Marina Sirota, PhD

Associate Professor

Marina is currently an Assistant Professor at the Bakar Computational Health Sciences Institute at UCSF. Prior to that she was the Lead Research Scientist in the Division of Systems Medicine at Stanford University and has worked as a Senior Research Scientist at Pfizer where she focused on developing Precision Medicine strategies in drug discovery. She completed her PhD in Biomedical Informatics at Stanford University, where her graduate work focused on predicting drug-disease relationships based on gene expression to identify novel therapeutic indications for known drugs. Her research interests lie in developing computational integrative methods and applying these approaches in the context of disease diagnostics and therapeutics. Her primary focus is on leveraging and integrating different types of omics and clinical data to better understand the role of the immune system in disease. The Sirota laboratory is funded by NIA, NLM, NIAMS, Pfizer, March of Dimes and the Burroughs Wellcome Fund. As a young leader in the field, she has been awarded the AMIA Young Investigator Award in 2017. Dr. Sirota also is the director of the AI4ALL program at UCSF, with the goal of introducing high school girls to applications of AI and machine learning in biomedicine.
Education
Ph.D., 2010 - Biomedical Informatics, Stanford University
B.S., 2006 - Biomedical Computation, Stanford University
M.S., 2006 - Biomedical Informatics, Stanford University
Websites
Publications

  1. 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. Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach. 2024. PMID: 38510116


  2. 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. Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights. 2024. PMID: 38383858


  3. Guy Amit, Chen Yanover, Maytal Bivas-Benita, Irena Girshovitz, Tal Helbitz, Tamar Sudry, Vered Bar, Alice S. Tang, Brian L. Le, Jacquelyn Roger, Sarah Woldemariam, Idit Kosti, Tomiko T. Oskotsky, Pinchas Akiva, Marina Sirota. Antidepressant use during pregnancy and the risk of preterm birth – a cohort study. 2024. PMID:


  4. Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach. 2023. PMID: 37703185


  5. Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A. Miscarriage risk assessment: a bioinformatic approach to identifying candidate lethal genes and variants. 2024. PMID: 38302665


  7. 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. Discovery of sparse, reliable omic biomarkers with Stabl. 2024. PMID: 38168992


  8. Alice S Tang, Katherine P Rankin, Gabriel Cerano, Silvia Miramontes, Hunter Mills, Tomiko Oskotsky, Billy Zeng, Charlotte Nelson, Karthik Soman, Sarah Woldemariam, Yaqiao Li, Albert M Lee, Zachary Miller, Isabel Elaine Allen, Stephan Sanders, Sergio Baranzini, Marina Sirota. Predictive Modeling Leveraging Electronic Health Records Identifies Early Predictors of Alzheimer’s Disease. 2023. PMID:


  9. Yaqiao Li, Yanxia Hao, Seo Yeon Yoon, Brian Grone, Leonardo Ding, Jessica Blumenfeld, Tomiko Oskotsky, Yadong Huang, Marina Sirota. Transcriptomic Profiling Across Age, APOE and Sex for Models of Alzheimer’s Disease at a Single Cell Resolution. 2023. PMID:


  10. Bland GD, Abrahamsson D, Wang M, Zlatnik MG, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. Exploring applications of non-targeted analysis in the characterization of the prenatal exposome. 2023. PMID: 38142008


  11. 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. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. 2023. PMID: 38134931


  12. M. Binvignat, B. Miao, C. Wibrand, M. Yang, D. Rychkov, E. Flynn, J. Nititham, W. Tamaki, U. Khan, A. Carvidi, M. Krueger, E. Niemi, Y. Sun, G. Fragiadakis, J. Sellam, E. Mariotti-Ferrandiz, D. Klatzmann, A. Gross, J. Ye, A. Butte, L.A. Criswell, M. Nakamura, M. Sirota. Identification d’une signature en Single Cell transcriptomique associée à l’activité de la maladie dans la polyarthrite rhumatoïde. 2023. PMID:


  13. Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA. Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort. 2023. PMID: 38077057


  14. Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye C, Dall'Era M, Yazdany J, Criswell L, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. 2023. PMID: 38076936


  15. Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics. 2023. PMID: 37986917


  17. Minot SS, Garb B, Roldan A, Tang AS, Oskotsky TT, Rosenthal C, Hoffman NG, Sirota M, Golob JL. MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies. 2023. PMID: 37939711


  18. Kodama L, Woldemariam S, Tang A, Li Y, Oskotsky T, Raphael E, Sirota M. Sex-stratified phenotyping of comorbidities associated with an inpatient delirium diagnosis using real world data. 2023. PMID: 37961487


  19. CN Okorie, A Meghan, S Bejerano, A Rodriguez, M Sirota, T Oskotsky, L Giudice, J Opoku-Anane. 10456 Endometriosis or Chronic Pelvic Pain —Disparities in Inpatient Surgical Care on the National Level. 2023. PMID:


  20. Ana Laura Almonte, Wanxin Wang, Emily Flynn, Sahar Houshdaran, Júlia Vallvé-Juanico, Juan Irwin, Divyashree Kushnoor, Alexis Combes, Gabriela K. Fragiadakis, Marina Sirota, Linda C. Giudice. ENDOMETRIAL SUBCELLULAR ALTERATIONS IN ENDOMETRIOSIS IDENTIFIED BY SINGLE-CELL ANALYSIS ACROSS THE MENSTRUAL CYCLE. 2023. PMID:


  21. Sarah Woldemariam, Feng Xie, Alennie Roldan, Jacquelyn Roger, Alice Tang, Tomiko Oskotsky, Nima Aghaeepour, Michael Eisenberg, Marina Sirota. LEVERAGING ELECTRONIC MEDICAL RECORDS REVEALS COMORBIDITIES SIGNIFICANTLY ASSOCIATED WITH MALE INFERTILITY. 2023. PMID:


  22. Jacquelyn Roger, Jean Costello, Melissa G. Rosenstein, Aleksandar Rajkovic, Hakan Cakmak, Gary Shaw, David Stevenson, Maria Glymour, Ruth Bunker Lathi, Marina Sirota. MALE FIRSTBORN AND SUBSEQUENT PREGNANCY LOSS – A REAPPRAISAL USING REAL-WORLD DATA. 2023. PMID:


  24. Mortlock S, Houshdaran S, Kosti I, Rahmioglu N, Nezhat C, Vitonis AF, Andrews SV, Grosjean P, Paranjpe M, Horne AW, Jacoby A, Lager J, Opoku-Anane J, Vo KC, Manvelyan E, Sen S, Ghukasyan Z, Collins F, Santamaria X, Saunders P, Kober K, McRae AF, Terry KL, Vallvé-Juanico J, Becker C, Rogers PAW, Irwin JC, Zondervan K, Montgomery GW, Missmer S, Sirota M, Giudice L. Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function. 2023. PMID: 37587191


  25. Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N. Corrigendum to Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth [The Journal of Pediatrics 194(2018):40-46.e4]. 2023. PMID: 37495478


  26. Trowbridge J, Abrahamsson D, Bland GD, Jiang T, Wang M, Park JS, Morello-Frosch R, Sirota M, Lee H, Goin DE, Zlatnik MG, Woodruff TJ. Extending Nontargeted Discovery of Environmental Chemical Exposures during Pregnancy and Their Association with Pregnancy Complications-A Cross-Sectional Study. 2023. PMID: 37466315


  27. Yu K, Basu A, Yau C, Wolf DM, Goodarzi H, Bandyopadhyay S, Korkola JE, Hirst GL, Asare S, DeMichele A, Hylton N, Yee D, Esserman L, van 't Veer L, Sirota M. Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes. 2023. PMID: 37384294


  28. Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A. Preconception Genetic Carrier Screening for Miscarriage Risk Assessment: A Bioinformatic Approach to Identifying Candidate Lethal Genes and Variants. 2023. PMID: 37398382


  29. M. Binvignat, B. Miao, C. Wibrand, M. Yang, D. Rychkov, E. Flynn, J. Nititham, A. Carvidi, M. Krueger, E. Niemi, Y. Sun, E. Mariotti-Ferrandiz, J. Sellam, C. Ye, A. Butte, L. Criswell, M. Nakamura, M. Sirota. POS1044 SINGLE CELL TRANSCRIPTOMICS ANALYSIS OF BLOOD IMMUNE CELLS IDENTIFIES GENE SIGNATURES AND CELL SUBSETS ASSOCIATED WITH DISEASE ACTIVITY IN A DIVERSE POPULATION OF RHEUMATOID ARTHRITIS PATIENTS. 2023. PMID:


  30. Vora B, Wen A, Yee SW, Trinh K, Azimi M, Green EAE, Sirota M, Greenberg AS, Newman JW, Giacomini KM. The Effect of Trimethoprim on Thiamine Absorption: A Transporter-Mediated Drug-Nutrient Interaction. 2023. PMID: 37151050


  31. Baglaenko Y, Wagner C, Bhoj VG, Brodin P, Gershwin ME, Graham D, Invernizzi P, Kidd KK, Korsunsky I, Levy M, Mammen AL, Nizet V, Ramirez-Valle F, Stites EC, Williams MS, Wilson M, Rose NR, Ladd V, Sirota M. Making inroads to precision medicine for the treatment of autoimmune diseases: Harnessing genomic studies to better diagnose and treat complex disorders. 2023. PMID: 38550937


  32. 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. Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients. 2023. PMID: 37146076


  33. Laurent SA, Strauli NB, Eggers EL, Wu H, Michel B, Demuth S, Palanichamy A, Wilson MR, Sirota M, Hernandez RD, Cree BAC, Herman AE, von Büdingen HC. Effect of Ocrelizumab on B- and T-Cell Receptor Repertoire Diversity in Patients With Relapsing Multiple Sclerosis From the Randomized Phase III OPERA Trial. 2023. PMID: 37094998


  34. 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. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. 2023. PMID: 36945505


  36. 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. VMAP: Vaginal Microbiome Atlas During Pregnancy. 2023. PMID: 36993193


  37. 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. Leveraging electronic health records to identify risk factors for recurrent pregnancy loss across two medical centers: a case-control study. 2023. PMID: 36993325


  38. Rahmioglu N, Mortlock S, Ghiasi M, M?ller PL, Stefansdottir L, Galarneau G, Turman C, Danning R, Law MH, Sapkota Y, Christofidou P, Skarp S, Giri A, Banasik K, Krassowski M, Lepamets M, Marciniak B, N?ukas M, Perro D, Sliz E, Sobalska-Kwapis M, Thorleifsson G, Topbas-Selcuki NF, Vitonis A, Westergaard D, Arnadottir R, Burgdorf KS, Campbell A, Cheuk CSK, Clementi C, Cook J, De Vivo I, DiVasta A, Dorien O, Donoghue JF, Edwards T, Fontanillas P, Fung JN, Geirsson RT, Girling JE, Harkki P, Harris HR, Healey M, Heikinheimo O, Holdsworth-Carson S, Hostettler IC, Houlden H, Houshdaran S, Irwin JC, Jarvelin MR, Kamatani Y, Kennedy SH, Kepka E, Kettunen J, Kubo M, Kulig B, Kurra V, Laivuori H, Laufer MR, Lindgren CM, MacGregor S, Mangino M, Martin NG, Matalliotaki C, Matalliotakis M, Murray AD, Ndungu A, Nezhat C, Olsen CM, Opoku-Anane J, Padmanabhan S, Paranjpe M, Peters M, Polak G, Porteous DJ, Rabban J, Rexrode KM, Romanowicz H, Saare M, Saavalainen L, Schork AJ, Sen S, Shafrir AL, Siewierska-G?rska A, Slomka M, Smith BH, Smolarz B, Szaflik T, Szyllo K, Takahashi A, Terry KL, Tomassetti C, Treloar SA, Vanhie A, Vincent K, Vo KC, Werring DJ, Zeggini E, Zervou MI, DBDS Genomic Consortium, FinnGen Study, FinnGen Endometriosis Taskforce, Celmatix Research Team, 23andMe Research Team, Adachi S, Buring JE, Ridker PM, D'Hooghe T, Goulielmos GN, Hapangama DK, Hayward C, Horne AW, Low SK, Martikainen H, Chasman DI, Rogers PAW, Saunders PT, Sirota M, Spector T, Strapagiel D, Tung JY, Whiteman DC, Giudice LC, Velez-Edwards DR, Uimari O, Kraft P, Salumets A, Nyholt DR, M?gi R, Stefansson K, Becker CM, Yurttas-Beim P, Steinthorsdottir V, Nyegaard M, Missmer SA, Montgomery GW, Morris AP, Zondervan KT. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions. 2023. PMID: 36914876


  39. 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. Data-driven longitudinal characterization of neonatal health and morbidity. 2023. PMID: 36791208


  40. Ben?tez R, Yu K, Sirota M, Malats N, Pineda S. Characterization of the tumor-infiltrating immune repertoire in muscle invasive bladder cancer. 2023. PMID: 36817478


  41. Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MAV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities. 2023. PMID: 36711882


  43. Sigdel TK, Fields PA, Liberto J, Damm I, Kerwin M, Hood J, Towfighi P, Sirota M, Robins HS, Sarwal MM. Perturbations of the T-cell immune repertoire in kidney transplant rejection. 2022. PMID: 36466928


  44. Abraham A, Le B, Kosti I, Straub P, Velez-Edwards DR, Davis LK, Newton JM, Muglia LJ, Rokas A, Bejan CA, Sirota M, Capra JA. Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth. 2022. PMID: 36167547


  45. Jessica Trowbridge, Dimitri Abrahamsson, Ting Jiang, Miaomiao Wang, June-Soo Park, Rachel Morello-Frosch, Marina Sirota, Dana Going, Marya Zlatnick, Tracey Woodruff. Extending non-targeted exposure discovery of environmental chemical exposures during pregnancy and their association with pregnancy complications. 2022. PMID:


  46. Lanata CM, Nititham J, Taylor KE, Solomon O, Chung SA, Blazer A, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Barcellos LF, Criswell LA. The dynamics of methylation of CpG sites associated with SLE subtypes in a longitudinal cohort. 2022. PMID: 35635730


  47. Goin DE, Abrahamsson D, Wang M, Jiang T, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Zlatnik MG, Woodruff TJ. Disparities in chemical exposures among pregnant women and neonates by socioeconomic and demographic characteristics: A nontargeted approach. 2022. PMID: 36049512


