Tomiko Oskotsky, MD
Bioinformatics Programmer
Computational Health Scienc
School of Medicine

Education & Training

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• MD Medical College of Wisconsin
• BS Biochemistry University of California Los Angeles

Websites

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• March of Dimes Prematurity Research Database (pretermbirthdb.org)
• UCSF AI4ALL (ai4all.ucsf.edu)
• Sirota Lab (sirotalab.ucsf.edu)

Publications (32)

Top publication keywords:
Severity of Illness IndexMentoringMicrobiotaAntidepressive AgentsFluoxetineComputational BiologyInfant HealthBiomedical ResearchSertralineArtificial IntelligenceDrug RepositioningFluvoxamineCrowdsourcingDissociative DisordersCultural Diversity

• 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, …
• Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.
  Cell reports. Medicine 2023 Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, …
• Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.
  medRxiv : the preprint server for health sciences 2023 Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA

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• 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
• Sex-stratified phenotyping of comorbidities associated with an inpatient delirium diagnosis using real world data.
  medRxiv : the preprint server for health sciences 2023 Kodama L, Woldemariam S, Tang A, Li Y, Oskotsky T, Raphael E, Sirota M
• 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, …
• Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.
  medRxiv : the preprint server for health sciences 2023 Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, …
• 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
• VMAP: Vaginal Microbiome Atlas During Pregnancy.
  medRxiv : the preprint server for health sciences 2023 Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, 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, …
• 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 …
• Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients.
  medRxiv : the preprint server for health sciences 2022 Sperry MM, Oskotsky T, MariÄ 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, …
• 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, …
• Mortality Risk Among Patients With COVID-19 Prescribed Selective Serotonin Reuptake Inhibitor Antidepressants.
  JAMA network open 2021 Oskotsky T, Maric I, Tang A, Oskotsky B, Wong RJ, Aghaeepour N, Sirota M, Stevenson DK
• 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
• Personalizing routine lab tests with machine learning.
  Nature medicine 2021 Tang A, Oskotsky T, 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, host responses to SARS-CoV-2, and in vitro responses to sex steroid hormone treatment in COVID-19.
  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,…
• Deep posteromedial cortical rhythm in dissociation.
  Nature 2020 Vesuna S, Kauvar IV, Richman E, Gore F, Oskotsky T, Sava-Segal C, Luo L, Malenka RC, Henderson JM, Nuyujukian P, Parvizi J, Deisseroth K
• 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