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Spring 2026
Sometimes things get so busy I forget to update this page. We survived 2025 intact and are striving forward in 2026. We submitted papers and grant proposals, went to meetings, and continued to push our knowledge management, data science, AI, and digital health projects. New Trainees: Katya Vinokuroff – an MD-PhD student has just joined the lab to focus on AI and ML projects. Kim Lanaghen – an MS student has just signed up to do her capstone with us on an AI chatbot project for NBS. Chatbot Updates (NBSchat): Courtney Gauchel and I both presented our work on chatbots…
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End of Summer 2024
The last academic year went by like a flash. The fall was all about 2 students finishing up and defending. That is always bittersweet. Seonggyun and Amber are on to the next stage of their careers. The spring and summer we have been writing papers and going to meetings. We were really excited to finally see the hard work of Amber Kiser in the lab go into print. This work is an important contribution to women’s health and has spurred collaboration to validate the work with other labs. Kiser AC, Schliep KC, Hernandez EJ, Peterson CM, Yandell M, Eilbeck K. An…
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Summer 2023
The fall semester started this week and reminded me that I have not done a data dump in a long time. The lab has been busy since the last update – this time last year. It is amazing how time flies. Papers Kiser AC, Eilbeck K, Bucher BT. Developing an LSTM Model to Identify Surgical Site Infections using Electronic Healthcare Records. AMIA Jt Summits Transl Sci Proc. 2023 Jun 16;2023:330-339. PMID: 37350879; PMCID: PMC10283140. Watkins MT, Kohlmann WK, Berry TS, Sama NR, Koptiuch C, Rynearson SG, Eilbeck KL. LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant…
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Summer Update 2022
Students 2 PhD students, Evan Chistensen and Lourdez Valdez have joined the group. Michael Watkins successfully defended and is now continuing his work in biomedical standards and interoperability at the University of Chicago. Papers Wesołowski S, Lemmon G, Hernandez EJ, Henrie A, Miller TA, Weyhrauch D, Puchalski MD, Bray BE, Shah RU, Deshmukh VG, Delaney R, Yostl HJ, Eilbeck K, Tristani-Firouzi M, Yandell M. An explainable artificial intelligence approach for predicting cardiovascular outcomes using electronic health records. PLOS Digit Health. 2022;1(1):e0000004. doi: 10.1371/journal.pdig.0000004. Epub 2022 Jan 18. PMID: 35373216; PMCID: PMC8975108. https://pubmed.ncbi.nlm.nih.gov/35373216/ Conway M, Vuong TT, Hart K, Rohrwasser A,…
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Summer 2021 Updates
We have been busy working off-site for over a year and are getting ready to transition back to the office. We have a new Chair – Yves Lussier, which has freed up some of my time. Here are some updates from the past few months. Students: ResultsMyWay: combining Fast Healthcare Interoperability Resources (FHIR), Clinical Quality Language (CQL), and informational resources to create a newborn screening application Newborn screening (NBS) can be life-changing for the families of infants who test positive for a rare condition. While resources exist to support these families, there can be delays in sharing these resources due…
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Investigating the Role of Infertility in Endometriosis Risk
Whooohoooo! Amber Kiser has had a poster accepted for the upcoming American Society for Reproductive Medicine conference. Amber has been using various machine learning techniques to explore the potential of earlier diagnosis of Endometriosis.
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Redefining fundamental concepts of transcription initiation in bacteria
A collaborative paper with researchers across the globe came out in NRG as an ExpertRecommendation. My part was helping with the ontological definitions of the sequence features involved in bacterial gene regulation. Updates to the operon way of thinking. It was lovely to work with such thoughtful people. Redefining fundamental concepts of transcription initiation in bacteria
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Summer 2020 updates.
It has been a while since I last updated – but this time, it has been a combination of teaching load, COVID, budget season, grant writing, white coats for black lives, and teetering on the verge of burnout. DBMI has been working at home since March. In BMI we have all become adept at zoom – even having our weekly coffee break virtually. We have taught, collaborated, and attended conferences virtually. We have all worked hard these last few months. It has been a work-life without a lot of punctuation. The days all merge together, the kids are at home…
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Almost Spring updates
I feel guilty for neglecting my blog. A few updates Michael Watkins and Andrew Miller in the group are off to Houston to present at the AMIA summit. Michael will present work on a Fhir app for lab data and Andrew is presenting his work with the VA on limb implants. Congratulations to Michael Watkins for receiving the prestigious John D. Morgan award this year. Michael is a model student. He is a TA just about every semester, he sits on the curriculum committee, has produced two papers in the past year, lead a ClinGen working group and presented FHIR tutorials…
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All the other updates in one post
It has been a busy few months. I have become interim chair of my department. I am learning so much and have some great mentors and support network. I am now PI of two training grants – our NLM T15 Biomedical Informatics Training Grant and an NIDDK T32 for University of Utah Interdisciplinary Training Program in Computational Approaches to Diabetes and Metabolism Research. There is a paper on it’s way out in Bioinformatics – Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. – thanks to everyone who worked on this effort. My group is going to AMIA in…