Boris Oskotsky, PhD
Bioinformatics Systems Admin
Computational Health Scienc
School of Medicine

Publications (20)

Top publication keywords:
Electronic Health RecordsParenteral NutritionCardiomyopathiesFluvoxaminePremature BirthSoftwareCrowdsourcingPrecision MedicineFluoxetineHigh-Throughput Nucleotide SequencingDiagnosis, Computer-AssistedParenteral Nutrition, TotalAntidepressive AgentsIntensive Care Units, NeonatalArtificial Intelligence

• 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
• 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
• Author Correction: 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…
• 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…
• 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, …

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• 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, …
• A certified de-identification system for all clinical text documents for information extraction at scale.
  JAMIA open 2023 Radhakrishnan L, Schenk G, Muenzen K, Oskotsky B, Ashouri Choshali H, Plunkett T, Israni S, Butte AJ
• 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, …
• A biomedical open knowledge network harnesses the power of AI to understand deep human biology.
  AI magazine 2022 Baranzini SE, Börner K, Morris J, Nelson CA, Soman K, Schleimer E, Keiser M, Musen M, Pearce R, Reza T, Smith B, Herr BW, Oskotsky B, Rizk-Jackson A, Rankin KP, Sanders SJ, Bove R, Rose PW, Israni S, …
• 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
• Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
  Genome biology 2022 Kaur N, Oskotsky B, Butte AJ, Hu Z
• 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
• CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties.
  Scientific data 2020 Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA
• Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.
  NPJ digital medicine 2020 Norgeot B, Muenzen K, Peterson TA, Fan X, Glicksberg BS, Schenk G, Rutenberg E, Oskotsky B, Sirota M, Yazdany J, Schmajuk G, Ludwig D, Goldstein T, Butte AJ
• PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.
  Bioinformatics (Oxford, England) 2019 Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna VA, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, Israni S, Larsen …
• Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis.
  JAMA network open 2019 Norgeot B, Glicksberg BS, Trupin L, Lituiev D, Gianfrancesco M, Oskotsky B, Schmajuk G, Yazdany J, Butte AJ
• ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data.
  JAMIA open 2019 Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ
• Comparing Ethnicity-Specific Reference Intervals for Clinical Laboratory Tests from EHR Data.
  The journal of applied laboratory medicine 2018 Rappoport N, Paik H, Oskotsky B, Tor R, Ziv E, Zaitlen N, Butte AJ
• Comprehensive analysis of normal adjacent to tumor transcriptomes.
  Nature communications 2017 Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ
• Effect of band mixing on hole transport along the axis of a semiconductor superlattice.
  Physical review. B, Condensed matter 1994 Gerchikov LG, Oskotsky BD, Subashiev AV