Eilbeck Lab

Department of Biomedical Informatics, University of Utah

  • Graduation

    Two students from the lab walked on Friday at the graduation ceremony. Congrats to Shale Dames and Paris Vail, and the other BMI students. Lots of good memories of these folks: Jason Jacobs – your contribution to the Chlamydia paper was exceptional, David Jones – it was an honor to go to your weddings (note pleural), Doug Redd – We miss you, come home, Seth thank you for the star trek pin – I wear it with nerdy pride. Live long and Prosper.  Shale and Paris – we (meaning you) have a ton of work to do this summer. Big…

  • OmniSearch paper out in Journal of Biomedical Semantics

    Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan and Alan Ruttenberg OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data Journal of Biomedical Semantics20167:25DOI: 10.1186/s13326-016-0064-2© Huang et al. 2016Received: 15 December 2015Accepted: 12 April 2016Published: 10 May 2016

  • ncRO paper in Journal of Biomedical Semantics

    The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology Journal of Biomedical Semantics20167:24 DOI: 10.1186/s13326-016-0066-0 Another paper from our collaboration with Jingshang Huang, of the University of South Alabama.

  • New Post docs in lab

    Two new post docs started this week. They are both working on projects in conjunction with the Utah Genome Projects, the Program in Personalized Heath and the CCTS.

  • Taxonomer at the Natural History Museum

    The Natural History Museum of Utah will be hosting a new Exhibit, Genome: unlocking life’s code . Taxonomer, our metagenomic tool will be featured as part of this exhibit. Opens May 21, 2016 and runs through to September 5, 2016. “Genome: Unlocking Life’s Code begins to unravel the mystery behind the complete set of instructions needed for every living thing on Earth to grow and function: the genome. With cutting-edge interactives, 3D models, custom animations, and engaging videos of real-life stories, the exhibition examines both the benefits and the challenges that genomics presents to modern society. “

  • SAB of OMNISearch/OMIT group at University of Southern Alabama

    I spent a productive couple of days working with Jingshan Huang in Mobile Alabama. Jingshan has developed several ontologies to describe non-coding RNA molecules and has developed a semantic search tool for miRNA called OMNISearch. Also present at the meeting were Judy Blake, Alan Ruttenberg, Darren Natale, Ming Tan and Dejing Dou.

  • Brilliant Defense

    Keith Simmon successfully defended his thesis on the 26th February, to an enthusiastic audience. It was standing room only, and Keith treated us to some of the best visuals the department has seen – including this figure of some of the problems plaguing metagenomic analysis. The talk also featured several live demos of his software that went off without a hitch. Keith has gone on the take a position as a Bioinformatics Analyst at ARUP Laboratories, where his interest lies in the bioinformatics of infectious disease detection.

  • PhD defense and new metagenomics paper

    Keith Simmon will hold his defense on the 26th February at 4pm in the BMI classroom. He will discuss his work developing, and benchmarking the Taxonomer metagenomics tool and will explore data from clinical application. It was a pleasure having Keith in my lab. The project has been a roller coaster and there has not been a boring moment. I want to take this opportunity to thank the Fay family for their generous support of this project and also the department of Pathology for funding portions of Keith. The first of several papers describing this work is e-available: Graf EH,…

  • The genomic CDS sandbox: An assessment among domain experts.

    A new paper lead by Ayesha Aziz in the Welch lab is now available from the journal of biomedical Informatics: J Biomed Inform. 2016 Jan 15. pii: S1532-0464(15)00299-3. doi: 10.1016/j.jbi.2015.12.019. [Epub ahead of print]The genomic CDS sandbox: An assessment among domain experts.Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM. Highlights•There is a need to promote development of resources for genomic CDS.•The proposed sandbox will be available pre-configured with CDS and genome tools.•We present survey results to assess needs for a genomic CDS sandbox.•Results show strong interest…

  • Community engagement

    Yesterday I went to a local elementary school to give the 5th grade a class on genetics. They have completed a science module looking at traits and DNA. We looked at the genetic code and how that makes words from the sequence. We then looked at the pigonetics resource at learn.genetics and saw how a single base change can alter a signaling peptide and cause pigeons to develop the crest phenotype. The kids were great, asked lots of questions and loved the pigeon aspect. I have to thank Mike Shapiro in Biology and Louisa Stark and her group for providing such…