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 Smart Computers
21.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht AI implications: Engineer's model lays groundwork for machine-learning device
18.08.2017 | Washington University in St. Louis

All articles from Information Technology >>>

The most recent press releases about innovation >>>

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

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

Cholesterol-lowering drugs may fight infectious disease

22.08.2017 | Health and Medicine

Meter-sized single-crystal graphene growth becomes possible

22.08.2017 | Materials Sciences

Repairing damaged hearts with self-healing heart cells

22.08.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>