Recent Faculty Publications

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

Zheng J, Lin AY, Huffman A, Masci AM, Racz R, Wu G, Roan K, Ong E, Sarntivijai S, Hu J, Asfaw E, Kahn H, Li X, Zhang X, Monickaraj J, Kosar N, Li J, Manuel W, Abeysinghe R, Rehana H, Bansal B, Pan Y, Guo J, He V, Song J, Seleznev AI, Hur K, He A, Davydov A, Yang Q, Ostropolets A, Vita R, Peters B, Ruttenberg A, Diehl AD, Hoyt CT, Roncaglia P, Huntley RP, Scheuermann RH, Courtot M, Todd T, Sayers S, Chen F, Li X, Yeh FY, Xiang Z, Ozgur A, Whetzel PL, Musen MA, Mungall CJ, Leitner WW, Cui L, Colby LA, Mobley HLT, Athey BD, Omenn GS, Cowell LG, Tao C, Hur J, Smith B, He Y. (2026) VO: The Vaccine Ontology. Scientific data (Apr).
Duncan WD, Sabharwal A, Diehl AD, Dutta N, Diller M, Joachimiak MP, Chandrasekharan GM. (2026) Representing dental caries and dysbiosis within the oral microbiome in the Oral Health and Disease Ontology. Journal of biomedical semantics (Apr), 17(1).
Tan SZK, Puig-Barbe A, Goutte-Gattat D, Eastwood C, Aevermann B, Avola A, Balhoff JP, Bayindir IU, Belfiore J, Caron AR, Fischer DS, George N, Gyori BM, Haendel MA, Hoyt CT, Kir H, Lubiana T, Matentzoglu N, Overton JA, Peng B, Peters B, Quardokus EM, Ray PL, Roncaglia P, Rivera AD, Stefancsik R, Teh WK, Toro S, Vasilevsky N, Xu C, Zhang Y, Scheuermann RH, Mungall CJ, Diehl AD, Osumi-Sutherland D. (2026) The Cell Ontology in the age of single-cell omics. Scientific data (Apr).
Dutta N, DeBellis M, Chanda N, Diehl AD, Wilson F, Rocha M, Diller M, Chandrasekharan GM, Duncan WD. (2026) Representing dental restoration materials in the oral health and disease ontology. Journal of biomedical semantics (Apr), 17(1).
Pengput A, Diehl AD. (2026) Ontology development and use for cholangiocarcinoma risk factors and predictions: a term enrichment data analysis and machine learning classification. Journal of biomedical semantics (Jan), 17(1): 2.
Xu S, Jiang L, Zhang Z, Luo X, Wu W, Wu H, Huang Z, Falls Z, Samudrala R, Tan Z. (2025) Deciphering bisphenol A (BPA)-elicited osteoarthritis mechanisms through network toxicology and molecular docking, then de novo generation of novel therapeutic candidates. BMC pharmacology & toxicology (Dec), 27(1): 20.
Xu S, Jiang L, Zhang Z, Luo X, Wu W, Wu H, Huang Z, Falls Z, Samudrala R, Tan Z. (2025) Deciphering bisphenol A (BPA)-elicited osteoarthritis mechanisms through network toxicology and molecular docking, then de novo generation of novel therapeutic candidates. BMC pharmacology & toxicology (Dec), 27(1): 20.
Emeagui OD, Rebello G, Afzal RA, Hall KC, Pratt RE, Yu KOA. (2025) Bartonella Endocarditis in a Pediatric Patient With Aortic Valvular Disease and Embolic Stroke: A Case Report and Review of the Literature. Cureus (Dec), 17(12): e98965.
Van Norden M, Mangione W, Falls Z, Samudrala R. (2025) Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms. Bioinformatics (Oxford, England) (Nov), 41(11)
Van Norden M, Mangione W, Falls Z, Samudrala R. (2025) Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms. Bioinformatics (Oxford, England) (Nov), 41(11).
Duncan WD, Sabharwal A, Diehl AD, Dutta N, Diller M, Joachimiak MP, Chandrasekharan GM. (2025) Representing Dental Caries and Dysbiosis within the Oral Microbiome in the Oral Health and Disease Ontology. Research square (Sep).
Sang S, Sun Z, Zheng W, Wang W, Islam MT, Chen Y, Yuan Q, Cheng C, Xi S, Han Z, Zhang T, Wu L, Li W, Xie J, Feng W, Chen Y, Xiong W, Yu J, Li G, Li Z, Jiang Y. (2025) TME-guided deep learning predicts chemotherapy and immunotherapy response in gastric cancer with attention-enhanced residual Swin Transformer. Cell reports. Medicine (Aug), 6(8): 102242. doi:10.1016/j.xcrm.2025.102242
Zheng J, Lin AY, Huffman A, Masci AM, Racz R, Wu G, Roan K, Ong E, Sarntivijai S, Hu J, Asfaw E, Kahn H, Li X, Zhang X, Kosar N, Li J, Manuel W, Abeysinghe R, Rehana H, Bansal B, Pan Y, Guo J, He V, Song J, Seleznev AI, Hur K, He A, Davydov A, Yang Q, Vita R, Peters B, Ruttenberg A, Diehl AD, Hoyt CT, Roncaglia P, Huntley RP, Scheuermann RH, Courtot M, Todd T, Sayers S, Chen F, Li X, Yeh FY, Xiang Z, Ozgur A, Whetzel PL, Musen MA, Mungall CJ, Leitner WW, Cui L, Colby LA, Mobley HLT, Athey BD, Omenn GS, Cowell LG, Tao C, Hur J, Smith B, He Y. (2025) VO: The Vaccine Ontology. bioRxiv : the preprint server for biology (Aug).
Resnick MP, Hitt J, McCray W, Hall K, LeHouillier F, Brown SH, Campbell KE, Montella D, Nebeker J, Elkin PL. (2025) Semantic Relations: Extending SNOMED CT and Solor. Applied clinical informatics (Aug), 16(4): 1263-1270.
Beverley J, Babcock S, Benson C, De Colle G, Cohen S, Diehl AD, Challa RANR, Mavrovich RA, Billig J, Huffman A, He Y. (2025) A fourfold pathogen reference ontology suite. Journal of biomedical semantics (Jul), 16(1): 12.
Tan SZK, Puig-Barbe A, Goutte-Gattat D, Eastwood C, Aevermann B, Avola A, Balhoff JP, Bayindir IU, Belfiore J, Caron AR, Fischer DS, George N, Gyori BM, Haendel MA, Hoyt CT, Kir H, Lubiana T, Matentzoglu N, Overton JA, Peng B, Peters B, Quardokus EM, Ray PL, Roncaglia P, Rivera AD, Stefancsik R, Teh WK, Toro S, Vasilevsky N, Xu C, Zhang Y, Scheuermann RH, Mungall CJ, Diehl AD, Osumi-Sutherland D. (2025) The Cell Ontology in the age of single-cell omics. ArXiv (Jun).
Rachel Stephens, Gillian Franklin, Kevin B Taylor, Kaity H Tung, Vladyslav Ilchenko, Muhammad Piracha, Shmuel Tiosano, Kendria Hall, Irshad Ally, Peter L Elkin. (2025) Semantic Clinical Artificial Intelligence (SCAI) Usability Testing. (May), 12(326): 27-32. doi:0.3233/SHTI250230
Resnick M, Elkin A, Tiosano S, Koppel R, Franklin G, Piracha MU, Taylor K, Tung K, Brown S, Nebeker J, Elkin P. (2025) The Semantic Clinical Artificial Intelligence (SCAI) Chatbot: Preliminary Usability Testing. (May), 12(326): 22-26. doi:10.3233/SHTI250229
Ceusters W, Rabenberg M. (2025) Semantic Difficulties in FHIR 'Conditions. Studies in health technology and informatics (May), 327: 7-11.
Schwartz DG Morreale C. (2025) Advanced Public Health Informatics: A Best Practices Pathway to New Knowledge, Skills, and Understanding Via Asynchronous Learning. Stud Health Technol Inform (May), 15: 1090-1091. doi:10.3233/SHTI250553

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