisco, Johns Hopkins University and MIT.

Tom Conte is President-elect, IEEE Computer Society; Professor of Computer Science and Electrical & Computer Engineering, Georgia Institute of Technology; and Elie Track is President, IEEE Council on Superconductivity; CEO, nVizix.

Technology Time Machine Looks Far Ahead at Future of Processing

October 7, 2014 3:25 pm | by Tom Conte and Elie Track, IEEE | Blogs | Comments

The IEEE Technology Time Machine (TTM) is going further into the future. Now in its third year, the annual two-day IEEE meeting is mixing things up a little in terms of format and topics. Rather than just looking at how some technologies might evolve in the next decade, experts and visionaries are going to look out to 2035 and beyond.

This 600X photograph of a Drosophila melanogaster (fruit fly) seminal vesicle received an Image of Distinction designation in the 2013 Nikon Small World Photomicrophotography Competition, which recognizes excellence in photography with the optical microsc

Fruit Fly Privates

October 3, 2014 2:57 pm | News | Comments

This 600X photograph of a Drosophila melanogaster (fruit fly) seminal vesicle received an Image of Distinction designation in the 2013 Nikon Small World Photomicrophotography Competition, which recognizes excellence in photography with the optical microscope. The confocal image was created by Barbara Laurinyecz of University of Szeged, Department of Genetics, Szeged, Hungary using fluorescence.

Caris Life Sciences is accelerating precision medicine for cancer treatment using IBM technical computing and software defined storage solutions.  Courtesy of Caris Life Science

Accelerating Use of Molecular Profiling in Cancer Treatment Selection

September 25, 2014 4:43 pm | by IBM | News | Comments

IBM announced that Caris Life Sciences is using IBM technical computing and storage technology to accelerate the company’s molecular profiling services for cancer patients. The Caris tumor profiling database is one of the largest datasets in the application of advanced molecular profiling technologies to support clinicians in delivering personalized treatment recommendations — or precision oncology.

Scaffolded DNA origami utilizes numerous chemically synthesized, short DNA strands (staple strands) to direct the folding of a larger, biologically derived strand of DNA (scaffold strand). Molecular recognition (base pairing, i.e., A binds to T and G bind

Researchers Create World’s Largest DNA Origami

September 11, 2014 4:48 pm | by North Carolina State University | News | Comments

Researchers from North Carolina State University, Duke University and the University of Copenhagen have created the world’s largest DNA origami, which are nanoscale constructions with applications ranging from biomedical research to nanoelectronics. The standard for DNA origami has long been limited to a scaffold strand that is made up of 7,249 bases. The research team has now created DNA origami consisting of 51,466 bases

University of Chicago Paleontologist Paul C. Sereno looks inside the jaws of a 50-foot life-size model of a Spinosaurus dinosaur at the National Geographic Society exhibit in Washington. (AP Photo/Pablo Martinez Monsivais)

Bizarre, Alien-like Giant Dinosaur Unveiled

September 11, 2014 4:33 pm | by Seth Borenstein, AP Science Writer | News | Comments

Picture the fearsome creatures of "Jurassic Park" crossed with the shark from "Jaws." Then, super-size to the biggest predator ever to roam Earth. Now, add a crocodile snout as big as a person and feet like a duck's. The result gives you some idea of a bizarre dinosaur scientists unveiled September 11, 2014. This patchwork of critters, a 50-foot predator, is the only known dinosaur to live much of its life in the water.

Parents and physicians and scientists from the Neuroblastoma and Medulloblastoma Translational Research Consortium and TGen have teamed to launch a groundbreaking personalized medicine clinical trial investigation for pediatric cancer.

Providing Critical Child-cancer Research Tools to Speed Development of Personalized Treatments

September 11, 2014 3:25 pm | by TGen | News | Comments

Dell, Terascala and the Translational Genomics Research Institute are installing state-of-the-art computing and programing specialized for human genome investigations at the National Cancer Institute. The mission of the Oncogenomics Section at the NCI is to harness the power of high throughput genomic and proteomic methods to improve the outcome of children with high-risk metastatic, refractory and recurrent cancers.

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