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:5/18/2015)... Fingerprint Cards (FPC) has received an ... and FPC1035 from one if its module partners. Deliveries are ... 2015 and the sensors will be used by smartphone manufacturers ... 2015 hereby amount to 740 MSEK to date. In addition ... and a number of smaller orders not separately communicated amounting ...
(Date:5/14/2015)... 14, 2015  Verificient Technologies, Inc., a ... online remote proctoring, announced a new alliance ... and creator of the Canvas Learning Management ... companies will benefit from the seamless integration ... As a fully integrated multifactor biometrics behavioral ...
(Date:5/11/2015)... May 11, 2015  Through a well-rounded UAS delegation representing ... had a strong showing at AUVSI,s Unmanned 2015 conference last ... Ohio,s UAS industry met with over ... all points along the UAS ecosystem. "Our ... Vice President for Aerospace Rich Knoll . "If you ...
Breaking Biology News(10 mins):Fingerprint Cards Receives Touch Fingerprint Sensor Order of SEK 230 Million and Raises Revenue Guidance for 2015 2Verificient and Instructure Announce Alliance Partnership to Provide Online Proctoring for K-12 and Higher Education Institutions 2Ohio Flies High at Unmanned '15, Sets Stage for Ohio UAS Conference 2
... hydrogen gas the ultimate fuel for stars is ... Robert Braun has found.,This is the first accurate measurement of ... after the Big Bang the Universe,s matter was almost entirely ... and generated galaxies, stars and planets and the process ...
... a fjord in Canada scientists have found a landscape similar ... a frozen and sulphurous environment, where sulphur associated with Arctic ... for traces of life on Europa. It is ... and sulphur come together, supposedly like on Europa, Jupiter,s moon. ...
... LA JOLLA, CA----A new method for rapidly solving the ... as integral membrane proteins, may speed drug discovery by ... to a paper published May 20 in Nature ... the Salk Institute for Biological Studies, provides a shortcut ...
Cached Biology News:There's more star-stuff out there but it's not dark matter 2Arctic bacteria help in the search to find life on moon Europa 2Speeding up drug discovery with rapid 3-D mapping of proteins 2Speeding up drug discovery with rapid 3-D mapping of proteins 3
(Date:5/28/2015)... NORTH BRUNSWICK, N.J. , May 28, 2015 ... that PDS0101, a cancer immunotherapy treatment targeting HPV-16, ... patients.  Currently, pre-cervical cancer is ... could offer a simple and effective non-surgical alternative. ... body,s defense mechanisms (T-cells) to recognize, target, and ...
(Date:5/28/2015)... Md. , May 28, 2015  GenVec, Inc. ... and CEO, Douglas J. Swirsky , will present ... Conference at 11 a.m. EDT on Thursday, June 4, ... of Mr. Swirsky,s presentation will be available at the ... be available on GenVec,s website.  To access, visit ...
(Date:5/28/2015)... Sunnyvale, Californiaa (PRWEB) May 28, 2015 ... on “ The Changing Landscape of EMR/EHR Clinical Data ... Annual Meeting taking place in Washington, DC on June ... the challenges of integrating EMR/EHR systems with EDC, and ... the opportunities brought by eSource and electronic health records/electronic ...
(Date:5/28/2015)... American Process Inc. (Atlanta, GA) and ... signed a joint agreement to improve ... nanocellulose, a rapidly emerging high performance, bioderived nanomaterial. ... limited number of feedstock materials available. Traditionally used ... parts for load bearing applications. , The ...
Breaking Biology Technology:PDS Biotechnology reports positive Phase I clinical trial results in proprietary HPV-Cancer Immunotherapy 2GenVec To Present At The Jefferies Healthcare Conference 2Clinovo Presents at the DIA 2015 51st Annual Meeting in Washington, DC on June 14th-18th 2American Process Inc. Announces Partnership with Oak Ridge National Laboratory to Make 3D Printing Plastic Resins Stronger and More Sustainable 2American Process Inc. Announces Partnership with Oak Ridge National Laboratory to Make 3D Printing Plastic Resins Stronger and More Sustainable 3
... SOUTH SAN FRANCISCO, Calif., May 5 VaxGen,Inc. ... it has completed the sale of all assets ... anthrax vaccine product candidate and,related technology to Emergent ... BioSolutions paid VaxGen $2 million upon execution of,the ...
... May 2 Biopure Corporation,(Nasdaq: BPUR ) ... Kingdom,s,Medicines and Healthcare Products Regulatory Agency (MHRA) is ... The purpose of the meeting is to clarify ... April 2008 from the United Kingdom,s Commission,on Human ...
... Roche is pleased to announce that,Grace Ju, Ph.D., research ... an "Outstanding Woman of Science" by the New Jersey,Association ... Thank You,Research Gala held May 1 at the Bridgewater ... at this year,s event, which is also,marking the 20th ...
Cached Biology Technology:VaxGen Sells Anthrax Vaccine Program and Related Assets and Technology to Emergent BioSolutions, Inc. 2Biopure Announces Date to Meet with UK's Medicines and Healthcare Products Agency 2Biopure Announces Date to Meet with UK's Medicines and Healthcare Products Agency 3Roche Research Director Grace Ju Hailed as NJABR 'Outstanding Woman of Science' 2Roche Research Director Grace Ju Hailed as NJABR 'Outstanding Woman of Science' 3
Matrix for protein MALDI-MS...
Originally developed for the culture of Drosophila; suitable for culture of other dipteran cell lines. Powder, Insect cell culture tested...
... number is a new product ... Cornings product number. If showing ... under the old Sigma-Aldrich number ... for assistance. Mfr Desig: ...
Collected from calves that are 10 days old or less. Sterile, cell culture tested, US Origin...
Biology Products: