Marina Sirota, PhD

Professor In Residence
Pediatrics

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.

Publications: 

Insights into the Chemical Exposome during Pregnancy: A Non-Targeted Analysis of Preterm and Term Births.

Environmental science & technology

Ji X, Lakuleswaran M, Cowell W, Kahn LG, Sirota M, Abrahamsson D

Physical inactivity exacerbates pathologic inflammatory signalling at the single cell level in patients with systemic lupus.

EBioMedicine

Patterson SL, Van Phan H, Ye CJ, Lanata C, González SC, Park J, Criswell LA, Barbour KE, Yazdany J, Dall'Era M, Sirota M, Katz P, Langelier CR

A positive ReceptivaDx result for BCL6 does not correlate with abnormal ERA results or decreased expression of receptivity-associated markers: two sides of the endometrial receptivity coin in fertility evaluation and treatment.

F&S science

Huang D, Flynn E, Almonte-Loya A, Davidson B, Chan M, Casillas A, Irwin JC, Fragiadakis GK, Cakmak H, Combes AJ, Cedars MI, Sirota M, Giudice LC

PREVALENCE OF MENTAL HEALTH DIAGNOSES IN A RECURRENT PREGNANCY LOSS (RPL) POPULATION.

Fertility and sterility

Samantha L. Kruger, Sophia Miryam Schüssler-Fiorenza Rose, Brindha Bavan, Aleksandar Rajkovic, Marina Sirota, Ruth B. Lathi

VMAP: Vaginal Microbiome Atlas during Pregnancy.

JAMIA open

Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang AS, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob JL, Sirota M

Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.

ACR open rheumatology

Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM

Sex-stratified analyses of comorbidities associated with an inpatient delirium diagnosis using real world data.

Research square

Sirota M, Kodama L, Woldemariam S, Tang A, Li Y, Kornak J, Allen IE, Raphael E, Oskotsky T

Harnessing EHR data for health research.

Nature medicine

Tang AS, Woldemariam SR, Miramontes S, Norgeot B, Oskotsky TT, Sirota M

Single-cell RNA-seq analysis reveals cell subsets and gene signatures associated with Rheumatoid Arthritis Disease Activity.

JCI insight

Binvignat M, Miao BY, Wibrand C, Yang MM, Rychkov D, Flynn E, Nititham J, Tamaki W, Khan U, Carvidi A, Krueger M, Niemi EC, Sun Y, Fragiadakis GK, Sellam J, Mariotti-Ferrandiz E, Klatzmann D, Gross AJ, Ye CJ, Butte AJ, Criswell LA, Nakamura MC, Sirota M

Alzheimer's disease as a women's health challenge: a call for action on integrative precision medicine approaches.

npj Women's Health

Miramontes S, Pereda Serras C, Woldemariam SR, Khan U, Li Y, Tang AS, Tsoy E, Oskotsky TT, Sirota M

Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics.

JCI insight

Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Madubata C, Fragiadakis GK, Ye CJ, Kim S, Gartner ZJ, Sirota M, Neely J

Data-driven insights can transform women's reproductive health.

npj Women's Health

Oskotsky TT, Yin O, Khan U, Arnaout L, Sirota M

Exposure to autoimmune disorders increases Alzheimer's disease risk in a multi-site electronic health record analysis.

medRxiv : the preprint server for health sciences

Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M

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

iScience

Oskotsky TT, Bhoja A, Bunis D, Le BL, Tang AS, Kosti I, Li C, Houshdaran S, Sen S, Vallvé-Juanico J, Wang W, Arthurs E, Govil A, Mahoney L, Lang L, Gaudilliere B, Stevenson DK, Irwin JC, Giudice LC, McAllister SL, Sirota M

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

Nature Aging

Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, Baranzini S, Sirota M

Antidepressant use during pregnancy and the risk of preterm birth – a cohort study.

npj Women's Health

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

Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach.

Clinical cancer research : an official journal of the American Association for Cancer Research

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

Miscarriage risk assessment: a bioinformatic approach to identifying candidate lethal genes and variants.

Human genetics

Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A

Discovery of sparse, reliable omic biomarkers with Stabl.

Nature biotechnology

Hédou J, Maric I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Amar J, Cambriel A, Oskotsky TT, Roldan A, Golob JL, Sirota M, Bonham TA, Sato M, Diop M, Durand X, Angst MS, Stevenson DK, Aghaeepour N, Montanari A, Gaudillière B

Predictive Modeling Leveraging Electronic Health Records Identifies Early Predictors of Alzheimer’s Disease.

Alzheimer's & Dementia

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

Transcriptomic Profiling Across Age, APOE and Sex for Models of Alzheimer’s Disease at a Single Cell Resolution.

Alzheimer's & Dementia

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

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

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

Identification d’une signature en Single Cell transcriptomique associée à l’activité de la maladie dans la polyarthrite rhumatoïde.

Revue du Rhumatisme

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

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

medRxiv : the preprint server for health sciences

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

Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.

bioRxiv : the preprint server for biology

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

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

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

Minot SS, Garb B, Roldan A, Tang AS, Oskotsky TT, Rosenthal C, Hoffman NG, Sirota M, Golob JL

Sex-stratified phenotyping of comorbidities associated with an inpatient delirium diagnosis using real world data.

medRxiv : the preprint server for health sciences

Kodama L, Woldemariam S, Tang A, Li Y, Oskotsky T, Raphael E, Sirota M

10456 Endometriosis or Chronic Pelvic Pain —Disparities in Inpatient Surgical Care on the National Level.

Journal of minimally invasive gynecology

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

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

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

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

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

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

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

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

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

P-335 Nervous system drugs are predicted as potential repurposing candidates for treatment in endometrial failure.

Human Reproduction

A Parraga-Leo, P Sebastian-Leon, J M Sanchez-Reyes, C Vidal, I Sanchez-Ribas, N Pellicer, J Remohi, M Sirota, P Diaz-Gimeno

Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes.

Frontiers in oncology

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

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

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

The Effect of Trimethoprim on Thiamine Absorption: A Transporter-Mediated Drug-Nutrient Interaction.

Clinical pharmacology and therapeutics

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

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

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

PLoS computational biology

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

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

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

Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee Li YS, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M

VMAP: Vaginal Microbiome Atlas During Pregnancy.

medRxiv : the preprint server for health sciences

Leo AP, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M

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

Research square

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

The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions.

Nature genetics

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

Data-driven longitudinal characterization of neonatal health and morbidity.

Science translational medicine

De Francesco D, Reiss JD, Roger J, Tang AS, Chang AL, Becker M, Phongpreecha T, Espinosa C, Morin S, Berson E, Thuraiappah M, Le BL, Ravindra NG, Payrovnaziri SN, Mataraso S, Kim Y, Xue L, Rosenstein MG, Oskotsky T, Maric I, Gaudilliere B, Carvalho B, Bateman BT, Angst MS, Prince LS, Blumenfeld YJ, Benitz WE, Fuerch JH, Shaw GM, Sylvester KG, Stevenson DK, Sirota M, Aghaeepour N

Characterization of the tumor-infiltrating immune repertoire in muscle invasive bladder cancer.

Frontiers in immunology

Ben?tez 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

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

Perturbations of the T-cell immune repertoire in kidney transplant rejection.

Frontiers in immunology

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

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

Jessica Trowbridge, Dimitri Abrahamsson, Ting Jiang, Miaomiao Wang, June-Soo Park, Rachel Morello-Frosch, Marina Sirota, Dana Going, Marya Zlatnick, Tracey Woodruff

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

Disparities in chemical exposures among pregnant women and neonates by socioeconomic and demographic characteristics: A nontargeted approach.

Environmental research

Goin DE, Abrahamsson D, Wang M, Jiang T, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Zlatnik MG, 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

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

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 WT, Eaneff S, Grant T, Kanungo I, Lindquist K, Myers-Turnbull D, Naing ZZC, Tang A, Vora B, Wang J, Karim I, Swadling C, Yang J, AI4ALL Student Cohort 2020, Lindstaedt B, Sirota M

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

Taubes A, Nova P, Zalocusky KA, Kosti I, Bicak M, Zilberter MY, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Aery Jones EA, Choudhary K, Grone B, Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, Koutsodendris N, Chen N, Wang C, Chang W, An A, Glicksberg BS, Sirota M, Huang Y

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

JAMA network open

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

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

Molecular neurobiology

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

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

Taubes A, Nova P, Zalocusky KA, Kosti I, Bicak M, Zilberter MY, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Jones EAA, Choudhary K, Grone B, Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, Koutsodendris N, Chen N, Wang C, Chang W, An A, Glicksberg BS, Sirota M, Huang Y

Sex-Specific 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.

eLife

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 COVID-19 Clinical Trials: Predicting Transporter-Mediated Drug-Drug Interactions Using In Vitro Assays and Real-World Data.

Clinical pharmacology and therapeutics

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

Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures.

Communications biology

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)

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

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

Research square

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 Hematopoietic Cell Transplantation Identifies Post-HCT Lung Injury.

Blood

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

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 RR, 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.

Leukemia

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, March of Dimes Prematurity Research Centers

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, March of Dimes Prematurity Research Centers

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.

mAbs

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

An Integrative Bioinformatics Approach Identifies In Vivo Validated Drug Candidates with Novel Mechanisms of Action in Rheumatoid Arthritis.

The Journal of Immunology

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

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.

Medicine

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 ClinicalTrials.gov.

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 (S11.003).

Neurology

H. Von Budingen, Tracy Kuo, Marina Sirota, Christopher van Belle, Leonard Apeltsin, Jacob Glanville, Bruce Cree, Pierre-Antoine Gourraud, Amy von Schwartzburg, Gabriella Huerta, Dilduz Telman, Purnima Sundar, Tyler Casey, David Cox, Stephen Hauser

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.

Nature

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, 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, 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

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