Marina Sirota, PhD

Assoc Professor in Residence

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.



Fertility and sterility

Jacquelyn Roger, Alice Tang, Sarah Woldemariam, Tomiko Oskotsky, Timothy Wen, Jay Liu, Idit Kosti, Brian Le, Hakan Cakmak, Michael Snyder, Nima Aghaeepour, Gary Shaw, David Stevenson, Linda C. Giudice, Maria Glymour, Aleksandar Rajkovic, Ruth Bunker Lathi, Marina Sirota

235.4: Analyzing the Impact of T-Cell Receptor Diversity in Acute Kidney Transplant Rejection.


Tara Sigdel, Paul Fields, Juliane Liberto, Izabella Damm, Maggie Kerwin, Jill Hood, Parhom Towfighi, Marina Sirota, Harlan Robins, Minnie Sarwal

340.11: Flow Cytometric Pattern of Gamma Delta TCR Expression Identifies Outcomes in Kidney Transplantation.


Swastika Sur, Akshay Ravoor, Silvia Pineda San Juan, Tara Sigdel, Dmitry Rychkov, Oriol Bestard Matamoros, Marina Sirota, Minnie Sarwal

The dynamics of methylation of CpG sites associated with SLE subtypes in a longitudinal cohort.

Arthritis & rheumatology (Hoboken, N.J.)

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

Physical Activity Associates with Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis.

The Journal of rheumatology

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

Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota M

In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures.

Journal of the American Society for Mass Spectrometry

Abrahamsson D, Siddharth A, Young TM, Sirota M, Park JS, Martin JW, Woodruff TJ

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

medRxiv : the preprint server for health sciences

Sperry MM, Oskotsky T, MariÄ I, Kaushal S, Takeda T, Horvath V, Powers RK, Rodas M, Furlong B, Soong M, Prabhala P, Goyal G, Carlson KE, Wong RJ, Kosti I, Le B, Logue J, Hammond H, Frieman M, Stevenson DK, Ingber DE, Sirota M, Novak R

Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions.

Frontiers in aging neuroscience

Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M

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

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

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

Tang AS, Oskotsky T, Havaldar S, Mantyh WG, Bicak M, Solsberg CW, Woldemariam S, Zeng B, Hu Z, Oskotsky B, Dubal D, Allen IE, Glicksberg BS, Sirota M

Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students.

PLoS computational biology

Oskotsky T, Bajaj R, Burchard J, Cavazos T, Chen I, Connell 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

A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires.

Frontiers in immunology

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

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

Alice Taubes, Phil Nova, Kelly A. Zalocusky, Idit Kosti, Mesude Bicak, Misha Y. Zilberter, Yanxia Hao, Seo Yeon Yoon, Tomiko Oskotsky, Silvia Pineda, Bin Chen, Emily A. Aery Jones, Krishna Choudhary, Brian Grone, Maureen E. Balestra, Fayzan Chaudhry, Ishan Paranjpe, Jessica De Freitas, Nicole Koutsodendris, Nuo Chen, Celine Wang, William Chang, Alice An, Benjamin S. Glicksberg, Marina Sirota, Yadong Huang

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

JAMA network open

Oskotsky T, Maric I, Tang A, Oskotsky B, Wong RJ, Aghaeepour N, Sirota M, Stevenson DK

Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions.

Molecular neurobiology

Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M

Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development in Term and Preterm Infants.

Journal of immunology (Baltimore, Md. : 1950)

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

Alice Taubes, Phil Nova, Kelly A. Zalocusky, Idit Kosti, Mesude Bicak, Misha Y. Zilberter, Yanxia Hao, Seo Yeon Yoon, Tomiko Oskotsky, Silvia Pineda, Bin Chen, Emily A. Aery Jones, Krishna Choudhary, Brian Grone, Maureen E. Balestra, Fayzan Chaudhry, Ishan Paranjpe, Jessica De Freitas, Nicole Koutsodendris, Nuo Chen, Celine Wang, William Chang, Alice An, Benjamin S. Glicksberg, Marina Sirota, Yadong Huang

Sex-Specific Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease.

JAMA neurology

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

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

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.


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

Tang A, Oskotsky T, Sirota M

Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS.

Nature communications

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

Using non-targeted screening and silicone wristbands to investigate geographic differences in pollution exposures among maternal and cord sera.

ISEE Conference Abstracts

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

“Where do these chemicals come from?” Tracing-back chemical exposures to consumer products.

ISEE Conference Abstracts

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

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

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

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

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

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

Scientific reports

Le BL, Andreoletti G, Oskotsky T, Vallejo-Gracia A, Rosales R, Yu K, Kosti I, Leon KE, Bunis DG, Li C, Kumar GR, White KM, García-Sastre A, Ott M, Sirota M

Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis.

Frontiers in immunology

Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M

P0467 Characterization of the tumor-infiltrating immune repertoire in Muscle Invasive Bladder Cancer.

European Urology

R. Benítez Dorta, K. Yu, M. Sirota, N. Malats, S. Pineda

Drugs in COVID19 clinical trials: Predicting transporter-mediated drug-drug interactions using in vitro assays and real-world data.

