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 interpretation changes from ClinVar. AMIA Annu Symp Proc. 2023 Apr 29;2022:1145-1152. PMID: 37128447; PMCID: PMC10148312.
Lario R, Kawamoto K, Sottara D, Eilbeck K, Huff S, Del Fiol G, Soley R, Middleton B. A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare. J Biomed Inform. 2023 Jan;137:104251. doi: 10.1016/j.jbi.2022.104251. Epub 2022 Nov 15. PMID: 36400330.
Kiser AC, Eilbeck K, Ferraro JP, Skarda DE, Samore MH, Bucher B. Standard Vocabularies to Improve Machine Learning Model Transferability With Electronic Health Record Data: Retrospective Cohort Study Using Health Care-Associated Infection. JMIR Med Inform. 2022 Aug 30;10(8):e39057. doi: 10.2196/39057. PMID: 36040784; PMCID: PMC9472055.
Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, van Sant D, Stark Z, Whiffin N, Rehm HL, Ware JS. Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships – allelic requirement, inheritance modes and disease mechanisms. medRxiv [Preprint]. 2023 Apr 3:2023.03.30.23287948. doi: 10.1101/2023.03.30.23287948. PMID: 37066232; PMCID: PMC10104222.
Education
The new thing this year is that we have added Group Peer Review to the list of activities for PhD students. This is a great way to get balanced and deep reviews on manuscripts. We have students from diverse academic backgrounds that provide excellent insight. We wish more editors would allow this sort of review.
We have worked with the APHL and the UDHHS to enable fellowships for 2nd year MS students. This is a really great opportunity to get involved in public health. They also have online internships.
The NLM trainees joined me at Stanford for the training grant meeting. It is always good to meet peers.
Conferences
Medical Informatics Europe Conference
Engelsma T, Anders C, Oudbier SJ, Eilbeck K, Knaup P, Peute LW, Ganzinger M. Proposing a Novel Hybrid Short-Term Exchange Program in Biomedical and Health Informatics Education. Stud Health Technol Inform. 2023 May 18;302:498-499. doi: 10.3233/SHTI230189. PMID: 37203733.
ACMG meeting Salt Lake City Utah.
P385: Understanding clinician needs and preferences with respect to returned NBS results. K Eilbeck, N Ruiz-Schultz, E Christiansen, A Rohrwasser. Genetics in Medicine Open 1
P648: A generalized model to describe sequence feature annotation. E Christensen, K Eilbeck, S Upchurch.Genetics in Medicine Open 1 (1)
RNASeq Analysis Identifies the Pathogenicity of Inherited Synonymous Splice-Region Variant in NEB, Confirming a Diagnosis of Neonatal Nemaline Myopathy 2. Barry Moore, Thomas J Nicholas, Rong Mao, Brian J Shayota, Steven E Boyden, Chelsea Solorzano, Rachel Palmquist, Pinar Bayrak-Toydemir, Andrew Farrell, Edgar J Hernandez, Bennet Peterson, Shawn Rynearson, Carson Holt, Alistair Ward, Eric Fredrickson, Kelsey Nicholson, David Pattison, Jian Zhao, Makenzie Fulmer, Lucilla Pizzo, Ting Wen, John O’Shea, Robert Lewis, Hayley Reynolds, Betsy Ostrander, Hunter Best, Luca Brunelli, Karen Eilbeck, Mark Yandell, Gabor Marth, Aaron R Quinlan, John C Carey, Martin Tristani-Firouzi, Joshua L Bonkowsky, Sabrina Malone Jenkins
American Society for reproductive Medicine.
A BAYESIAN NETWORK FOR COMPLEX PAIN-RELATED FEATURES OF ENDOMETRIOSIS https://www.fertstert.org/article/S0015-0282(22)01151-7/fulltext AC Kiser, KC Schliep, M Yandell, K Eilbeck. Fertility and Sterility 118 (4), e222
Honors
I became a fellow of the American College of Medical Informatics. This involved a trip to Puerto Rico. The best thing was putting a slide deck together that mentioned everyone who contributed to my journey.
I became a fellow of the American College of Medical Informatics. This involved a trip to Puerto Rico. The best thing was putting a slide deck together that mentioned everyone who contributed to my journey.
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