Pre-Prints
Sperry MM, Oskotsky T, Marić 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.
Different HMGCR-inhibiting statins vary in their association with increased survival in patients with COVID-19.
medRxiv. 2022. DOI Name:
10.1101/2022.04.12.22273802
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 M, Oskotsky T, Marić 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.
AI-Driven Longitudinal Characterization of Neonatal Health and Morbidity. medRxiv. 2022. DOI Name:
10.1101/2022.03.31.22273233
Trowbridge J, Abrahamsson D, Jiang T, Wang M, Park JS, Morello-Frosch R,
Sirota M, Goin DE, Zlatnick M, Woodruff TJ.
Extending non-targeted exposure discovery of environmental chemical exposures during pregnancy and their association with pregnancy complications—a cross-sectional study.
medRxiv. 2022. DOI Name:
10.1101/2022.03.07.22272040v1
Cuyler L, Yu K, Okimoto RA,
Sirota M.
Transcriptional fidelity enhances cancer cell line selection in pediatric cancers.
bioRxiv. 2021. DOI Name:
10.1101/2021.10.01.462682v1
Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye J,
Sirota M.
Multi-modal single-cell sequencing identifies cellular immunophenotypes associated with juvenile dermatomyositis disease activity.
medRxiv. 2021. DOI Name:
10.1101/2021.09.18.21263581v1
Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier C, and
Sirota M.
Physical Activity Moderates Inflammatory Gene Expression in Rheumatoid Arthritis
medRxiv. 2021. DOI Name:
10.1101/2021.08.27.21262729
Andrews S, Yang IJ, Froehlich K, Oskotsky T, and
Sirota M.
Large-scale placenta DNA methylation mega-analysis reveals fetal sex-specific differentially methylated CpG sites and regions.
bioRxiv. 2021. DOI Name:
10.1101/2021.03.04.433985
Sun M, Shankar R, Ko M, Chang CD, Yeh S, Li S, Liu K, Zhou G, Xing J, VanVelsen A, VanVelsen T, Paithankar S, Feng BY,
Young K, Strug M, Turco L, Wang Z, Schadt E, Chen R, Li X, Oskotsky T,
Sirota M, Glicksberg BS, Nadkarni GN, Moeser AJ,
Li L, Kim S, Zhou J, Chen B.
Sex differences in viral entry protein expression, host responses to SARS-CoV-2,
and in vitro responses to sex steroid hormone treatment in COVID-19.
Research Square. 2020. DOI name:
10.21203/rs.3.rs-100914/v2
Abraham A, Le BL, Kosti I, Straub P, Velez Edwards DR, Davis LK, Muglia L, Rokas A, Bejan A,
Sirota M, Capra JA.
Dense phenotyping from electronic health records enables machine-learning-based prediction of preterm birth.
bioRxiv. 2020. DOI name:
10.1101/2020.07.15.20154864
Rahmioglu N, Banasik K, Christofidou P, Danning R, Galarneau G, Giri A, MacGregor S, Mortlock S, Sapkota Y,
Schork AJ, Sobalska-Kwapis M, Stefansdottir L, Turman C, Uimari O, Adachi S, Andrews S, Arnadottir R, Burgdorf KS,
Campbell A, Cheuk CS, Clementi C, Cook J, De IV, DiVasta A, O D, Edwards T, Fontanillas P, Fung JN, Geirsson RT,
Girling J, Harris HR, Holdsworth-Carson S, Houshdaran S, Hu-Seliger T, Jaqrvelin M, Kepka E, Kulig B, Laufer MR,
Law M, Low S, Mangino M, Marciniak B, Matalliotaki C, Matalliotakis M, Murray AD, Nezhat C, Nõukas M, Olsen C,
Padmanabhan S, Paranjpe M, Parfitt D, Peters M, Polak G, Porteous DJ, Romanowicz H, Saare M, Shafrir A, Siewierska-Górska A,
Skarp S, Slomka M, Smith BH, Smolarz B, Szaflik T, Szyllo K, Terry K, Thorleifsson G, Tomassetti C, Vanhie A,
Vincent K, Vitonis A, Werge T, DBDS Genetic Consortium Andersen S, Banasik K, Brunak S, Burgdorf KS, Erikstrup C,
Hansen TF, Hjalgrim H, Jemec G, Jennum P, Nielsen KR, Nyegaard M, Paarup HM, Pedersen OB, Petersen M, Sorensen E,
Ullum H, Werge T, Gudbjartsson D, Stefansson K, Stefansson H, Þorsteinsdottir U, iPSYCH-Broad Consortium Mortensen PB,
Hougaard DM, Borglum AD, the Celmatix Research Team the 23andMe Research Team Chasman DI, D’Hooghe T, Giudice LC,
Goulielmos GN, Hapangama DK, Hayward C, Horne AW, Kamatani Y, Kubo M, Martikainen H, Rogers PA, Saunders PT,
Sirota M, Spector T, Strapagiel D, Tung JY, Whiteman D, Becker CM, Salumets A, Magi R, Kraft P,
Nyegaard M, Nyholt DR, Steinthorsdottir V, Stefansson K, Velez-Edwards DR, Yurttas PB, Missmer SA, Montgomery GW,
Morris AP, Zondervan KT.
Large-scale genome-wide association meta-analysis of endometriosis reveals 13 novel loci and genetically-associated comorbidity with other pain conditions.
bioRxiv. 2018.
DOI name:
10.1101/406967
Daugherty AC, Farrington C, Hakim I, Mujahid S, Noblin ES, Radin AM, Chua MS, Rabe M, Fernald G, Ford D,
Sirota M, Schaevitz L, Radin AA.
Rapid Identification and Validation of Novel Rheumatoid Arthritis Drug Treatments using an Integrative Bioinformatics Platform.
bioRxiv. 2018. DOI name:
10.1101/243998
Publications
2022
Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y,
Sirota M. Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease
Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions.
Frontiers in Aging Neuroscience. 2022.
Pubmed PMID:
35572130
Goin DE, Abrahamsson D, Wang M, Park JS,
Sirota M, Morello-Frosch R, DeMicco E, Trowbridge J, August L, O’Connell S, Ladella S,
Zlatnik MG, Woodruff TJ.
Investigating geographic differences in environmental chemical exposures in maternal and cord sera using non-targeted screening and
silicone wristbands in California.
Journal of Exposure Science & Environmental Epidemiology. 2022.
Pubmed PMID:
35449448
Zinter MS, Versluys AB, Lindemans CA, Mayday MY, Reyes G, Sunshine S, Chan M, Fiorino EK, Cancio M, Prevaes S,
Sirota M,
Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL.
Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates.
Sci Transl Med. 2022. Pubmed PMID:
35263147
Ishiyama K, Arakawa-Hoyt J, Aguilar OA, Damm I, Towfighi P, Sigdel T, Tamaki S, Babdor J, Spitzer MH, Reed EF, Sarwal MM, Lanier LL;
CMV Systems Immunobiology Group. Mass cytometry reveals single-cell kinetics of cytotoxic lymphocyte evolution in CMV-infected
renal transplant patients. Proc Natl Acad Sci USA. 2022. Pubmed PMID:
35181606
Tang AS, Oskotsky T, Havaldar S, Mantyh W, Bicak M, Warly-Solsberg C, Woldemariam S, Zeng B, Hu Z, Oskotsky B, Dubal D, Allen IE,
Glicksberg B, and
Sirota M.
Deep phenotyping of Alzheimer's Disease Leveraging Electronic Medical Records Data Identifies Sex-Specific Clinical Associations.
Nat Commun. 2022. PubMed PMID:
35115528
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*, Lindstaedt B and
Sirota M.
Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students.
PLOS Computational Biology. 2022. PubMed PMID:
35100256
Bunis D, Wang W, Vallve-Juanico J, Houshdaran S, Sen S, Soltane IB, Kosti I, Vo KC, Irwin J, Giudice LC, and
Sirota M.
Whole-tissue deconvolution and scRNAseq analysis identify altered endometrial cellular compositions and
functionality associated with endometriosis.
Front. Immunol. 2022. PubMed PMID:
35069565
Yu K, Ravoor A, Malats N, Pineda S, and
Sirota M.
A pan-cancer analysis of tumor-infiltrating B cell repertoires.
Front. Immunol. 2022. PubMed PMID:
35069569
2021
Ahn R, Schaenman J, Qian Z, Pickering H, Groysberg V, Rossetti M, Llamas M, Hoffmann A, Gjertson D,
Deng M, Bunnapradist S, Reed EF; CMV Systems Immunobiology Group.
Acute and Chronic Changes in Gene Expression After CMV DNAemia in Kidney Transplant Recipients.
Front Immunol. 2021 PubMed PMID:
34867983
Oskotsky T*, Marić I*, Tang A, Oskotsky B, Wong RJ, Aghaeepour N,
Sirota M**, Stevenson DK**.
Mortality Risk Among Patients With COVID-19 Prescribed Selective Serotonin Reuptake Inhibitor Antidepressants.
JAMA Network Open. 2021. PubMed PMID:
34779847
Belonwu S, Li Y, Bunis D, Rao AA, Warly-Solsberg C, Tang A, Fragiadakis G, Dubal D, Oskotsky T, and
Sirota M.
Sex-stratified single-cell RNA-Seq analysis identifies sex-specific and cell type-specific transcriptional responses in
Alzheimer's disease across two brain regions.
Mol Neurobiol. 2021. PubMed PMID:
34669146
Le BL, Sper R, Nielsen SCA, Pineda S, Nguyen, QH, Lee JY, Boyd SD, Mackenzie, TC and
Sirota M.
Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development
in Term and Preterm Infants.
J Immunol. 2021. PubMed PMID:
34654689
Taubes A Nova P, Zalocusky K. A, Kosti I, Bicak M, Zilberter M. Y, Hao Y, Yoon SY, Oskotsky T, Pineda S, Chen B, Jones AEA, Choudhary K, Grone B,
Balestra ME, Chaudhry F, Paranjpe I, De Freitas J, Koutsodendris N, Chen N, Wang C, Chang W, An A, Glicksberg BS, Sirota M, Huang Y.
Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease.
Nature Aging. 2021. DOI:
10.1038/s43587-021-00122-7
Kim GJ, Mo H, Liu H, Wu Z, Chen S, Zheng J, Zhao X, Nucum D, Shortland J, Peng L, Elepano M, Tang B, Olson S, Paras N, Li H, Renslo AR,
Arkin MR, Huang B, Lu B,
Sirota M, Guo S. A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial
restoration in dopamine neurons. Elife. 2021. PubMed PMID:
34550070
Pineda S, López De Maturana E, Yu K, Ravoor A, Wood I, Malats N and
Sirota M.
Tumor-infiltrating B and T cell repertoire in pancreatic cancer associated with host and tumor features. Front Immunol. 2021.
PubMed PMID:
34630409
Paranjpe MD, Belonwu S, Wang JK, Oskotsky T, Gupta A, Taubes A, Zalocusky K, Paranjpe I, Glicksberg BS, Huang Y,
Sirota M.
Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women with Alzheimer's Disease. Front Aging Neurosci. 2021.
PubMed PMID:
34658838
Tang A, Oskotsky T,
Sirota M.
Personalizing routine lab tests with machine learning.
Nat Med. 2021. PubMed PMID:
34518677
Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F,
Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER,
Sirota M, DeRisi JL, Matthay MA; COMET Consortium, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ,
Calfee CS, Langelier CR.
Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS.
Nat Commun. 2021. PubMed PMID:
34446707
Davis EJ, Solsberg CW, White CC, Miñones-Moyano E,
Sirota M, Chibnik L, Bennett DA, De Jager PL, Yokoyama JS, Dubal, DB.
Sex-Specific Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease.
JAMA Neurol. 2021. PubMed PMID:
34424272
Gillis-Buck E, Miller H,
Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC.
Extrathymic Aire-expressing cells support maternal-fetal tolerance.
Sci Immunol. 2021. PubMed PMID:
34272228
Abrahamsson D, Wang A, Jiang T, Wang M, Siddharth A, Morello-Frosch R, Park JS,
Sirota M, Woodruff TJ.
Comprehensive Non-Targeted Analysis Study of the Prenatal Exposome.
Environ Sci Technol. 2021. PubMed PMID:
34260856
Tarca AL, Pataki BA, Romero R,
Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T, The DREAM Preterm Birth Prediction Challenge Consortium, Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC.
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth.
Cell Reports Medicine. 2021. PubMed PMID:
34195686
Le BL*, Andreoletti G*, Oskotsky T*, Vallejo-Gracia A, Rosales R, Yu KZ, Kosti I, Leon KE,
Bunis DG, Li C, Kumar GR, White KM, García-Sastre AE, Ott M,
Sirota M.
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. Scientific Reports. 2021.
PubMed PMID:
34112877
Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF,
Sirota M.
Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis.
Frontiers in Immunology. 2021. PubMed PMID:
34177888
Vora B, Brackman DJ, Zou L, Garcia‐Cremades M,
Sirota M, Savic RM, Giacomini KM.
Oxypurinol pharmacokinetics and pharmacodynamics in healthy volunteers: Influence of BCRP Q141K polymorphism and patient characteristics.
Clinical and Translational Science. 2021. PubMed PMID:
33931953
Andreoletti G, Lanata CM, Trupin L, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Era MD, Yazdany J, Criswell LA,
Sirota M.
Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and
disease-specific expression signatures.
Communications Biology. 2021. PubMed PMID:
33883687
Yee SW, Vora B, Oskotsky T, Zou L, Jakobsen S, Enogieru OJ, Koleske ML, Kosti I, Rödin M,
Sirota M, Giacomini KM.
Drugs in COVID19 clinical trials: Predicting transporter‐mediated drug‐drug interactions using in vitro assays and real‐world data.
Clinical Pharmacology and Therapeutics. 2021. PubMed PMID:
33759449
Wang A, Abrahamsson D, Jiang T, Wang M, Morello-Frosch R, Park JS,
Sirota M, Woodruff TJ.
Suspect Screening, Prioritization, and Confirmation of Environmental Chemicals in Maternal-Newborn Pairs from San Francisco.
Environ Sci Technol. 2021. PubMed PMID:
33726493
Enogieru OJ, Koleske ML, Vora B, Ngo H, Yee SW, Chatad D,
Sirota M, Giacomini KM.
The Effects of Genetic Mutations and Drugs on the Activity of the Thiamine Transporter, SLC19A2.
AAPS. 2021. DOI:
10.1208/s12248-021-00562-4
Marić I*, Oskotsky T*, Kosti I, Le B, Wong RJ, Shaw GM,
Sirota M**, Stevenson DK**.
Decreased Mortality Rate Among COVID-19 Patients Prescribed Statins: Data From Electronic Health Records In The US.
Frontiers in Medicine. 2021. PubMed PMID:
33614688
Rychkov D, Sur S,
Sirota M, Sarwal MM.
Molecular Diversity of Clinically Stable Human Kidney Allografts.
JAMA Network Open. 2021. PubMed PMID:
33492376
Bunis D, Bronevetsky Y, Krow-Lucal E, Bhakta NR, Kim CC, Nerella S, Jones N, Mendoza VF, Bryson YJ, Gern JE, Rutishauser RL, Ye CJ,
Sirota M, McCune JM, Burt TD.
Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Hematopoiesis. Cell Reports. 2021.
Pubmed PMID:
33406429
Zinter MS, Lindemans C, Versluys B, Mayday MY, Sunshine S, Reyes G,
Sirota M, Sapru A, Matthay MA, Kharbanda S, Dvorak CC, Jan Boelens JJ, DeRisi JL.
The Pulmonary Metatranscriptome Prior to Pediatric Hematopoietic Cell Transplantation Identifies Post-HCT Lung Injury.
Blood. 2021. DOI name:
10.1182/blood.2020009246
2020
Bunis DG, Andrews J, Fragiadakis GK, Burt TD,
Sirota M.
dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit.
Bioinformatics. 2020. DOI name:
10.1093/bioinformatics/btaa1011
Pineda S, Sur S, Sigdel T, Nguyen M, Crespo E, Torija A, Meneghini M, Gomà M,
Sirota M, Bestard O, Sarwal MM.
Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection.
Kidney International Reports. 2020. DOI name:
10.1016/j.ekir.2020.07.023
Kober KM, Lee M-C, Olshen A, Conley YP,
Sirota M, Keiser M, Hammer MJ, Abrams G, Schumacher M, Levine JD, Miaskowski C.
Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with
paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain.
Molecular Pain. 2020.
Pubmed PMID:
32586194
Pineda S, Bunis D, Kosti I,
Sirota M.
Data Integration for Immunology.
Annual Review of Biomedical Data Science. 2020. DOI name:
10.1146/annurev-biodatasci-012420-122454
Abrahamsson D, Park JS, Singh R,
Sirota M, Woodruff T.
Applications of Machine Learning to in silico Quantification of Chemicals without Analytical Standards.
Journal of Chemical Information and Modeling. 2020. Pubmed PMID:
32379974
Stevenson DK, Wong RJ, Aghaeepour N, Maric I, Angst MS, Contrepois K, Darmstadt GL, Druzin ML, Eisenberg ML, Gaudilliere B, Gibbs RS, Gotlib IH, Gould JB, Lee HC, Ling XB, Mayo JA, Moufarrej MN,
Quaintance CC, Quake SR, Relman DA,
Sirota M, Snyder MP, Sylvester KG, Hao S, Wise PH, Shaw GM, Katz M.
Towards personalized medicine in maternal and child health: integrating biologic and social determinants.
Pediatr Res. 2020. Pubmed PMID:
32454518
Norgeot B, Muenzen K, Peterson TA, Fan X, Glicksberg B, Schenk G, Rutenberg E, Oskotsky B,
Sirota M, Yazdany J, Schmajuk G, Ludwig D, Goldstein T, Butte AJ.
Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.
Nature Partner Journals Digital Medicine. 2020. DOI name:
10.1038/s41746-020-0258-y
Kosti I, Lyalina S, Pollard KS, Butte AJ,
Sirota M.
Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth.
Frontiers in Microbiology. 2020. PubMed PMID:
32322240
Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B,
Sirota M, Wiita AP .
Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis.
Leukemia. 2020. PubMed PMID:
32123307
Le BL, Iwatani S, Wong RJ, Stevenson DK,
Sirota M.
Computational discovery of therapeutic candidates for preventing preterm birth.
JCI Insight. 2020. PubMed PMID:
32051340
Garg A, Fazio S, Duell PB, Baass A, Udata C, Joh T, Riel T,
Sirota M, Dettling D, Liang H, Garzone PD, Gumbiner B, Wan H.
Molecular Characterization of Familial Hypercholesterolemia in a North American Cohort.
J Endocr Soc. 2019. PubMed PMID:
31993549
2019
Neely J, Rychkov D, Paranjpe M, Waterfield M, Kim S,
Sirota M.
Gene Expression Meta‐Analysis Reveals Concordance in Gene Activation, Pathway, and Cell‐Type Enrichment in Dermatomyositis Target Tissues
ACR Open Rheumatology. PubMed PMID
31872188.
Vora B, Green EAE, Khuri N, Ballgren F,
Sirota M, Giacomini KM. Drug-nutrient
interactions: discovering prescription drug inhibitors of the thiamine
transporter ThTR-2 (SLC19A3). Am J Clin Nutr. 2019. PubMed PMID:
31764942.
Paik H, Kan MJ, Rappoport N, Hadley D,
Sirota M, Chen B, Manber U, Cho SB,
Butte AJ. Tracing diagnosis trajectories over millions of patients reveal an
unexpected risk in schizophrenia. Sci Data. 2019. PubMed PMID:
31615985.
Tsur A, Batsry L, Toussia-Cohen S, Rosenstein MG, Barak O, Brezinov Y,
Yoeli-Ullman R, Sivan E,
Sirota M, Druzin ML, Stevenson DK, Blumenfeld YJ, Aran
D. Development and validation of a machine learning model for prediction of
shoulder dystocia. Ultrasound Obstet Gynecol. 2019. PubMed PMID:
31587401.
Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M,
Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany
J,
Sirota M, Criswell LA. A phenotypic and genomics approach in a multi-ethnic
cohort to subtype systemic lupus erythematosus. Nat Commun. 2019. PubMed PMID:
31467281.
Ashouri JF, Hsu LY, Yu S, Rychkov D, Chen Y, Cheng DA,
Sirota M, Hansen E, Lattanza L, Zikherman J, Weiss A.
Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis.
Proc Natl Acad Sci U S A. 2019. PubMed PMID:
31455730.
Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ,
Goldstein T,
Sirota M. Comprehensive transcriptomic analysis of cell lines as
models of primary tumors across 22 tumor types. Nat Commun. 2019. PubMed PMID:
31395879.
Paranjpe MD, Taubes A,
Sirota M. Insights into Computational Drug Repurposing
for Neurodegenerative Disease. Trends Pharmacol Sci. 2019. PubMed PMID:
31326236.
Pineda S, Sigdel TK, Liberto JM, Vincenti F,
Sirota M, Sarwal MM.
Characterizing pre-transplant and post-transplant kidney rejection risk by B cell
immune repertoire sequencing. Nat Commun. 2019. PubMed PMID:
31015506.