Clinical pharmacology and therapeutics

Yee SW, Vora B, Oskotsky TT, Zou L, Jakobsen S, Enogieru OJ, Koleske ML, Kosti I, Rödin M, Sirota M, Giacomini KM

The Pulmonary Metatranscriptome Prior to Pediatric Hematopoietic Cell Transplantation Identifies Post-HCT Lung Injury.


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

Suspect Screening, Prioritization, and Confirmation of Environmental Chemicals in Maternal-Newborn Pairs from San Francisco.

Environmental science & technology

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

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

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

Decreased Mortality Rate Among COVID-19 Patients Prescribed Statins: Data From Electronic Health Records in the US.

Frontiers in medicine

Maric I, Oskotsky T, Kosti I, Le B, Wong RJ, Shaw GM, Sirota M, Stevenson DK

COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone.

Research square

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

Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells.

Cell reports

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

Rychkov D, Sur S, Sirota M, Sarwal MM

dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit.

Bioinformatics (Oxford, England)

Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M

Sex differences in viral entry protein expression, host responses to SARS-CoV-2, and in vitro responses to sex steroid hormone treatment in COVID-19.

Research square

Sun M, Shankar R, Ko M, Chang CD, Yeh SJ, Li S, Liu K, Zhou G, Xing J, VanVelsen A, VanVelsen T, Paithankar S, Feng BY, Young K, Strug M, Turco L, Wang Z, Schadt E, Chen R, Li X, Oskotsky T, Sirota M, Glicksberg BS, Nadkarni GN, Moeser AJ, Li L, Kim S, Zhou J, Chen B

A method for comprehensively characterizing chemical exposures of pregnant women in San Francisco using non-targeted analysis.

ISEE Conference Abstracts

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

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

Silvia Pineda, Daniel G. Bunis, Idit Kosti, Marina Sirota

Towards personalized medicine in maternal and child health: integrating biologic and social determinants.

Pediatric Research

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

Applications of Machine Learning to in silico Quantification of Chemicals without Analytical Standards.

Journal of chemical information and modeling

Panagopoulos Abrahamsson D, Park JS, Singh R, Sirota M, Woodruff TJ

Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.

NPJ digital medicine

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

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.


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

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

Le BL, Iwatani S, Wong RJ, Stevenson DK, Sirota M

Drug-nutrient interactions: discovering prescription drug inhibitors of the thiamine transporter ThTR-2 (SLC19A3).

The American journal of clinical nutrition

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

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

Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia.

Scientific data

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

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

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

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

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

Paranjpe MD, Taubes A, Sirota M

Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing.

Nature communications

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

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

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

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)

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

Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research.

Scientific data

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

Enabling precision medicine in neonatology, an integrated repository for preterm birth research.

Scientific data

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

Pre-pregnancy or first-trimester risk scoring to identify women at high risk of preterm birth.

European journal of obstetrics, gynecology, and reproductive biology

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

Pineda S, Sirota M

Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease.

Journal of pediatric gastroenterology and nutrition

Kosti I, Sirota M

Cumulative Risk and Impacts Modeling on Environmental/Chemical and Social Stressors.

ISEE Conference Abstracts

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

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

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

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

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

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

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

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

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

Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Dudley RA, Yazdany J

Are minor alleles more likely to be risk alleles?

BMC medical genomics

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

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

Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth.

The Journal of pediatrics

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.


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

Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment.

JCI insight

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

Comprehensive analysis of normal adjacent to tumor transcriptomes.

Nature communications

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

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

Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety.

Rheumatology international

Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Yazdany J

Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets.

Nature communications

Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ

Synergistic drug combinations from electronic health records and gene expression.

Journal of the American Medical Informatics Association : JAMIA

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

Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab.


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

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

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

Paik H, Chen B, Sirota M, Hadley D, Butte AJ

Novel Chemicals Identified in Pregnant Women in Northern California.

ISEE Conference Abstracts

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

Wang A, Padula A, Sirota M, Woodruff TJ

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.

Scientific reports

Kosti I, Jain N, Aran D, Butte AJ, Sirota M

Systematic pan-cancer analysis of tumour purity.

Nature communications

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

Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ

Fighting disease with data.

XRDS Crossroads The ACM Magazine for Students

Marina Sirota, Bin Chen

Effect of genome and environment on metabolic and inflammatory profiles.

PloS one

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

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

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

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

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

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

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

Khatri P, Sirota M, Butte AJ

Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.

Science translational medicine

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

Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

PLoS computational biology

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S

Drug discovery in a multidimensional world: systems, patterns, and networks.

Journal of cardiovascular translational research

Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E

Autoimmune disease classification by inverse association with SNP alleles.

PLoS genetics

Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ

A Classifier-based approach to identify genetic similarities between diseases.

Bioinformatics (Oxford, England)

Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S

Evolution of genes and genomes on the Drosophila phylogeny.


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

Global Assessment of B Cell Alloimmunity Using Human Protein Microarrays.

Clinical Immunology

Persis P. Wadia, Marc Coram, Marina Sirota, David B. Miklos, Atul Butte