Eilbeck Lab

 

 

DECART: DATA SCIENCE FOR THE HEALTH SCIENCES

July 10-12, 2017 The python at the end of the galaxy (A play on the restaurant at the end of the universe) (

Galaxy is an open source, web-based platform for data intensive biomedical research. Thousands of bioinformatics tools have been imported into this graphical user interface. This tool enables biomedical informatics exploration and the building and sharing of reusable workflows. Ipython notebooks are now an integral part of galaxy.

Dissertation award entry

Recently graduated doctoral students who have published a dissertation may apply for the CGS/ProQuest Distinguished Dissertation Award, which recognizes excellence in dissertation writing. For 2017, dissertations in the Biological Sciences & Humanities/Fine Arts will be considered.

The BMI department submitted Keith Simmon’s thesis.

Upcoming posters at Curating the Clinical Genome

• ClinVar Miner: Enabling deep exploration of the ClinVar archive

Alexander R. Henrie,¹ Brandon Cushman,² Sarah Hemphill,² Steven Harrison,² Marina DiStefano,² Danielle Azzariti,² Justin Aronson,³ Lisa M. Vincent,⁴ Scott R. Goehringer,⁵ Erin Rooney Riggs,⁵ Christa Lese Martin,⁵ Heidi L. Rehm,^2,6 Karen Eilbeck¹

¹Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA

²Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA.

³Pierce Middle School, Brookline, MA, USA

⁴GeneDx, Gaithersburg, MD, USA

⁵Geisinger Health System, Danville, PA, USA

⁶Department of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA USA

• A community-developed data model for representing sequence variation

Karen Eilbeck¹, Shawn Rynearson¹, Gil Alterovitz², Larry J. Babb³, Robert R. Freimuth⁴, Sarah E. Hunt⁵, David Kreda⁶, Jennifer Lee¹⁷, Peter N. Robinson⁸, David Haussler⁹, Heidi Rehm^10,11, Peter Goodhand¹², Reece K. Hart¹³

¹University of Utah School of Medicine, Salt Lake City, Utah, USA. ²Harvard Medical School, Boston, MA, USA. ³Sunquest Information Systems, Boston, MA, USA . ⁴Mayo Clinic, Rochester, MN, USA. ⁵EBI, Wellcome Campus, Hinxton, UK. ⁶Independent Consultant, New York, NY, USA. ⁷NCBI, National Library of Medicine, Bethesda, MD, USA. ⁸Jackson Laboratory, Jax Genomic Medicine, Farmington, CT USA. ⁹University of California, Santa Cruz, CA, USA. ¹⁰Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA. ¹¹Department of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA USA. ¹²Ontario Institute for Cancer Research, Toronto, CA. ¹³Invitae, San Francisco, CA, USA.

• hgvs-eval: automated evaluation suite to assess HGVS-formatting tools

Nicole Ruiz¹, Justin Paschall², Xing Xu³, David Caplan³, Carolyn Ch’ng⁴, Karen Eilbeck¹, Reece Hart⁵

¹Department of Biomedical Informatics, University of Utah, 421 Wakara Way, Salt Lake City, UT 84108

²University of California Berkeley, Berkeley, CA 94720

³SolveBio, 285 West Broadway, Suite 630, New York, NY 10013

⁴British Columbia Cancer Agency, Canada’s Michael Smith Genome Sciences Centre, Vancouver

⁵Invitae, Inc. 475 Brannan St., San Francisco, CA 94107

New Student

Michael Watkins joined the lab from the BYU bioinformatics program to work on variant annotation and representation issues. We are really pleased to have Michael hit the ground running and hope to entice more students from that program to BMI.

 

Upcoming Med School class

A certificate in Precision Medicine will be offered to the Med school students in the fall, and I will be teaching a session on phenotyping and variant interpretation in September. This will be a hands-on practical class with lots of doing rather than sitting.

Promotion

This summer I was promoted to full professor. There are a lot of people who have been part of the process that I need to thank. First, thanks to my department faculty and admin for their support. Thank you to Joyce Mitchell for hiring me. Thanks to everyone I have worked with over the years, to numerous to name, but this is a nice graph of some of my network: https://utah.pure.elsevier.com/en/persons/karen-eilbeck/network/ . The list goes on, CCTS, BMI DAC and SAC, program for personalized medicine, SOM RPT committee…