  48. 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. Different HMGCR-inhibiting statins vary in their association with increased survival in patients with COVID-19. 2022. PMID: 35441166


  49. Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier CR, Sirota M. Physical Activity Associates with Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis. 2022. PMID: 35777820


  50. Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota M. Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity. 2022. PMID: 35799782


  52. Abrahamsson D, Siddharth A, Young TM, Sirota M, Park JS, Martin JW, Woodruff TJ. In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures. 2022. PMID: 35649165


  53. Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, 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. 2022. PMID: 35572130


  54. Goin DE, Abrahamsson D, Wang M, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Trowbridge J, August L, O'Connell S, Ladella S, Zlatnik MG, Woodruff TJ. Investigating geographic differences in environmental chemical exposures in maternal and cord sera using non-targeted screening and silicone wristbands in California. 2022. PMID: 35449448


  55. Zinter MS, Versluys AB, Lindemans CA, Mayday MY, Reyes G, Sunshine S, Chan M, Fiorino EK, Cancio M, Prevaes S, Sirota M, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL. Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates. 2022. PMID: 35263147


  56. 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. Deep phenotyping of Alzheimer's disease leveraging electronic medical records identifies sex-specific clinical associations. 2022. PMID: 35115528


  57. Oskotsky T, Bajaj R, Burchard J, Cavazos T, Chen I, Connell W, 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. Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students. 2022. PMID: 35100256


  58. Yu K, Ravoor A, Malats N, Pineda S, Sirota M. A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires. 2022. PMID: 35069569


  59. Bunis DG, Wang W, Vallvé-Juanico J, Houshdaran S, Sen S, Ben Soltane I, Kosti I, Vo KC, Irwin JC, Giudice LC, Sirota M. Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis. 2022. PMID: 35069565


  60. 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. Author Correction: Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease. 2021. PMID: 37117528


  61. Oskotsky T, Maric I, Tang A, Oskotsky B, Wong RJ, Aghaeepour N, Sirota M, Stevenson DK. Mortality Risk Among Patients With COVID-19 Prescribed Selective Serotonin Reuptake Inhibitor Antidepressants. 2021. PMID: 34779847


  62. Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M. Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions. 2021. PMID: 34669146


  63. Le BL, Sper R, Nielsen SCA, Pineda S, Nguyen QH, Lee JY, Boyd SD, MacKenzie TC, Sirota M. Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development in Term and Preterm Infants. 2021. PMID: 34654689


  64. 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. Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease. 2021. PMID: 36172600


  65. Davis EJ, Solsberg CW, White CC, Miñones-Moyano E, Sirota M, Chibnik L, Bennett DA, De Jager PL, Yokoyama JS, Dubal DB. Sex-Specific Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease. 2021. PMID: 34424272


  66. Paranjpe MD, Belonwu S, Wang JK, Oskotsky T, Gupta A, Taubes A, Zalocusky KA, Paranjpe I, Glicksberg BS, Huang Y, Sirota M. Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer's Disease. 2021. PMID: 34658838


  67. Pineda S, López de Maturana E, Yu K, Ravoor A, Wood I, Malats N, Sirota M. Tumor-Infiltrating B- and T-Cell Repertoire in Pancreatic Cancer Associated With Host and Tumor Features. 2021. PMID: 34630409


  68. Kim GJ, Mo H, Liu H, Wu Z, Chen S, Zheng J, Zhao X, Nucum D, Shortland J, Peng L, Elepano M, Tang B, Olson S, Paras N, Li H, Renslo AR, Arkin MR, Huang B, Lu B, Sirota M, Guo S. A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons. 2021. PMID: 34550070


  69. Tang A, Oskotsky T, Sirota M. Personalizing routine lab tests with machine learning. 2021. PMID: 34518677


  70. Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, COMET Consortium , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS. 2021. PMID: 34446707


  71. Dana E. Goin, Dimitri Abrahamsson, Miaomiao Wang, June Soo Park, Marina Sirota, Rachel Morello Frosch, Erin DeMicco, Jessica Trowbridge, Laura August, Steven O’Connell, Subhashini Ladella, Tracey J. Woodruff. Using non-targeted screening and silicone wristbands to investigate geographic differences in pollution exposures among maternal and cord sera. 2021. PMID:


  72. Dimitri Abrahamsson, Ting Jiang, Miaomiao Wang, June Soo Park, Rachel Morello Frosch, Marina Sirota, Tracey Woodruff. “Where do these chemicals come from?” Tracing-back chemical exposures to consumer products. 2021. PMID:


  73. Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC. Extrathymic Aire-expressing cells support maternal-fetal tolerance. 2021. PMID: 34272228


  74. Panagopoulos Abrahamsson D, Wang A, Jiang T, Wang M, Siddharth A, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. A Comprehensive Non-targeted Analysis Study of the Prenatal Exposome. 2021. PMID: 34260856


