Jacobs School of Medicine and Biomedical Sciences

Recent Faculty Publications

Our contributions to the scholarly literature demonstrate our commitment to advancing the field of biomedical informatics.

Ceusters W, Bona JP. Analyzing SNOMED CT's Historical Data: Pitfalls and Possibilities. AMIA Annu Symp Proc. 2017; 2016
Ceusters W, Jensen M, Diehl AD. Ontological Realism for the Research Domain Criteria for Mental Disorders. Stud Health Technol Inform. 2017; 235
Blaisure J, Ceusters W. Business Rules to Improve Secondary Data Use of Electronic Healthcare Systems. Stud Health Technol Inform. 2017; 235
Dubovsky SL, Antonius D, Ellis DG, Ceusters W, Sugarman RC, Roberts R, Kandifer S, Phillips J, Daurignac EC, Leonard KE, Butler LD, Castner JP and Braen GR. A preliminary study of a novel emergency department nursing triage simulation for research applications. BMC Research Notes. 2017
Ceusters W, Blaisure J. A Realism-Based View on Counts in OMOP's Common Data Model. Stud Health Technol Inform. 2017; 237
Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 2016
Hogan WR, Ceusters W. Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis. J Biomed Semantics. 2016; 7(1)
Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK, Subramanian S, Samudrala R, Van Voorhis WC. Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target. J Biomol Screen. 2016; 21(7)
Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016; 7(1)
Ray PL, Cox AP, Jensen M, Allen T, Duncan W, Diehl AD. Representing vision and blindness. J Biomed Semantics. 2016; 7
Ceusters W, Bona J. Ontological Foundations for Tracking Data Quality through the Internet of Things. Stud Health Technol Inform. 2016; 221
Elkin PL, Schlegel DR, Anand E. Recruiting Participants to Local Clinical Trials using Ontology and the IoT. Stud Health Technol Inform. 2016; 221
Chopra G, Samudrala R. Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform. Curr Pharm Des. 2016; 22(21)
Durham J, Raphael KG, Benoliel R, Ceusters W, Michelotti A, Ohrbach R. Perspectives on next steps in classification of oro-facial pain - part 2: role of psychosocial factors. J Oral Rehabil. 2015; 42(12)
Manocheewa S, Mittler JE, Samudrala R, Mullins JI. Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development. Viruses. 2015; 7(11)
Durham J, Raphael KG, Benoliel R, Ceusters W, Michelotti A, Ohrbach R. Perspectives on next steps in classification of oro-facial pain - part 2: role of psychosocial factors. J Oral Rehabil. 2015
Ceusters W, Benoliel R, Durham J, Raphael KG, Michelotti A, Ohrbach R. Perspectives on next steps in classification of oro-facial pain - part 1: role of ontology.. J Oral Rehabil. 2015; 42
Ceusters W, Nasri-Heir C, Alnaas D, Cairns BE, Michelotti A, Ohrbach R. Perspectives on next steps in classification of oro-facial pain - Part 3: biomarkers of chronic oro-facial pain - from research to clinic. J Oral Rehabil. 2015
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A,. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015; 347(6225)
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A,. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015; 347(6225)

Research Funding

Clinical Translational Science Award (CTSA). John Canty, Jr. (Co-Principal Investigator), Margarita Dubocovich (Principal Investigator), Peter Elkin (Co-Investigator), Leonard Epstein (Co-Investigator), Steven Fliesler (Co-Investigator), Alan Hutson (Co-Investigator), Gene Morse (Co-Investigator), Timothy Murphy (Principal Investigator), Sanjay Sethi (Co-Investigator), Laurene Tumiel Berhalter (Co-Investigator). National Institutes of Health. $16,000,000. 1/1/2016-1/1/2020.
Natural Language Processing (NLP) to enhance structured data in identifying nonvalvular atrial fibrillation patients and their stroke and bleed risk (B0660170). Peter Elkin (Principal Investigator). Pfizer Inc. 9/1/2015-12/1/2016.
Big data scientist training enhancement program (BD-STEP): to provide training and research opportunities to enable next-generation patient-centered outcomes research. Peter Elkin (Co-Investigator). Veteran's Administration. 9/1/2015-8/1/2016.

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