Navigation Links
Computers 'taught' to ID regulating gene sequences
Date:11/5/2012

Johns Hopkins researchers have succeeded in teaching computers how to identify commonalities in DNA sequences known to regulate gene activity, and to then use those commonalities to predict other regulatory regions throughout the genome. The tool is expected to help scientists better understand disease risk and cell development.

The work was reported in two recent papers in Genome Research, published online on July 3 and Sept. 27.

"Our goal is to understand how regulatory information is encrypted and to learn which sequence variations contribute to medical risks," says Andrew McCallion, Ph.D., associate professor of molecular and comparative pathobiology in the McKusick-Nathans Institute of Genetic Medicine at Hopkins. "We give data to a computer and 'teach it' to distinguish between data that has no biological value versus data that has this or that biological value. It then establishes a set of rules, which allows it to look at new sets of data and apply what it learned. We're basically sending our computers to school."

These state-of-the-art "machine learning" techniques were developed by Michael Beer, Ph.D., assistant professor of biomedical engineering at the Johns Hopkins School of Medicine, and by Ivan Ovcharenko, Ph.D., at the National Center for Biotechnology Information. The researchers began both studies by creating "training sets" for their computers to "learn" from. These training sets were lists of DNA sequences taken from regions of the genome, called enhancers, that are known to increase the activity of particular genes in particular cells.

For the first of their studies, McCallion's team created a training set of enhancer sequences specific to a particular region of the brain by compiling a list of 211 published sequences that had been shown, by various studies in mice and zebrafish, to be active in the development or function of that part of the brain.

For a second study, the team gen
'/>"/>

Contact: Catherine Kolf
ckolf@jhmi.edu
443-287-2251
Johns Hopkins Medicine
Source:Eurekalert  

Page: 1 2

Related biology news :

1. Computers can predict effects of HIV policies
2. 2 NASA visualizations selected for computers graphics showcase
3. BUSM study identifies receptors role in regulating obesity, type 2 diabetes
4. Scientists identify mechanism for regulating plant oil production
5. New screening technique yields elusive compounds to block immune-regulating enzyme
6. DNA sequences need quality time too - guidelines for quality control published
7. Research reveals contrasting consequences of a warmer Earth
8. Revolutionary project will obtain entire genome sequences in fight against Alzheimers
9. New approach to spell checking gene sequences
10. Long-term research reveals causes and consequences of environmental change
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Computers 'taught' to ID regulating gene sequences
(Date:4/17/2014)... Our eyes not ... with a continuous stream of information about our own movements. ... a car the world glides by us and leaves ... our brain calculates self-motion from this "optic flow". This way, ... during our own movements. Together with biologists from the University ...
(Date:4/17/2014)... to produce hydrogen sulfide in order to properly multiply ... from the Center for Craniofacial Molecular Biology at the ... Songtao Shi, principal investigator on the project, said the ... the flow of calcium ions. The essential ions activate ... or the creation of new bone tissue, and keeps ...
(Date:4/17/2014)... Singh Thursday as a "Champion of Change" for ... in the residential, commercial and industrial sectors. , ... and Computer Engineering and director of Clemson,s Center ... leading the charge across the country to create ... driving policy changes at the local level to ...
Breaking Biology News(10 mins):How vision makes sure that little fish do not get carried away 2How vision makes sure that little fish do not get carried away 3How vision makes sure that little fish do not get carried away 4White House honors Clemson professor as 'Champion of Change' for solar deployment 2
... international team of scientists led by King,s College London has ... (short-sightedness). Myopia is a major cause of ... cure. These findings, published today in the journal Nature ... lead to finding better treatments or ways of preventing the ...
... (NGS) technology has revolutionized biomedical research, making complete ... for a wide variety of research applications. Bioinformatics ... critical bottleneck for many researchers and organizations wishing ... DNA Sequencing Informatics provides a thorough introduction ...
... throughout Vienna it was impossible not to notice that the ... around the courtyards of the inner city nor woke tired ... no longer there. Thankfully, they gradually reappeared and a ... levels. But the sudden crash in numbers was alarming ...
Cached Biology News:New genes for short-sightedness identified 2Forensic pathology: tracing the origin of the Usutu Virus 2
(Date:1/14/2014)... WASHINGTON , Jan. 14, 2014  3D Communications, a leading provider ... scientific, regulatory, business, and media events in the United ... its former associate Virginia Cox , JD, is returning to ... Virginia Cox re-joins 3D after more than two years ...
(Date:1/14/2014)... , Jan. 14, 2014 The largest international ... medicinal plants and therapeutic derivatives thereof has endorsed ... and researchers about the challenges of adulterated herb ... ) The Society for Medicinal ...
(Date:1/14/2014)... Canada (PRWEB) January 14, 2014 In ... its motives and methods in product development and promotion ... the industry. This mistrust, fueled by concerns about the ... fed by reports of spectacular fines to the world’s ...
(Date:1/14/2014)... ®, provider of RapidResponse ®, a cloud-based supply chain ... S&OP ) service, is proud to be a gold sponsor ... at the Hilton San Diego Bayfront, January 30 – 31, ... , Director of Supply Chain at Amgen, as she presents ...
Breaking Biology Technology:Former FDA Associate Commissioner Returns To 3D Communications 2World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 2World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 3World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 4World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 5World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 6World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 7World's Largest Group of Medicinal Plant Researchers Endorses ABC-AHP-NCNPR Botanical Adulterants Program 8The Sunshine Act: Necessary Regulation or Unnecessary Dysregulation? New Life Science Webinar Hosted by Xtalks and IRB Services 2The Sunshine Act: Necessary Regulation or Unnecessary Dysregulation? New Life Science Webinar Hosted by Xtalks and IRB Services 3Event Alert: Kinaxis Customer to Present at the Biomanufacturing Summit "Supply Chain: Improving Network Effectiveness" 2
... New sol-gel inks developed by researchers at the University ... three-dimensional structures of metal oxides with nanoscale features. , ... nanoscale opens a new avenue to functional devices. Potential ... The researchers describe the new inks in a paper ...
... Calif., Oct. 11 CompareNetworks,Media Group, the leading ... industries, today announced the launch of Acuity Medical,Education, ... CompareNetworks. With the arrival of two key new ... Liza Frenzik as Special,Projects Director, the CompareNetworks team ...
... Fisher,Scientific Inc. (NYSE: TMO ), the world ... construct an $11 million, state-of-the-art BioCenter,for the manufacture ... the site of its existing bioprocess production business ... a response to the increasing demand for,disposable bioprocessing ...
Cached Biology Technology:Sol-gel inks produce complex shapes with nanoscale features 2CompareNetworks Media Group Delivers CME/CE Through Acuity Medical Education 2Thermo Fisher Scientific to Expand Manufacturing Operation for Single-Use Bioprocessing Containers 2Thermo Fisher Scientific to Expand Manufacturing Operation for Single-Use Bioprocessing Containers 3Thermo Fisher Scientific to Expand Manufacturing Operation for Single-Use Bioprocessing Containers 4
iEMS Thermal Microplate Holder...
Improve inventory management with stainless steel red cell canisters; ensure product safety with CO2 or LN2 backup systems. A complete solution for your blood banking needs....
Improve inventory management with stainless steel red cell canisters; ensure product safety with CO2 or LN2 backup systems. A complete solution for your blood banking needs....
... RNase H- Reverse Transcriptase (RT) is an ... RT. It is a DNA polymerase that ... RNA DNA or an RNA:DNA hybrid. This ... of point mutations rather than a deletion ...
Biology Products: