Tomiko Oskotsky, MD

Bioinformatics Programmer,
Computational Health Sciences
Computational Health Scienc
[email protected]
Publications: 

Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach.

iScience

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, McAllister SL, Sirota M

Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights.

Nature Aging

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, Baranzini S, Sirota M

Discovery of sparse, reliable omic biomarkers with Stabl.

Nature biotechnology

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, Sirota M, Bonham TA, Sato M, Diop M, Durand X, Angst MS, Stevenson DK, Aghaeepour N, Montanari A, Gaudillière B

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.

Cell reports. Medicine

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, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M

Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.

medRxiv : the preprint server for health sciences

Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA

MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies.

Cell reports methods

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

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

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

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, Stevenson DK, Ingber DE, Sirota M, Novak R

Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.

medRxiv : the preprint server for health sciences

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, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee Li YS, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M

VMAP: Vaginal Microbiome Atlas During Pregnancy.

medRxiv : the preprint server for health sciences

Leo AP, 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, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M

Leveraging electronic health records to identify risk factors for recurrent pregnancy loss across two medical centers: a case-control study.

Research square

Roger J, Xie F, Costello J, Tang A, Liu J, Oskotsky T, Woldemariam S, Kosti I, Le B, Snyder M, Giudice L, Torgerson D, Shaw G, Stevenson D, Rajkovic A, Aghaeepour N, Glymour M, Cakmak H, Lathi R, Sirota M

Data-driven longitudinal characterization of neonatal health and morbidity.

Science translational medicine

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 MG, Oskotsky T, Maric I, Gaudilliere B, Carvalho B, Bateman BT, Angst MS, Prince LS, Blumenfeld YJ, Benitz WE, Fuerch JH, Shaw GM, Sylvester KG, Stevenson DK, Sirota M, Aghaeepour N

Different HMGCR-inhibiting statins vary in their association with increased survival in patients with COVID-19.

medRxiv : the preprint server for health sciences

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 B, Logue J, Hammond H, Frieman M, Stevenson DK, Ingber DE, Sirota M, Novak R

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

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

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

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 Student Cohort 2020, Lindstaedt B, Sirota M

Author Correction: Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease.

Nature Aging

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, Koutsodendris N, Chen N, Wang C, Chang W, An A, Glicksberg BS, Sirota M, Huang Y

Mortality Risk Among Patients With COVID-19 Prescribed Selective Serotonin Reuptake Inhibitor Antidepressants.

JAMA network open

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

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

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, Koutsodendris N, Chen N, Wang C, Chang W, An A, Glicksberg BS, Sirota M, Huang Y

Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer's Disease.

Frontiers in aging neuroscience

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

Tang A, Oskotsky T, Sirota M

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19.

Scientific reports

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

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

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

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

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, Glicksberg BS, Nadkarni GN, Moeser AJ, Li L, Kim S, Zhou J, Chen B

Deep posteromedial cortical rhythm in dissociation.

Nature

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

Chi J, Kugler J, Chu IM, Loftus PD, Evans KH, Oskotsky T, Basaviah P, Braddock CH

Custom People Group: 
UCSF Microbiome Researchers