  75. Silvia Pineda, Katharine Yu, Nuria Malats, Marina Sirota. Abstract 2787: Landscape of tumor-infiltrating B and T cell repertoire in pancreatic cancer. 2021. PMID:


  76. Tarca AL, Pataki BÁ, Romero R, Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T, DREAM Preterm Birth Prediction Challenge Consortium , Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC. Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. 2021. PMID: 34195686


  77. 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. Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. 2021. PMID: 34112877


  78. Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M. Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. 2021. PMID: 34177888


  79. R. Benítez Dorta, K. Yu, M. Sirota, N. Malats, S. Pineda. P0467 Characterization of the tumor-infiltrating immune repertoire in Muscle Invasive Bladder Cancer. 2021. PMID:


  80. Yee SW, Vora B, Oskotsky TT, Zou L, Jakobsen S, Enogieru OJ, Koleske ML, Kosti I, Rödin M, Sirota M, Giacomini KM. Drugs in COVID19 clinical trials: Predicting transporter-mediated drug-drug interactions using in vitro assays and real-world data. 2021. PMID: 33759449


  83. Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M. dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit. 2020. PMID: 33313640


  85. Zinter MS, Lindemans C, Versluys B, Mayday MY, Sunshine S, Reyes G, Sirota M, Sapru A, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJJ, DeRisi JL. The Pulmonary Metatranscriptome Prior to Pediatric Hematopoietic Cell Transplantation Identifies Post-HCT Lung Injury. Volume 137 of Issue 12. 2020. PMID: 33512420


  86. Wang A, Abrahamsson DP, Jiang T, Wang M, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. Suspect Screening, Prioritization, and Confirmation of Environmental Chemicals in Maternal-Newborn Pairs from San Francisco. 2021. PMID: 33726493


  87. Enogieru OJ, Koleske ML, Vora B, Ngo H, Yee SW, Chatad D, Sirota M, Giacomini KM. The Effects of Genetic Mutations and Drugs on the Activity of the Thiamine Transporter, SLC19A2. Volume 23 of Issue 2. 2021. PMID: 33649974


  88. Katharine Yu, Amrita Basu, Christina Yau, Denise Wolf, Gillian Hirst, Laura Sit, Nicholas O’Grady, Thelma Brown, Angela DeMichele, Don Berry, Nola Hylton, Doug Yee, Laura Esserman, Laura van 't Veer, Marina Sirota. Abstract PS11-04: Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatment arms and molecular subtypes. 2021. PMID:


  89. Maric I, Oskotsky T, Kosti I, Le B, Wong RJ, Shaw GM, Sirota M, Stevenson DK. Decreased Mortality Rate Among COVID-19 Patients Prescribed Statins: Data From Electronic Health Records in the US. Volume 8. 2021. PMID: 33614688


  90. Sarma A, Christenson S, Mick E, Deiss T, DeVoe C, Pisco A, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha B, Neff N, Tan M, Serpa PH, Ansel KM, Wilson J, Leligdowicz A, Seigel E, Sirota M, DeRisi J, Matthay M, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Calfee C, Langelier C. COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone. 2021. PMID: 33469573


  91. Bunis DG, Bronevetsky Y, Krow-Lucal E, Bhakta NR, Kim CC, Nerella S, Jones N, Mendoza VF, Bryson YJ, Gern JE, Rutishauser RL, Ye CJ, Sirota M, McCune JM, Burt TD. Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. Volume 34 of Issue 1. 2021. PMID: 33406429


  92. Rychkov D, Sur S, Sirota M, Sarwal MM. Molecular Diversity of Clinically Stable Human Kidney Allografts. Volume 4 of Issue 1. 2021. PMID: 33492376


  93. 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. 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. 2020. PMID: 33173861


  94. D. Abrahamsson, A. Wang, T. Jiang, M. Wang, R. Morello-Frosch, J. Park, M. Sirota, T. Woodruff. A method for comprehensively characterizing chemical exposures of pregnant women in San Francisco using non-targeted analysis. 2020. PMID:


  95. Pineda S, Sur S, Sigdel T, Nguyen M, Crespo E, Torija A, Meneghini M, Gomà M, Sirota M, Bestard O, Sarwal MM. Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection. Volume 5 of Issue 10. 2020. PMID: 33102963


  96. Silvia Pineda, Daniel G. Bunis, Idit Kosti, Marina Sirota. Data Integration for Immunology. 2020. PMID:


  97. Stevenson DK, Wong RJ, Aghaeepour N, Maric I, Angst MS, Contrepois K, Darmstadt GL, Druzin ML, Eisenberg ML, Gaudilliere B, Gibbs RS, Gotlib IH, Gould JB, Lee HC, Ling XB, Mayo JA, Moufarrej MN, Quaintance CC, Quake SR, Relman DA, Sirota M, Snyder MP, Sylvester KG, Hao S, Wise PH, Shaw GM, Katz M. Towards personalized medicine in maternal and child health: integrating biologic and social determinants. Volume 89 of Issue 2. 2020. PMID: 32454518


  98. Panagopoulos Abrahamsson D, Park JS, Singh RR, Sirota M, Woodruff TJ. Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards. Volume 60 of Issue 6. 2020. PMID: 32379974


  99. 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. Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. Volume 3. 2020. PMID: 32337372


  100. Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M. Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Volume 11. 2020. PMID: 32322240


  101. Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B, Sirota M, Wiita AP. Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis. Volume 34 of Issue 10. 2020. PMID: 32123307


  102. Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M, Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Criswell LA. Author Correction: A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Volume 11 of Issue 1. 2020. PMID: 32109229


  103. Le BL, Iwatani S, Wong RJ, Stevenson DK, Sirota M. Computational discovery of therapeutic candidates for preventing preterm birth. Volume 5 of Issue 3. 2020. PMID: 32051340


  105. Vora B, Green EAE, Khuri N, Ballgren F, Sirota M, Giacomini KM. Drug-nutrient interactions: discovering prescription drug inhibitors of the thiamine transporter ThTR-2 (SLC19A3). Volume 111 of Issue 1. 2020. PMID: 31764942


  106. Garg A, Fazio S, Duell PB, Baass A, Udata C, Joh T, Riel T, Sirota M, Dettling D, Liang H, Garzone PD, Gumbiner B, Wan H. Molecular Characterization of Familial Hypercholesterolemia in a North American Cohort. 2019. PMID: 31993549


  107. Neely J, Rychkov D, Paranjpe M, Waterfield M, Kim S, Sirota M. Gene Expression Meta-Analysis Reveals Concordance in Gene Activation, Pathway, and Cell-Type Enrichment in Dermatomyositis Target Tissues. Volume 1 of Issue 10. 2019. PMID: 31872188


  108. Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ. Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia. Volume 6 of Issue 1. 2019. PMID: 31615985


  110. Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M, Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Criswell LA. A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Volume 10 of Issue 1. 2019. PMID: 31467281


  111. Ashouri JF, Hsu LY, Yu S, Rychkov D, Chen Y, Cheng DA, Sirota M, Hansen E, Lattanza L, Zikherman J, Weiss A. Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis. Volume 116 of Issue 37. 2019. PMID: 31455730


  112. Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types. Volume 10 of Issue 1. 2019. PMID: 31395879


  113. Paranjpe MD, Taubes A, Sirota M. Insights into Computational Drug Repurposing for Neurodegenerative Disease. Volume 40 of Issue 8. 2019. PMID: 31326236


  115. Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM. Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing. Volume 10 of Issue 1. 2019. PMID: 31015506


  116. Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ. Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets. Volume 2 of Issue 4. 2019. PMID: 30977847


  117. Matt S. Zinter, Caroline A Lindemans, Madeline Y Mayday, Birgitta Versluys, Marina Sirota, Christopher C. Dvorak, Jaap-Jan Boelens, Joseph L DeRisi, Chan Zuckerberg Biohub. Metatranscriptomic Evaluation of Pulmonary Complications after Pediatric Hematopoietic Cell Transplantation Reveals Pathogenic Microbes Linked to Dysregulated Human Immunologic Gene Expression. 2019. PMID:


  118. Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M. A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm. Volume 132. 2019. PMID: 30852461


  119. Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Volume 35 of Issue 1. 2019. PMID: 30561547


  120. Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, Muglia LJ, Ober C, England SK, Macones G, Driscoll D, Parry S, Shaw GM, Stevenson DK, Simpson JL, Thomson E, Butte AJ. Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Volume 5 of Issue 1. 2018. PMID: 30563979


  121. Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, England SK, Parry S, Shaw GM, Simpson JL, Thomson E, Butte AJ. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Volume 5. 2018. PMID: 30398470


  122. Baer RJ, McLemore MR, Adler N, Oltman SP, Chambers BD, Kuppermann M, Pantell MS, Rogers EE, Ryckman KK, Sirota M, Rand L, Jelliffe-Pawlowski LL. Pre-pregnancy or first-trimester risk scoring to identify women at high risk of preterm birth. Volume 231. 2018. PMID: 30439652


  123. Pineda S, Sirota M. Determining Significance in the New Era for P Values. Volume 67 of Issue 5. 2018. PMID: 30052572


  124. Kosti I, Sirota M. Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease. Volume 67 of Issue 4. 2018. PMID: 29746345


  125. Hongtai Huang, Aolin Wang, Rachel Morello-Frosch, Juleen Lam, Marina Sirota, Amy M. Padula, Tracey Woodruff. Cumulative Risk and Impacts Modeling on Environmental/Chemical and Social Stressors. 2018. PMID:


  126. Aolin Wang, Jackie M. Schwartz, Roy Gerona, Thomas Lin, Rachel Morello-Frosch, Marina Sirota, Tracey Woodruff. The Pregnancy Chemisome in Relation to Birth Outcomes and Consumer Product Use: Suspect Screening of Industrial Chemicals. 2018. PMID:


  127. Padula AM, Huang H, Baer RJ, August LM, Jankowska MM, Jellife-Pawlowski LL, Sirota M, Woodruff TJ. Environmental pollution and social factors as contributors to preterm birth in Fresno County. Volume 17 of Issue 1. 2018. PMID: 30157858


  128. Huang H, Woodruff TJ, Baer RJ, Bangia K, August LM, Jellife-Palowski LL, Padula AM, Sirota M. Investigation of association between environmental and socioeconomic factors and preterm birth in California. Volume 121 of Issue Pt 2. 2018. PMID: 30075861


  129. Wang A, Gerona RR, Schwartz JM, Lin T, Sirota M, Morello-Frosch R, Woodruff TJ. A Suspect Screening Method for Characterizing Multiple Chemical Exposures among a Demographically Diverse Population of Pregnant Women in San Francisco. Volume 126 of Issue 7. 2018. PMID: 30044231


  130. Silvia Pineda, Tara K Sigdel, Juliane Liberto, Krishna Roskin, Scott Boyd, Marina Sirota, Minnie M Sarwal. B Cell Immune Repertoire Sequencing Identifies Pre-transplant Rejection Risk. 2018. PMID:


  131. Silvia Pineda, Tara K Sigdel, Jieming Chen, Annette M Jackson, Marina Sirota, Minnie M Sarwal. Pre-Transplant Assessment of AMR Risk by Novel Donor/Recipient Non-HLA Variants. 2018. PMID:


  132. Vora B, Wang A, Kosti I, Huang H, Paranjpe I, Woodruff TJ, MacKenzie T, Sirota M. Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. Volume 9. 2018. PMID: 29867970


  133. Huang H, Wang A, Morello-Frosch R, Lam J, Sirota M, Padula A, Woodruff TJ. Cumulative Risk and Impact Modeling on Environmental Chemical and Social Stressors. Volume 5 of Issue 1. 2018. PMID: 29441463


  134. Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Dudley RA, Yazdany J. Correction to: Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Volume 38 of Issue 2. 2018. PMID: 29273937


  136. Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ. Are minor alleles more likely to be risk alleles? Volume 11 of Issue 1. 2018. PMID: 29351777


  137. Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ, Sirota M. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Volume 8 of Issue 1. 2018. PMID: 29317701


  138. Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N. Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth. Volume 194. 2017. PMID: 29249523


  139. Van Blarcom T, Lindquist K, Melton Z, Cheung WL, Wagstrom C, McDonough D, Valle Oseguera C, Ding S, Rossi A, Potluri S, Sundar P, Pitts S, Sirota M, Galindo Casas M, Yan Y, Jones J, Roe-Zurz Z, Srivatsa Srinivasan S, Zhai W, Pons J, Rajpal A, Chaparro-Riggers J. Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies. Volume 10 of Issue 2. 2017. PMID: 29227213


  140. Pineda S, Sigdel TK, Chen J, Jackson AM, Sirota M, Sarwal MM. Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant. Volume 8. 2017. PMID: 29259604


  141. Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, Chen B, Lee A, Brown AS, Aasi SZ, Hollmig T, Ator MA, Dorsey BD, Ruggeri BR, Zificsak CA, Sirota M, Tang JY, Butte A, Epstein E, Sarin KY, Oro AE. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. Volume 2 of Issue 21. 2017. PMID: 29093271


  142. Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ. Comprehensive analysis of normal adjacent to tumor transcriptomes. Volume 8 of Issue 1. 2017. PMID: 29057876


  143. Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, Bhattacharya S, Sirota M, Musen MA, Butte AJ. Precision annotation of digital samples in NCBI's gene expression omnibus. Volume 4. 2017. PMID: 28925997


  144. Sirota M, Sarwal MM. Transplantomics: Toward Precision Medicine in Transplantation Research. Volume 101 of Issue 8. 2017. PMID: 28121910


  145. Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Yazdany J. Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Volume 37 of Issue 10. 2017. PMID: 28748425


  146. Apeltsin L, Wang S, von Büdingen HC, Sirota M. A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data. Volume 7 of Issue 1. 2017. PMID: 28706301


  147. Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Volume 8. 2017. PMID: 28699633


  148. Elizabeth S Noblin, Aaron C Daugherty, Carl Farrington, Isaac Hakim, Andrew M Radin, Mei-Sze Chua, Mark Rabe, Guy Fernald, Daniel Ford, Marina Sirota, Laura Schaevitz, Andrew A Radin. An Integrative Bioinformatics Approach Identifies In Vivo Validated Drug Candidates with Novel Mechanisms of Action in Rheumatoid Arthritis. 2017. PMID:


  149. Low YS, Daugherty AC, Schroeder EA, Chen W, Seto T, Weber S, Lim M, Hastie T, Mathur M, Desai M, Farrington C, Radin AA, Sirota M, Kenkare P, Thompson CA, Yu PP, Gomez SL, Sledge GW, Kurian AW, Shah NH. Synergistic drug combinations from electronic health records and gene expression. Volume 24 of Issue 3. 2017. PMID: 27940607


  150. Schmajuk G, Tonner C, Trupin L, Li J, Sarkar U, Ludwig D, Shiboski S, Sirota M, Dudley RA, Murray S, Yazdany J. Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab. Volume 96 of Issue 13. 2017. PMID: 28353614


  151. Rebecca J. Baer, Scott P. Oltman, Miriam Kuppermann, Matthew Pantell, Elizabeth E. Rogers, Kelli K. Ryckman, Marina Sirota, Larry Rand, Laura L. Jelliffe-Pawlowski. 313: Development of a first-trimester risk score to predict preterm birth for black women in California. 2017. PMID:


  152. Yeung YA, Foletti D, Deng X, Abdiche Y, Strop P, Glanville J, Pitts S, Lindquist K, Sundar PD, Sirota M, Hasa-Moreno A, Pham A, Melton Witt J, Ni I, Pons J, Shelton D, Rajpal A, Chaparro-Riggers J. Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Volume 7. 2016. PMID: 27857134


  153. Paik H, Chen B, Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. Volume 5 of Issue 11. 2016. PMID: 27860440


  154. Aolin Wang*, Jackie Schwartz, Roy Gerona, Thomas Lin, Marina Sirota, Tracey Woodruff. Novel Chemicals Identified in Pregnant Women in Northern California. 2016. PMID:


  155. Wang A, Padula A, Sirota M, Woodruff TJ. Environmental influences on reproductive health: the importance of chemical exposures. Volume 106 of Issue 4. 2016. PMID: 27513554


  156. Kosti I, Jain N, Aran D, Butte AJ, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Volume 6. 2016. PMID: 27142790


  158. Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. Volume 12 of Issue 4. 2016. PMID: 27115429


  160. Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Volume 6. 2015. PMID: 26634437


  161. Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. Volume 4 of Issue 10. 2015. PMID: 26535158


  162. Marina Sirota, Bin Chen. Fighting disease with data. 2015. PMID:


  163. Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. Volume 8 Suppl 2. 2015. PMID: 26043652


  164. Sirota M, Willemsen G, Sundar P, Pitts SJ, Potluri S, Prifti E, Kennedy S, Ehrlich SD, Neuteboom J, Kluft C, Malone KE, Cox DR, de Geus EJ, Boomsma DI. Effect of genome and environment on metabolic and inflammatory profiles. Volume 10 of Issue 4. 2015. PMID: 25853885


  165. Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. 2015. PMID: 25592598


  167. Palanichamy A, Apeltsin L, Kuo TC, Sirota M, Wang S, Pitts SJ, Sundar PD, Telman D, Zhao LZ, Derstine M, Abounasr A, Hauser SL, von Büdingen HC. Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis. Volume 6 of Issue 248. 2014. PMID: 25100740


  168. von Büdingen HC, Kuo TC, Sirota M, van Belle CJ, Apeltsin L, Glanville J, Cree BA, Gourraud PA, Schwartzburg A, Huerta G, Telman D, Sundar PD, Casey T, Cox DR, Hauser SL. B cell exchange across the blood-brain barrier in multiple sclerosis. Volume 122 of Issue 12. 2012. PMID: 23160197


  169. Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Volume 109 of Issue 18. 2012. PMID: 22499789


  170. Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. Volume 8 of Issue 2. 2012. PMID: 22383865


  171. Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Volume 131 of Issue 3. 2011. PMID: 21858542


  172. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Volume 3 of Issue 96. 2011. PMID: 21849664


  173. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Volume 3 of Issue 96. 2011. PMID: 21849665


  174. Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Volume 7 of Issue 8. 2011. PMID: 21691330


  175. Liu LY, Schaub MA, Sirota M, Butte AJ. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Volume 18 of Issue 2. 2011. PMID: 21618365


  176. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. Volume 6 of Issue 12. 2010. PMID: 21152010


  177. Chen R, Davydov EV, Sirota M, Butte AJ. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. Volume 5 of Issue 10. 2010. PMID: 21042586


  178. Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. Volume 3 of Issue 5. 2010. PMID: 20677029


  179. Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. Volume 5 of Issue 12. 2009. PMID: 20041220


  180. Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Volume 25 of Issue 12. 2009. PMID: 19477990


  181. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, et al. Evolution of genes and genomes on the Drosophila phylogeny. Volume 450 of Issue 7167. 2007. PMID: 17994087


  182. Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Volume 8 of Issue 12. 2007. PMID: 18096039


  183. Persis P. Wadia, Marc Coram, Marina Sirota, David B. Miklos, Atul Butte. Global Assessment of B Cell Alloimmunity Using Human Protein Microarrays. 2007. PMID: