Marina Sirota, PhD
Associate Professor
Pediatrics
School of Medicine

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.

• Gene expression meta-analysis reveals aging and cellular senescence signatures in scleroderma-associated interstitial lung disease.
  Frontiers in immunology 2024 Yang MM, Lee S, Neely J, Hinchcliff M, Wolters PJ, Sirota M
• 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, …
• Predictive Modeling Leveraging Electronic Health Records Identifies Early Predictors of Alzheimer’s Disease.
  Alzheimer's & Dementia 2023 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 …
• Transcriptomic Profiling Across Age, APOE and Sex for Models of Alzheimer’s Disease at a Single Cell Resolution.
  Alzheimer's & Dementia 2023 Yaqiao Li, Yanxia Hao, Seo Yeon Yoon, Brian Grone, Leonardo Ding, Jessica Blumenfeld, Tomiko Oskotsky, Yadong Huang, Marina Sirota
• Exploring applications of non-targeted analysis in the characterization of the prenatal exposome.
  The Science of the total environment 2023 Bland GD, Abrahamsson D, Wang M, Zlatnik MG, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ
• 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, …
• Identification d’une signature en Single Cell transcriptomique associée à l’activité de la maladie dans la polyarthrite rhumatoïde.
  Revue du Rhumatisme 2023 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. …
• 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
• Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.
  bioRxiv : the preprint server for biology 2023 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
• Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics.
  bioRxiv : the preprint server for biology 2023 Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J
• Gene Expression Meta-Analysis Reveals Aging and Cellular Senescence Signatures in Scleroderma-associated Interstitial Lung Disease.
  bioRxiv : the preprint server for biology 2023 Yang MM, Lee S, Neely J, Hinchcliff M, Wolters PJ, Sirota M
• 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
• 10456 Endometriosis or Chronic Pelvic Pain —Disparities in Inpatient Surgical Care on the National Level.
  Journal of Minimally Invasive Gynecology 2023 CN Okorie, A Meghan, S Bejerano, A Rodriguez, M Sirota, T Oskotsky, L Giudice, J Opoku-Anane
• ENDOMETRIAL SUBCELLULAR ALTERATIONS IN ENDOMETRIOSIS IDENTIFIED BY SINGLE-CELL ANALYSIS ACROSS THE MENSTRUAL CYCLE.
  Fertility and Sterility 2023 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
• LEVERAGING ELECTRONIC MEDICAL RECORDS REVEALS COMORBIDITIES SIGNIFICANTLY ASSOCIATED WITH MALE INFERTILITY.
  Fertility and Sterility 2023 Sarah Woldemariam, Feng Xie, Alennie Roldan, Jacquelyn Roger, Alice Tang, Tomiko Oskotsky, Nima Aghaeepour, Michael Eisenberg, Marina Sirota
• MALE FIRSTBORN AND SUBSEQUENT PREGNANCY LOSS – A REAPPRAISAL USING REAL-WORLD DATA.
  Fertility and Sterility 2023 Jacquelyn Roger, Jean Costello, Melissa G. Rosenstein, Aleksandar Rajkovic, Hakan Cakmak, Gary Shaw, David Stevenson, Maria Glymour, Ruth Bunker Lathi, Marina Sirota
• 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
• Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function.
  Communications biology 2023 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,…
• 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].
  The Journal of pediatrics 2023 Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N
• Extending Nontargeted Discovery of Environmental Chemical Exposures during Pregnancy and Their Association with Pregnancy Complications-A Cross-Sectional Study.
  Environmental health perspectives 2023 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
• Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes.
  Frontiers in oncology 2023 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
• Preconception Genetic Carrier Screening for Miscarriage Risk Assessment: A Bioinformatic Approach to Identifying Candidate Lethal Genes and Variants.
  medRxiv : the preprint server for health sciences 2023 Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A
• 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.
  Annals of the Rheumatic Diseases 2023 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.…
• The Effect of Trimethoprim on Thiamine Absorption: A Transporter-Mediated Drug-Nutrient Interaction.
  Clinical pharmacology and therapeutics 2023 Vora B, Wen A, Yee SW, Trinh K, Azimi M, Green EAE, Sirota M, Greenberg AS, Newman JW, Giacomini KM
• Making inroads to precision medicine for the treatment of autoimmune diseases: Harnessing genomic studies to better diagnose and treat complex disorders.
  Cambridge prisms. Precision medicine 2023 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, …
• 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, …
• Effect of Ocrelizumab on B- and T-Cell Receptor Repertoire Diversity in Patients With Relapsing Multiple Sclerosis From the Randomized Phase III OPERA Trial.
  Neurology(R) neuroimmunology & neuroinflammation 2023 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
• 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…
• The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions.
  Nature genetics 2023 Rahmioglu N, Mortlock S, Ghiasi M, Møller 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, …
• 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 …
• Characterization of the tumor-infiltrating immune repertoire in muscle invasive bladder cancer.
  Frontiers in immunology 2023 Benítez R, Yu K, Sirota M, Malats N, Pineda S
• Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities.
  bioRxiv : the preprint server for biology 2023 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 …
• Translational Bioinformatics to Enable Precision Medicine for All: Elevating Equity across Molecular, Clinical, and Digital Realms.
  Yearbook of medical informatics 2022 Tang A, Woldemariam S, Roger J, Sirota M
• Perturbations of the T-cell immune repertoire in kidney transplant rejection.
  Frontiers in immunology 2022 Sigdel TK, Fields PA, Liberto J, Damm I, Kerwin M, Hood J, Towfighi P, Sirota M, Robins HS, Sarwal MM
• Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth.
  BMC medicine 2022 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
• Extending non-targeted exposure discovery of environmental chemical exposures during pregnancy and their association with pregnancy complications.
  ISEE Conference Abstracts 2022 Jessica Trowbridge, Dimitri Abrahamsson, Ting Jiang, Miaomiao Wang, June-Soo Park, Rachel Morello-Frosch, Marina Sirota, Dana Going, Marya Zlatnick, Tracey Woodruff
• Dynamics of Methylation of CpG Sites Associated With Systemic Lupus Erythematosus Subtypes in a Longitudinal Cohort.
  Arthritis & rheumatology (Hoboken, N.J.) 2022 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
• Disparities in chemical exposures among pregnant women and neonates by socioeconomic and demographic characteristics: A nontargeted approach.
  Environmental research 2022 Goin DE, Abrahamsson D, Wang M, Jiang T, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Zlatnik MG, Woodruff TJ
• 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, …
• Physical Activity Associates With Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis.
  The Journal of rheumatology 2022 Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier CR, Sirota M
• Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity.
  Frontiers in immunology 2022 Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota 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
• In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures.
  Journal of the American Society for Mass Spectrometry 2022 Abrahamsson D, Siddharth A, Young TM, Sirota M, Park JS, Martin JW, Woodruff TJ
• 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
• Investigating geographic differences in environmental chemical exposures in maternal and cord sera using non-targeted screening and silicone wristbands in California.
  Journal of exposure science & environmental epidemiology 2022 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
• Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates.
  Science translational medicine 2022 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
• 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 …
• A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires.
  Frontiers in immunology 2022 Yu K, Ravoor A, Malats N, Pineda S, Sirota M
• Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis.
  Frontiers in immunology 2022 Bunis DG, Wang W, Vallvé-Juanico J, Houshdaran S, Sen S, Ben Soltane I, Kosti I, Vo KC, Irwin JC, Giudice LC, Sirota M
• 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
• Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development in Term and Preterm Infants.
  Journal of immunology (Baltimore, Md. : 1950) 2021 Le BL, Sper R, Nielsen SCA, Pineda S, Nguyen QH, Lee JY, Boyd SD, MacKenzie TC, 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 Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease.
  JAMA neurology 2021 Davis EJ, Solsberg CW, White CC, Miñones-Moyano E, Sirota M, Chibnik L, Bennett DA, De Jager PL, Yokoyama JS, Dubal DB
• 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
• Tumor-Infiltrating B- and T-Cell Repertoire in Pancreatic Cancer Associated With Host and Tumor Features.
  Frontiers in immunology 2021 Pineda S, López de Maturana E, Yu K, Ravoor A, Wood I, Malats N, Sirota M
• A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons.
  eLife 2021 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
• Personalizing routine lab tests with machine learning.
  Nature medicine 2021 Tang A, Oskotsky T, Sirota M
• Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS.
  Nature communications 2021 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, …
• Using non-targeted screening and silicone wristbands to investigate geographic differences in pollution exposures among maternal and cord sera.
  ISEE Conference Abstracts 2021 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. …
• “Where do these chemicals come from?” Tracing-back chemical exposures to consumer products.
  ISEE Conference Abstracts 2021 Dimitri Abrahamsson, Ting Jiang, Miaomiao Wang, June Soo Park, Rachel Morello Frosch, Marina Sirota, Tracey Woodruff
• Extrathymic Aire-expressing cells support maternal-fetal tolerance.
  Science immunology 2021 Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC
• A Comprehensive Non-targeted Analysis Study of the Prenatal Exposome.
  Environmental science & technology 2021 Panagopoulos Abrahamsson D, Wang A, Jiang T, Wang M, Siddharth A, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ
• Abstract 2787: Landscape of tumor-infiltrating B and T cell repertoire in pancreatic cancer.
  Cancer Research 2021 Silvia Pineda, Katharine Yu, Nuria Malats, Marina Sirota
• Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth.
  Cell reports. Medicine 2021 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…
• 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
• P0467 Characterization of the tumor-infiltrating immune repertoire in Muscle Invasive Bladder Cancer.
  European Urology 2021 R. Benítez Dorta, K. Yu, M. Sirota, N. Malats, S. Pineda
• 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
• Oxypurinol pharmacokinetics and pharmacodynamics in healthy volunteers: Influence of BCRP Q141K polymorphism and patient characteristics.
  Clinical and translational science 2021 Vora B, Brackman DJ, Zou L, Garcia-Cremades M, Sirota M, Savic RM, Giacomini KM
• Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures.
  Communications biology 2021 Andreoletti G, Lanata CM, Trupin L, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Dall'Era M, Yazdany J, Criswell LA, Sirota M
• dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit.
  Bioinformatics (Oxford, England) 2021 Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M
• Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19.
  Research square 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
• The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury.
  Blood 2021 Zinter MS, Lindemans CA, Versluys BA, Mayday MY, Sunshine S, Reyes G, Sirota M, Sapru A, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL
• Suspect Screening, Prioritization, and Confirmation of Environmental Chemicals in Maternal-Newborn Pairs from San Francisco.
  Environmental science & technology 2021 Wang A, Abrahamsson DP, Jiang T, Wang M, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ
• The Effects of Genetic Mutations and Drugs on the Activity of the Thiamine Transporter, SLC19A2.
  The AAPS journal 2021 Enogieru OJ, Koleske ML, Vora B, Ngo H, Yee SW, Chatad D, Sirota M, Giacomini KM
• Abstract PS11-04: Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatment arms and molecular subtypes.
  Cancer Research 2021 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, …
• 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
• COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone.
  Research square 2021 Sarma A, Christenson SA, Mick E, DeVoe C, Deiss T, Pisco AO, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha BS, Neff N, Tan M, Serpa PH, Ansel KM, Wilson JG, Leligdowicz A, …
• Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells.
  Cell reports 2021 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
• Molecular Diversity of Clinically Stable Human Kidney Allografts.
  JAMA network open 2021 Rychkov D, Sur S, Sirota M, Sarwal MM
• 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,…
• A method for comprehensively characterizing chemical exposures of pregnant women in San Francisco using non-targeted analysis.
  ISEE Conference Abstracts 2020 D. Abrahamsson, A. Wang, T. Jiang, M. Wang, R. Morello-Frosch, J. Park, M. Sirota, T. Woodruff
• Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection.
  Kidney international reports 2020 Pineda S, Sur S, Sigdel T, Nguyen M, Crespo E, Torija A, Meneghini M, Gomà M, Sirota M, Bestard O, Sarwal MM
• Data Integration for Immunology.
  Annual Review of Biomedical Data Science 2020 Silvia Pineda, Daniel G. Bunis, Idit Kosti, Marina Sirota
• Towards personalized medicine in maternal and child health: integrating biologic and social determinants.
  Pediatric research 2020 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, …
• Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards.
  Journal of chemical information and modeling 2020 Panagopoulos Abrahamsson D, Park JS, Singh RR, Sirota M, Woodruff TJ
• 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
• Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth.
  Frontiers in microbiology 2020 Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M
• Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis.
  Leukemia 2020 Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B, Sirota M, Wiita AP
• Author Correction: A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus.
  Nature communications 2020 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
• Computational discovery of therapeutic candidates for preventing preterm birth.
  JCI insight 2020 Le BL, Iwatani S, Wong RJ, Stevenson DK, Sirota M
• Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain.
  Molecular pain 2020 Kober KM, Lee MC, Olshen A, Conley YP, Sirota M, Keiser M, Hammer MJ, Abrams G, Schumacher M, Levine JD, Miaskowski C
• Drug-nutrient interactions: discovering prescription drug inhibitors of the thiamine transporter ThTR-2 (SLC19A3).
  The American journal of clinical nutrition 2020 Vora B, Green EAE, Khuri N, Ballgren F, Sirota M, Giacomini KM
• Molecular Characterization of Familial Hypercholesterolemia in a North American Cohort.
  Journal of the Endocrine Society 2019 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
• Gene Expression Meta-Analysis Reveals Concordance in Gene Activation, Pathway, and Cell-Type Enrichment in Dermatomyositis Target Tissues.
  ACR open rheumatology 2019 Neely J, Rychkov D, Paranjpe M, Waterfield M, Kim S, Sirota M
• Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia.
  Scientific data 2019 Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ
• Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis.
  Clinical Lymphoma Myeloma & Leukemia 2019 Vishesh Sarin, Katharine Yu, Marina Sirota, Arun Wiita
• A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus.
  Nature communications 2019 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
• Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Ashouri JF, Hsu LY, Yu S, Rychkov D, Chen Y, Cheng DA, Sirota M, Hansen E, Lattanza L, Zikherman J, Weiss A
• Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types.
  Nature communications 2019 Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M
• Insights into Computational Drug Repurposing for Neurodegenerative Disease.
  Trends in pharmacological sciences 2019 Paranjpe MD, Taubes A, Sirota M
• ASSOCIATION BETWEEN POLYGENIC RISK SCORE AND INCREASED BRAIN TAU DEPOSITION IN COGNITIVELY NORMAL AND MCI INDIVIDUALS.
  Alzheimer's & Dementia 2019 Manish Paranjpe, Min Liu, Yun Zhou, Marina Sirota
• Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing.
  Nature communications 2019 Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM
• Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets.
  JAMA network open 2019 Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ
• Metatranscriptomic Evaluation of Pulmonary Complications after Pediatric Hematopoietic Cell Transplantation Reveals Pathogenic Microbes Linked to Dysregulated Human Immunologic Gene Expression.
  Biology of Blood and Marrow Transplantation 2019 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
• A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm.
  Journal of reproductive immunology 2019 Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M
• Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.
  Bioinformatics (Oxford, England) 2019 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, …
• Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research.
  Scientific data 2018 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, …
• Enabling precision medicine in neonatology, an integrated repository for preterm birth research.
  Scientific data 2018 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…
• Pre-pregnancy or first-trimester risk scoring to identify women at high risk of preterm birth.
  European journal of obstetrics, gynecology, and reproductive biology 2018 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
• Determining Significance in the New Era for P Values.
  Journal of pediatric gastroenterology and nutrition 2018 Pineda S, Sirota M
• Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease.
  Journal of pediatric gastroenterology and nutrition 2018 Kosti I, Sirota M
• Cumulative Risk and Impacts Modeling on Environmental/Chemical and Social Stressors.
  ISEE Conference Abstracts 2018 Hongtai Huang, Aolin Wang, Rachel Morello-Frosch, Juleen Lam, Marina Sirota, Amy M. Padula, Tracey Woodruff
• The Pregnancy Chemisome in Relation to Birth Outcomes and Consumer Product Use: Suspect Screening of Industrial Chemicals.
  ISEE Conference Abstracts 2018 Aolin Wang, Jackie M. Schwartz, Roy Gerona, Thomas Lin, Rachel Morello-Frosch, Marina Sirota, Tracey Woodruff
• Environmental pollution and social factors as contributors to preterm birth in Fresno County.
  Environmental health : a global access science source 2018 Padula AM, Huang H, Baer RJ, August LM, Jankowska MM, Jellife-Pawlowski LL, Sirota M, Woodruff TJ
• Investigation of association between environmental and socioeconomic factors and preterm birth in California.
  Environment international 2018 Huang H, Woodruff TJ, Baer RJ, Bangia K, August LM, Jellife-Palowski LL, Padula AM, Sirota M
• A Suspect Screening Method for Characterizing Multiple Chemical Exposures among a Demographically Diverse Population of Pregnant Women in San Francisco.
  Environmental health perspectives 2018 Wang A, Gerona RR, Schwartz JM, Lin T, Sirota M, Morello-Frosch R, Woodruff TJ
• B Cell Immune Repertoire Sequencing Identifies Pre-transplant Rejection Risk.
  Transplantation Journal 2018 Silvia Pineda, Tara K Sigdel, Juliane Liberto, Krishna Roskin, Scott Boyd, Marina Sirota, Minnie M Sarwal
• Pre-Transplant Assessment of AMR Risk by Novel Donor/Recipient Non-HLA Variants.
  Transplantation Journal 2018 Silvia Pineda, Tara K Sigdel, Jieming Chen, Annette M Jackson, Marina Sirota, Minnie M Sarwal
• Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth.
  Frontiers in immunology 2018 Vora B, Wang A, Kosti I, Huang H, Paranjpe I, Woodruff TJ, MacKenzie T, Sirota M
• Cumulative Risk and Impact Modeling on Environmental Chemical and Social Stressors.
  Current environmental health reports 2018 Huang H, Wang A, Morello-Frosch R, Lam J, Sirota M, Padula A, Woodruff TJ
• Correction to: Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety.
  Rheumatology international 2018 Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Dudley RA, Yazdany J
• Corrigendum: Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant.
  Frontiers in immunology 2018 Pineda S, Sigdel TK, Chen J, Jackson AM, Sirota M, Sarwal MM
• Are minor alleles more likely to be risk alleles?
  BMC medical genomics 2018 Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ
• A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth.
  Scientific reports 2018 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, …
• Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth.
  The Journal of pediatrics 2017 Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N
• Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies.
  mAbs 2017 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, …
• Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant.
  Frontiers in immunology 2017 Pineda S, Sigdel TK, Chen J, Jackson AM, Sirota M, Sarwal MM
• Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment.
  JCI insight 2017 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 …
• 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
• Precision annotation of digital samples in NCBI's gene expression omnibus.
  Scientific data 2017 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 …
• Transplantomics: Toward Precision Medicine in Transplantation Research.
  Transplantation 2017 Sirota M, Sarwal MM
• Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety.
  Rheumatology international 2017 Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Yazdany J
• A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data.
  Scientific reports 2017 Apeltsin L, Wang S, von Büdingen HC, Sirota M
• Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets.
  Nature communications 2017 Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ
• An Integrative Bioinformatics Approach Identifies In Vivo Validated Drug Candidates with Novel Mechanisms of Action in Rheumatoid Arthritis.
  The Journal of Immunology 2017 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
• Synergistic drug combinations from electronic health records and gene expression.
  Journal of the American Medical Informatics Association : JAMIA 2017 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 …
• Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab.
  Medicine 2017 Schmajuk G, Tonner C, Trupin L, Li J, Sarkar U, Ludwig D, Shiboski S, Sirota M, Dudley RA, Murray S, Yazdany J
• 313: Development of a first-trimester risk score to predict preterm birth for black women in California.
  American Journal of Obstetrics and Gynecology 2017 Rebecca J. Baer, Scott P. Oltman, Miriam Kuppermann, Matthew Pantell, Elizabeth E. Rogers, Kelli K. Ryckman, Marina Sirota, Larry Rand, Laura L. Jelliffe-Pawlowski
• Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire.
  Nature communications 2016 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
• Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses.
  CPT: pharmacometrics & systems pharmacology 2016 Paik H, Chen B, Sirota M, Hadley D, Butte AJ
• Novel Chemicals Identified in Pregnant Women in Northern California.
  ISEE Conference Abstracts 2016 Aolin Wang*, Jackie Schwartz, Roy Gerona, Thomas Lin, Marina Sirota, Tracey Woodruff
• Environmental influences on reproductive health: the importance of chemical exposures.
  Fertility and sterility 2016 Wang A, Padula A, Sirota M, Woodruff TJ
• Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.
  Scientific reports 2016 Kosti I, Jain N, Aran D, Butte AJ, Sirota M
• 251 Identification of alpha-adrenergic agonists as potential therapeutic agents for dermatomyositis through drug-repurposing using public expression datasets.
  Journal of Investigative Dermatology 2016 H.G. Cho, D. Fiorentino, M. Lewis, M. Sirota, K. Sarin
• Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.
  PLoS computational biology 2016 Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB
• Identification of Alpha-Adrenergic Agonists as Potential Therapeutic Agents for Dermatomyositis through Drug-Repurposing Using Public Expression Datasets.
  The Journal of investigative dermatology 2016 Cho HG, Fiorentino D, Lewis M, Sirota M, Sarin KY
• Systematic pan-cancer analysis of tumour purity.
  Nature communications 2015 Aran D, Sirota M, Butte AJ
• Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds.
  CPT: pharmacometrics & systems pharmacology 2015 Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ
• Fighting disease with data.
  XRDS Crossroads The ACM Magazine for Students 2015 Marina Sirota, Bin Chen
• Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research.
  BMC medical genomics 2015 Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ
• Effect of genome and environment on metabolic and inflammatory profiles.
  PloS one 2015 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
• A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2015 Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ
• Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2015 Wu M, Sirota M, Butte AJ, Chen B
• Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis.
  Science translational medicine 2014 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
• B cell exchange across the blood-brain barrier in multiple sclerosis.
  The Journal of clinical investigation 2012 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
• Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes.
  Proceedings of the National Academy of Sciences of the United States of America 2012 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
• Ten years of pathway analysis: current approaches and outstanding challenges.
  PLoS computational biology 2012 Khatri P, Sirota M, Butte AJ
• Sex differences in disease risk from reported genome-wide association study findings.
  Human genetics 2011 Liu LY, Schaub MA, Sirota M, Butte AJ
• Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.
  Science translational medicine 2011 Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ
• Discovery and preclinical validation of drug indications using compendia of public gene expression data.
  Science translational medicine 2011 Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ
• The role of bioinformatics in studying rheumatic and autoimmune disorders.
  Nature reviews. Rheumatology 2011 Sirota M, Butte AJ
• Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association.
  Inflammatory bowel diseases 2011 Liu LY, Schaub MA, Sirota M, Butte AJ
• Identifying a high fraction of the human genome to be under selective constraint using GERP++.
  PLoS computational biology 2010 Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S
• Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association.
  PloS one 2010 Chen R, Davydov EV, Sirota M, Butte AJ
• Drug discovery in a multidimensional world: systems, patterns, and networks.
  Journal of cardiovascular translational research 2010 Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E
• Autoimmune disease classification by inverse association with SNP alleles.
  PLoS genetics 2009 Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ
• A Classifier-based approach to identify genetic similarities between diseases.
  Bioinformatics (Oxford, England) 2009 Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S
• Evolution of genes and genomes on the Drosophila phylogeny.
  Nature 2007 Drosophila 12 Genomes Consortium, 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, …
• CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.
  Genome biology 2007 Gross SS, Do CB, Sirota M, Batzoglou S
• Global Assessment of B Cell Alloimmunity Using Human Protein Microarrays.
  Clinical Immunology 2007 Persis P. Wadia, Marc Coram, Marina Sirota, David B. Miklos, Atul Butte