Tomiko Oskotsky, MD
Associate Professor of Medicine
Computational Health Scienc
School of Medicine

She has expansive expertise in harnessing clinical and multi-omics datasets and applying bioinformatics approaches to drive therapeutic and diagnostic breakthroughs in Alzheimer’s disease, endometriosis, and preterm birth. She directs the March of Dimes Prematurity Research Data Repository and the UCSF AI4ALL program, expanding the reach of machine learning and AI in both biomedical discovery and education. Dr. Oskotsky has advanced the field through pioneering initiatives, including co-leading a DREAM Challenge on the vaginal microbiome, publishing extensively, and forging collaborations across academia. Her work centers on computational approaches to precision medicine, with a focus on women’s health and complex diseases.

• Transcriptomic comparison of early onset preeclampsia and placenta accreta identifies inverse trophoblast and decidua functions at the maternal-fetal interface.
  npj women's health 2025 Yin O, Almonte-Loya A, Appierdo R, Yang M, Yilmaz BD, Oskotsky TT, Gonzalez-Velez JM, Giudice LC, Afshar Y, Sirota M
• Delirium in hospitalized COVID-19 patients is associated with dynamic changes in peripheral immune gene expression.
  GeroScience 2025 LaHue SC, Takegami N, Simmasalam R, Baqai A, Munoz E, Sikri A, de Courson TDB, Singhal NS, Eckalbar W, Langelier CR, Hendrickson CM, Calfee CS, Erle DJ, Krummel MF, Woodruff PG, Oskotsky T, Sirota M, …
• Decoding subphenotypes in electronic medical records within late-onset Alzheimer's disease reveals heterogeneity and sex-specific differences.
  medRxiv : the preprint server for health sciences 2025 Katsuhara Y, Khan U, Miller ZA, Allen IE, Oskotsky TT, Sirota M, Tang AS
• Leveraging electronic health records from two hospital systems identifies male infertility-associated comorbidities across time.
  Communications medicine 2025 Woldemariam SR, Xie F, Roldan A, Roger J, Tang AS, Oskotsky TT, Stevenson DK, Lathi RB, Rajkovic A, Allen IE, Aghaeepour N, Eisenberg M, Sirota M
• Anticlustering for sample allocation to minimize batch effects.
  Cell reports methods 2025 Papenberg M, Wang C, Diop M, Bukhari SH, Oskotsky B, Davidson BR, Vo KC, Liu B, Irwin JC, Combes AJ, Gaudilliere B, Li J, Stevenson DK, Klau GW, Giudice LC, Sirota M, Oskotsky TT
• Single-Cell Profiling Reveals Altered Endometrial Cellular Features Across the Menstrual Cycle in Endometriosis Patients.
  bioRxiv : the preprint server for biology 2025 Almonte-Loya A, Wang W, Houshdaran S, Tang X, Flynn E, Liu B, Kushnoor D, Nezhat C, Vilella F, Simon C, Vo KC, Casillas A, Khan U, Serras CP, Oskotsky TT, Huang D, Vallve-Juanico J, Irwin J, Combes A,…
• Comorbidity analysis and clustering of endometriosis patients using electronic health records.
  Cell reports. Medicine 2025 Khan U, Oskotsky TT, Yilmaz BD, Roger J, Gjoni K, Irwin JC, Opoku-Anane J, Elhadad N, Giudice LC, Sirota M
• Comorbidities associated with a clinically-recognized delirium diagnosis in the hospital using real world data.
  Communications medicine 2025 Kodama L, Woldemariam SR, Tang AS, Li Y, Kornak J, Allen IE, Raphael E, Oskotsky TT, Sirota M
• Cell-type-directed network-correcting combination therapy for Alzheimer's disease.
  Cell 2025 Li Y, Pereda Serras C, Blumenfeld J, Xie M, Hao Y, Deng E, Chun YY, Holtzman J, An A, Yoon SY, Tang X, Rao A, Woldemariam S, Tang A, Zhang A, Simms J, Lo I, Oskotsky T, Keiser MJ, Huang Y, Sirota M
• Diagnostic Reversion in Dementia Care: A Real-World Analysis of Mild Cognitive Impairment Diagnoses Following Dementia in a Large Electronic Medical Record System.
  medRxiv : the preprint server for health sciences 2025 Miramontes S, Khan U, Zimmerman S, Ferguson EL, Mills H, Oskotsky B, Phelps E, Oskotsky TT, Capra AJ, Glymour MM, Sirota M, Tsoy E
• InSight: AI Mobile Screening Tool for Multiple Eye Disease Detection using Multimodal Fusion
  arXiv 2025 Raghu Ananya, Raghu Anisha, Tang AS, Paulus YM, Kim TN, Oskotsky TT
• Benchmarking Large Language Models for Predictive Modeling in Biomedical Research With a Focus on Reproductive Health.
  bioRxiv : the preprint server for biology 2025 Sarwal R, Tarca V, Dubin C, Kalavros N, Bhatti G, Bhattacharya S, Butte A, Romero R, Stolovitzky G, Oskotsky TT, Tarca AL, Sirota M
• A Transcriptomics-Based Computational Drug Repositioning Pipeline Identifies Simvastatin And Primaquine As Novel Therapeutics For Endometriosis Pain.
  bioRxiv : the preprint server for biology 2025 Oskotsky TT, Tang X, Arthurs E, Govil A, Abbasi F, Bhoja A, Bunis DJ, Lau A, Einhaus J, Diop M, Irwin JC, Gaudilliere B, Stevenson DK, Giudice LC, McAllister SL, Sirota M
• AI-guided precision parenteral nutrition for neonatal intensive care units.
  Nature medicine 2025 Phongpreecha T, Ghanem M, Reiss JD, Oskotsky TT, Mataraso SJ, De Francesco D, Reincke SM, Espinosa C, Chung P, Ng T, Costello JM, Sequoia JA, Razdan S, Xie F, Berson E, Kim Y, Seong D, Szeto MY, Myers…
• Exposure to autoimmune disorders is associated with increased Alzheimer's disease risk in a multi-site electronic health record analysis.
  Cell reports. Medicine 2025 Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M
• Peripheral blood mononuclear cell transcriptomic trajectories reveal dynamic regulation of inflammatory actors in delirium.
  medRxiv : the preprint server for health sciences 2025 LaHue SC, Takegami N, Simmasalam R, Baqai A, Munoz E, Sikri A, de Courson TDB, Singhal NS, Eckalbar W, Langelier CR, Hendrickson CM, Calfee CS, Erle DJ, Krummel MF, Woodruff PG, Oskotsky T, Sirota M, …
• Pre-conception clinical risk factors differ between spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.
  BMC pregnancy and childbirth 2025 Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA
• Real world perspectives on endometriosis disease phenotyping through surgery, omics, health data, and artificial intelligence.
  npj women's health 2025 Nezhat CR, Oskotsky TT, Robinson JF, Fisher SJ, Tsuei A, Liu B, Irwin JC, Gaudilliere B, Sirota M, Stevenson DK, Giudice LC
• VMAP: Vaginal Microbiome Atlas during Pregnancy.
  JAMIA open 2024 Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang AS, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, …
• Harnessing EHR data for health research.
  Nature medicine 2024 Tang AS, Woldemariam SR, Miramontes S, Norgeot B, Oskotsky TT, Sirota M
• A scalable platform for acquisition of high-fidelity human intracranial EEG with minimal clinical burden.
  PloS one 2024 Yamada L, Oskotsky T, Nuyujukian P, Stanford Comprehensive Epilepsy Center, Stanford Pediatric Epilepsy Center
• Alzheimer's disease as a women's health challenge: a call for action on integrative precision medicine approaches.
  npj women's health 2024 Miramontes S, Pereda Serras C, Woldemariam SR, Khan U, Li Y, Tang AS, Tsoy E, Oskotsky TT, Sirota M
• Data-driven insights can transform women's reproductive health.
  npj women's health 2024 Oskotsky TT, Yin O, Khan U, Arnaout L, Sirota M
• Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach.
  iScience 2024 Oskotsky TT, Bhoja A, Bunis D, Le BL, Tang AS, Kosti I, Li C, Houshdaran S, Sen S, Vallvé-Juanico J, Wang W, Arthurs E, Govil A, Mahoney L, Lang L, Gaudilliere B, Stevenson DK, Irwin JC, Giudice LC, …
• Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights.
  Nature aging 2024 Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, …
• Discovery of sparse, reliable omic biomarkers with Stabl.
  Nature biotechnology 2024 Hédou J, Maric I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Amar J, Cambriel A, Oskotsky TT, Roldan A, Golob JL, …
• MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies.
  Cell reports methods 2023 Minot SS, Garb B, Roldan A, Tang AS, Oskotsky TT, Rosenthal C, Hoffman NG, Sirota M, Golob JL
• Endometriosis in the era of precision medicine and impact on sexual and reproductive health across the lifespan and in diverse populations.
  FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2023 Giudice LC, Oskotsky TT, Falako S, Opoku-Anane J, Sirota M
• Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients.
  PLoS computational biology 2023 Sperry MM, Oskotsky TT, Maric I, Kaushal S, Takeda T, Horvath V, Powers RK, Rodas M, Furlong B, Soong M, Prabhala P, Goyal G, Carlson KE, Wong RJ, Kosti I, Le BL, Logue J, Hammond H, Frieman M, …
• Similarities and differences in Alzheimer's dementia comorbidities in racialized populations identified from electronic medical records.
  Communications medicine 2023 Woldemariam SR, Tang AS, Oskotsky TT, Yaffe K, Sirota M
• Leveraging electronic health records to identify risk factors for recurrent pregnancy loss across two medical centers: a case-control study.
  Research square 2023 Roger J, Xie F, Costello J, Tang A, Liu J, Oskotsky T, Woldemariam S, Kosti I, Le B, Snyder MP, Giudice LC, Torgerson D, Shaw GM, Stevenson DK, Rajkovic A, Glymour MM, Aghaeepour N, Cakmak H, Lathi RB…
• Data-driven longitudinal characterization of neonatal health and morbidity.
  Science translational medicine 2023 De Francesco D, Reiss JD, Roger J, Tang AS, Chang AL, Becker M, Phongpreecha T, Espinosa C, Morin S, Berson E, Thuraiappah M, Le BL, Ravindra NG, Payrovnaziri SN, Mataraso S, Kim Y, Xue L, Rosenstein …
• Large-scale placenta DNA methylation integrated analysis reveals fetal sex-specific differentially methylated CpG sites and regions.
  Scientific reports 2022 Andrews SV, Yang IJ, Froehlich K, Oskotsky T, Sirota M
• Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions.
  Frontiers in aging neuroscience 2022 Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M
• Deep phenotyping of Alzheimer's disease leveraging electronic medical records identifies sex-specific clinical associations.
  Nature communications 2022 Tang AS, Oskotsky T, Havaldar S, Mantyh WG, Bicak M, Solsberg CW, Woldemariam S, Zeng B, Hu Z, Oskotsky B, Dubal D, Allen IE, Glicksberg BS, Sirota M
• Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students.
  PLoS computational biology 2022 Oskotsky T, Bajaj R, Burchard J, Cavazos T, Chen I, Connell WT, Eaneff S, Grant T, Kanungo I, Lindquist K, Myers-Turnbull D, Naing ZZC, Tang A, Vora B, Wang J, Karim I, Swadling C, Yang J, AI4ALL …
• Author Correction: Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease.
  Nature aging 2021 Taubes A, Nova P, Zalocusky KA, Kosti I, Bicak M, Zilberter MY, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Aery Jones EA, Choudhary K, Grone B, Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, …
• Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions.
  Molecular neurobiology 2021 Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M
• Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease.
  Nature aging 2021 Taubes A, Nova P, Zalocusky KA, Kosti I, Bicak M, Zilberter MY, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Jones EAA, Choudhary K, Grone B, Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, …
• Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer's Disease.
  Frontiers in aging neuroscience 2021 Paranjpe MD, Belonwu S, Wang JK, Oskotsky T, Gupta A, Taubes A, Zalocusky KA, Paranjpe I, Glicksberg BS, Huang Y, Sirota M
• Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19.
  Scientific reports 2021 Le BL, Andreoletti G, Oskotsky T, Vallejo-Gracia A, Rosales R, Yu K, Kosti I, Leon KE, Bunis DG, Li C, Kumar GR, White KM, García-Sastre A, Ott M, Sirota M
• Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis.
  Frontiers in immunology 2021 Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M
• Drugs in COVID-19 Clinical Trials: Predicting Transporter-Mediated Drug-Drug Interactions Using In Vitro Assays and Real-World Data.
  Clinical pharmacology and therapeutics 2021 Yee SW, Vora B, Oskotsky T, Zou L, Jakobsen S, Enogieru OJ, Koleske ML, Kosti I, Rödin M, Sirota M, Giacomini KM
• Decreased Mortality Rate Among COVID-19 Patients Prescribed Statins: Data From Electronic Health Records in the US.
  Frontiers in medicine 2021 Maric I, Oskotsky T, Kosti I, Le B, Wong RJ, Shaw GM, Sirota M, Stevenson DK
• Sex differences in viral entry protein expression and host transcript responses to SARS-CoV-2.
  Research square 2020 Sun M, Shankar R, Ko M, Chang CD, Yeh SJ, Li S, Liu K, Zhou G, Xing J, VanVelsen A, VanVelsen T, Paithankar S, Feng BY, Young K, Strug M, Turco L, Wang Z, Schadt E, Chen R, Li X, Oskotsky T, Sirota M,…
• Medical students and the electronic health record: 'an epic use of time'.
  The American journal of medicine 2014 Chi J, Kugler J, Chu IM, Loftus PD, Evans KH, Oskotsky T, Basaviah P, Braddock CH