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:8/31/2015)... 31, 2015 Research and Markets ( http://www.researchandmarkets.com/research/st5b3m/saudi_arabia ... Arabia Biomedical Sensors Market - Growth, Trends & Forecasts ... The Saudi Arabia Biomedical Sensors market is estimated at ... over the period 2014-2020 The near future ... genetic formulation of each individual. These sensors can be ...
(Date:8/25/2015)... BELLEVUE, Wash. , Aug. 25, 2015 ... systems, announced today it will unveil its "Guardian S" ... at the National Tactical Officers Association Conference on August ... Guardian S is the first-ever commercially available energetically autonomous ... research and in-field trials and is protected by more ...
(Date:8/20/2015)... , Aug. 20, 2015 The wearable ... that are active and healthy. However, wearable technology ... hospital environment to help improve diagnostic capabilities and ... from the Wearable Technologies Conference 2015 , ... applications for wearables in healthcare.    ...
Breaking Biology News(10 mins):Saudi Arabia Biomedical Sensors Market Report 2015 - Growth, Trends & Forecasts (2014-2020) 2Sarcos to Debut First-of-its-Kind Snake Robot 2Sarcos to Debut First-of-its-Kind Snake Robot 3Leaf Healthcare Releases Video from Wearable Technology Conference on New Applications for Wearables in the Hospital Environment 2Leaf Healthcare Releases Video from Wearable Technology Conference on New Applications for Wearables in the Hospital Environment 3
... mentioned as pack animals in the biblical stories of Abraham, ... not domesticated in the Land of Israel until centuries after ... challenging the Bible,s historicity, this anachronism is direct proof that ... Now Dr. Erez Ben-Yosef and Dr. Lidar Sapir-Hen of ...
... TORONTO, February 3, 2014 Women with schizophrenia are ... and other serious pregnancy and delivery complications as women ... the Institute for Clinical Evaluative Sciences (ICES) and Women,s ... today in the British Journal of Obstetrics and ...
... 2014) Those two crooked beady eyes peeking out of a ... food in the murky waters of the Chesapeake Bay. They ... of a crab from an adolescent into a full-fledged adult. ... Maryland recently discovered a new hormone in those eyestalks responsible ...
Cached Biology News:Finding Israel's first camels 2Finding Israel's first camels 3Women with schizophrenia at higher risk of pregnancy and delivery complications: Study 2Hormone in crab eyes makes it possible for females to mate and care for their young 2
(Date:9/2/2015)... , Sept. 2, 2015 Research ... the addition of Jain PharmaBiotech,s new report ... to their offering. An ... and biotechnology industries is anticipated. Nanotechnology will ... development - from formulations for optimal delivery ...
(Date:9/2/2015)... Sep. 02, 2015 ... the addition of Jain PharmaBiotech,s new report ... their offering. This report follows the ... that can be objectively measured and evaluated as ... as well as pharmacological responses to a therapeutic ...
(Date:9/2/2015)... R.I. , Sept. 2, 2015  Neurotech ... been enrolled in the multicenter Phase 2 clinical ... the long-term treatment of recurrent subfoveal choroidal neovascularization ... NT-503 is a unique vascular endothelial growth factor ... ECT implant. "This landmark proof-of-concept study ...
(Date:9/2/2015)... ZIONA, Israel , September 2, ... TASE: BVXV) today announced the intent of the National Institute ... National Institutes of Health (NIH) within the Department of Health ... trial to be held in the United States ... the use of BiondVax,s universal flu vaccine candidate, Multimeric-001 (M-001), ...
Breaking Biology Technology:Global Nanobiotechnology Applications, Markets and Companies Report 2015-2024 2Global Nanobiotechnology Applications, Markets and Companies Report 2015-2024 3Updated 2015 Biomarkers Report - Latest Technologies, Markets and Companies Insights to 2024 with over 1,000 References 2Updated 2015 Biomarkers Report - Latest Technologies, Markets and Companies Insights to 2024 with over 1,000 References 3Neurotech Announces First Patient Enrolled in Novel Anti-VEGF Encapsulated Cell Therapy Study 2Neurotech Announces First Patient Enrolled in Novel Anti-VEGF Encapsulated Cell Therapy Study 3Neurotech Announces First Patient Enrolled in Novel Anti-VEGF Encapsulated Cell Therapy Study 4BiondVax Announces Intent to Launch a Phase 2 Trial in the United States in Collaboration with the U.S. National Institutes of Health 2BiondVax Announces Intent to Launch a Phase 2 Trial in the United States in Collaboration with the U.S. National Institutes of Health 3
... Functional Analysis in Yeast ,,, Regulation of ... Tanya Hosfield ,Stratagene , Stratagene ... express,and functionally analyze eukaryotic genes in the budding ... one of four different yeast,selective markers in the ...
... Cycler allows rapid,amplification of rare mRNA , , Donald D. ... University of Illinois at Chicago , , , ... Figure 1: RoboCycler 40 Temperature Cycler In Situ, ... situ adapter system for the RoboCycler 40, ...
... thermoshaker , Jeff Braman ,Stratagene , , ... , , ... round-bottom plate were used to cultivate bacterial clones ... phase rates of bacterial growth, were equivalent ...
Cached Biology Technology:Epitope-Tagging Vectors for Functional Analysis in Yeast 2Epitope-Tagging Vectors for Functional Analysis in Yeast 3Epitope-Tagging Vectors for Functional Analysis in Yeast 4Epitope-Tagging Vectors for Functional Analysis in Yeast 5Epitope-Tagging Vectors for Functional Analysis in Yeast 6Detecting Gastrin-Releasing Peptide Receptor by in situ PCR on Archived,Tissue 2Detecting Gastrin-Releasing Peptide Receptor by in situ PCR on Archived,Tissue 3Detecting Gastrin-Releasing Peptide Receptor by in situ PCR on Archived,Tissue 4Detecting Gastrin-Releasing Peptide Receptor by in situ PCR on Archived,Tissue 5Detecting Gastrin-Releasing Peptide Receptor by in situ PCR on Archived,Tissue 6High-Throughput Cultivation of Bacterial Clones 2High-Throughput Cultivation of Bacterial Clones 3
C1-inhibitor (C1-INH)...
Procollagen type I C-terminal propeptide (human, PICP)...
... provides a comprehensive microarray service for ... embedded within non-coding RNAs (ncRNAs) using ... probe design, which enables highly sensitive ... RNAs (1). This comprehensive service includes ...
... LC micro-fractionation, spotting and preparation for ... LC eluent can be accurately and ... trace amounts. This allows for automatic ... measurements. When used in conjunction with ...
Biology Products: