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bioinformatics blog
Keith Bradnam – Manchester University Bioinformatics Masters alum, asked me to answer some questions for his popular nerdy blog http://www.acgt.me. You can read my replies here. For some reason, maybe the fact that it was the first course in the UK to bring bioinformatics students together, there is a lively community of ex students, spanning […]
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micro RNA search tool grant
Jingshan Huang was awarded a 3 year NIH grant to further develop OMIT, reported in genomeweb. I am happy to be part of this exciting project, and look forward to students in my department using OMIT for their analysis.
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Birth of identity: understanding changes to birth certificates and their value for identity resolution
A paper with the Staes lab came out today: Birth of identity: understanding changes to birth certificates and their value for identity resolution Jeffrey Duncan1, Scott P Narus1,2, Stephen Clyde3, Karen Eilbeck1, Sidney Thornton1,2, Catherine Staes1. J Am Med Inform Assoc doi:10.1136/amiajnl-2014-002774 Abstract Introduction Identity information is often used to link records within or among information systems in public […]
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OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain
The micro RNA ontology paper with the Huang lab is now available from PLOS ONE. OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain Jingshan Huang, Jiangbo Dang, Glen M. Borchert, Karen Eilbeck, He Zhang, Min Xiong, Weijian Jiang, Hao Wu, Judith A. Blake, Darren A. Natale, Ming Tan.
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RCKMS paper update
We have been accepted by AMIA to present our paper ‘Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System’. Thanks to the RCKMS working group for all of the work last year and to Catherine Staes, Shu McGarvey and Julie Lipstein.
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genomic CDS paper
Technical desiderata for the integration of genomic data with clinical decision support. Another paper from our collaboration with the Kawamoto lab has been accepted and the unedited version is now available here. Highlights
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Scholarship news
I am pleased to announce that Keith in my lab has been awarded a scholarship from U of U donors: Dick and Carol Fay. The Fays have long been supporters of biomedical informatics and I am thrilled they chose to fund Keith.
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The Clinical Genome Conference
I attended the Clinical Genome conference last week in San Francisco and presented in the NGS REFERENCES AND STANDARDS ARE NOT STATIC session. My talk described the work of the CDC’s workgroup to support the development of a clinical variant file. This was a great opportunity to disseminate the work of the group and to meet […]
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Summer Undergraduate Research Project
This year BMI got two undergrads for 10 weeks. Rolando from UT Brownsville will be working with Julio Facelli, and Adam Grant from BYU will be in my group. Adam is double majoring in Genetics and Bioinformatics and we will keep him busy. The whole group is off to Moab for the weekend before the hard work starts. The URP’s are administered through MBP and are a great opportunity for students to get lab experience.
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more USTAR media
The USTAR Genetic Discovery Program is has been in the media lately: The Scope: Using Computer Logic to Diagnose Rare Diseases Apr 15, 2014It’s impossible to treat a patient effectively without knowing what’s wrong. Published this month in the American Journal for Human Genetics, computational biologist Dr. Mark Yandell reports a novel method for diagnosing […]