Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Computer scientists develop tool for mining genomic data

16.02.2004


Equipped with cutting-edge techniques to track the activity of tens of thousands of genes in a single experiment, biologists now face a new challenge - determining how to analyze this tidal wave of data. Stanford Associate Professor of Computer Science Daphne Koller and her colleagues have come to the rescue with a strategic approach that reduces the trial-and-error aspect of genetic sequence analysis.



’’What we’re developing is a suite of computational tools that take reams of data and automatically extract a picture of what’s happening in the cell,’’ says Koller. ’’It tells you where to look for good biology.’’

Koller presented her statistical approach for mining genomic data at a Feb. 14 symposium - ’’Machine Learning in the Sciences’’ - at the annual meeting of the American Association for the Advancement of Science (AAAS) in Seattle.


Several years ago, before Koller came onto the scene, a new generation of high-throughput assays revolutionized molecular biology. In the most stunning example of this technology, scientists began using thumbnail-sized ’’gene chips’’ to monitor the activities of thousands of genes at once. In October 2003, Santa Clara-based Affymetrix took this breakthrough to a new level when it began marketing whole-genome chips packed with all 30,000 to 50,000 known human genes. Genome chips can reveal, for instance, that in kidney cells treated with a certain drug, 116 genes spring into action while another 255 get shut off.

But this state-of-the-art DNA microarray technology provides only a single snapshot of the cell. ’’It’s a very partial view,’’ Koller says.

What scientists really want to know is how groups of genes work together to control specific biological processes, such as muscle development or cancer progression. Unraveling these regulatory networks - for example, determining that Gene A gets activated by Gene B but repressed by Gene C - is a daunting task.

Sifting through whopping amounts of DNA microarray data to cull the hundreds of activator and repressor candidates is actually the easy part. The real challenge is figuring out which of these genes, if any, are biologically meaningful. This requires a bewildering array of hit-or-miss wet-lab experiments that examine protein-protein and protein-DNA interactions among the candidate genes.

Koller’s computational tools will make this scheme less formidable by providing scientists with targeted hypotheses in the form of ’’Gene A regulates Gene B under Condition C.’’ These predictions are generated from a probabilistic framework that integrates data from a variety of sources, including microarrays, DNA sequences, and protein-protein and protein-DNA interactions.

As Koller sees it, each of these sources offers a glimpse into what is happening in the cell: ’’a snapshot from this angle, a shot from another angle, data from a third, and so on.’’ Her computational scheme creates ’’the best picture we can construct from putting all of these snapshots together.’’

The proof of concept for Koller’s targeted hypotheses came in a June 2003 Nature Genetics publication, which described the application of her tools to predict gene regulatory networks in a variety of biological processes in yeast. Three of these predictions were confirmed in wet-lab experiments, suggesting regulatory roles for previously uncharacterized proteins.

’’The creativity and computer science perspective brought to these problems by Koller and her collaborators provide a tremendous boost to biology,’’ says Matthew Scott, a developmental biologist at Stanford and chair of the scientific leadership council of Bio-X, an interdisciplinary initiative. His research group has used Koller’s approach to identify genes involved in specific processes during embryonic development, to determine which genes are key regulators of other genes and to track changes in gene activities during disease progression.

Scott adds that while the computational methods suggest interesting hypotheses, their ultimate validation relies upon lab experiments.

In the future, Koller hopes to develop her scheme to handle multi-species analysis - for instance, to identify gene regulatory networks that appear in both human and mouse genomes. ’’When a regulatory module is conserved across multiple species, that indicates it’s playing a significant role,’’ Koller says.

Koller’s collaborators include Eran Segal and Michael Shapira (both of Stanford), Nir Friedman (Hebrew University of Jerusalem), Aviv Regev (Harvard Center for Genome Research), Dana Pe’er (Harvard-Lipper Center for Computational Genetics), Roman Yelensky (Massachusetts Institute of Technology) and David Botstein (Princeton University).

Esther Landhuis | EurekAlert!
Further information:
http://robotics.stanford.edu/~koller/index.html
http://dags.stanford.edu
http://www.stanford.edu/news/

More articles from Information Technology:

nachricht Researchers illuminate the path to a new era of microelectronics
23.04.2018 | Boston University College of Engineering

nachricht Researchers achieve HD video streaming at 10,000 times lower power
20.04.2018 | University of Washington

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Molecules Brilliantly Illuminated

Physicists at the Laboratory for Attosecond Physics, which is jointly run by Ludwig-Maximilians-Universität and the Max Planck Institute of Quantum Optics, have developed a high-power laser system that generates ultrashort pulses of light covering a large share of the mid-infrared spectrum. The researchers envisage a wide range of applications for the technology – in the early diagnosis of cancer, for instance.

Molecules are the building blocks of life. Like all other organisms, we are made of them. They control our biorhythm, and they can also reflect our state of...

Im Focus: Spider silk key to new bone-fixing composite

University of Connecticut researchers have created a biodegradable composite made of silk fibers that can be used to repair broken load-bearing bones without the complications sometimes presented by other materials.

Repairing major load-bearing bones such as those in the leg can be a long and uncomfortable process.

Im Focus: Writing and deleting magnets with lasers

Study published in the journal ACS Applied Materials & Interfaces is the outcome of an international effort that included teams from Dresden and Berlin in Germany, and the US.

Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) together with colleagues from the Helmholtz-Zentrum Berlin (HZB) and the University of Virginia...

Im Focus: Gamma-ray flashes from plasma filaments

Novel highly efficient and brilliant gamma-ray source: Based on model calculations, physicists of the Max PIanck Institute for Nuclear Physics in Heidelberg propose a novel method for an efficient high-brilliance gamma-ray source. A giant collimated gamma-ray pulse is generated from the interaction of a dense ultra-relativistic electron beam with a thin solid conductor. Energetic gamma-rays are copiously produced as the electron beam splits into filaments while propagating across the conductor. The resulting gamma-ray energy and flux enable novel experiments in nuclear and fundamental physics.

The typical wavelength of light interacting with an object of the microcosm scales with the size of this object. For atoms, this ranges from visible light to...

Im Focus: Basel researchers succeed in cultivating cartilage from stem cells

Stable joint cartilage can be produced from adult stem cells originating from bone marrow. This is made possible by inducing specific molecular processes occurring during embryonic cartilage formation, as researchers from the University and University Hospital of Basel report in the scientific journal PNAS.

Certain mesenchymal stem/stromal cells from the bone marrow of adults are considered extremely promising for skeletal tissue regeneration. These adult stem...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

Unique scope of UV LED technologies and applications presented in Berlin: ICULTA-2018

12.04.2018 | Event News

IWOLIA: A conference bringing together German Industrie 4.0 and French Industrie du Futur

09.04.2018 | Event News

 
Latest News

Structured light and nanomaterials open new ways to tailor light at the nanoscale

23.04.2018 | Physics and Astronomy

On the shape of the 'petal' for the dissipation curve

23.04.2018 | Physics and Astronomy

Clean and Efficient – Fraunhofer ISE Presents Hydrogen Technologies at the HANNOVER MESSE 2018

23.04.2018 | Trade Fair News

VideoLinks
Science & Research
Overview of more VideoLinks >>>