Chen J, Bhattacharya S,
Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser
J, Sarwal MM, Butte AJ. Assessment of Postdonation Outcomes in US Living Kidney
Donors Using Publicly Available Data Sets. JAMA Netw Open. 2019. PubMed PMID:
30977847.
Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ,
Sirota M.
A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm. J Reprod Immunol.
2019. PubMed PMID:
30852461.
BGhaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B,
Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance
C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K,
McNeil L, Tingle M, Wise P, Maric I,
Sirota M, Wyss-Coray T, Winn VD, Druzin ML,
Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G,
Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B,
Aghaeepour N. Multiomics modeling of the immunome, transcriptome, microbiome,
proteome and metabolome adaptations during human pregnancy. Bioinformatics. 2019. PubMed PMID:
30561547.
2018
Baer RJ, McLemore MR, Adler N, Oltman SP, Chambers BD, Kuppermann M, Pantell
MS, Rogers EE, Ryckman KK,
Sirota M, Rand L, Jelliffe-Pawlowski LL. Pre-pregnancy
or first-trimester risk scoring to identify women at high risk of preterm birth.
Eur J Obstet Gynecol Reprod Biol. 2018. PubMed PMID:
30439652.
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 L, Ober C, England
SK, Parry S, Macones G, Driscol D, 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. Sci Data. 2018. PubMed PMID:
30398470.
Padula AM, Huang H, Baer RJ, August LM, Jankowska MM, Jellife-Pawlowski LL,
Sirota M, Woodruff TJ. Environmental pollution and social factors as contributors
to preterm birth in Fresno County. Environ Health. 2018. PubMed PMID:
30157858 .
Huang H, Woodruff TJ, Baer RJ, Bangia K, August LM, Jellife-Palowski LL, Padula AM,
Sirota M.
Investigation of association between environmental and socioeconomic factors and preterm birth in California.
Environ Int. 2018. PubMed PMID:
30075861.
Pineda S,
Sirota M . Determining Significance in the New Era for p-Values.
J Pediatr Gastroenterol Nutr. 2018. PubMed PMID:
30052572.
Wang A, Gerona RR, Schwartz JM, Lin T,
Sirota M , Morello-Frosch R, Woodruff TJ.
A Suspect Screening Method for Characterizing Multiple Chemical Exposures among a Demographically Diverse Population of Pregnant Women in San Francisco.
Environ Health Perspect. 2018. PubMed PMID:
30044231.
Vora B, Wang A, Kosti I, Huang H, Paranjpe I, Woodruff TJ, MacKenzie T,
Sirota M.
Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth.
Front Immunol. 2018. PubMed PMID:
29867970.
Kosti I,
Sirota M. Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease. J Pediatr Gastroenterol Nutr. 2018. PubMed PMID:
29746345.
Huang H, Wang A, Morello-Frosch R, Lam J,
Sirota M, Padula A, Woodruff TJ.
Cumulative Risk and Impact Modeling on Environmental Chemical and Social
Stressors. Curr Environ Health Rep. 2018. PubMed PMID:
29441463.
Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A,
Chen R,
Sirota M, Kodama K, Hadley D, Butte AJ. Are minor alleles more likely to be risk alleles? BMC Med Genomics. PubMed PMID:
29351777.
Rappoport N*, Toung J*, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ,
Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ*,
Sirota M*. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Sci Rep. 2018. PubMed PMID:
29317701.
2017
Pineda S, Sigdel T, Chen J, Jackson A,
Sirota M*, Sarwal M*.
Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant.
Frontiers in Immunology, 2017. PubMed PMID:
29259604.
Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N,
Sirota M, Tishkoff SA, Sondheimer N. Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth. J Pediatr. 2017. PubMed PMID:
29249523.
Van Blarcom T, Lindquist K, Melton Z, Cheung WL, Wagstrom C, McDonough D, Oseguera CV, Ding S, Rossi A, Potluri S, Sundar P, Pitts S,
Sirota M, Casas MG, Yan Y, Jones J, Roe-Zurz Z, Srinivasan SS, Zhai W, Pons J, Rajpal A, Chaparro-Riggers J. Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies. MAbs. 2017. PubMed PMID:
29227213.
Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, Chen B, Lee A, Brown AS, Aasi SZ, Hollmig T, Ator MA, Dorsey BD, Ruggeri BR, Zificsak CA,
Sirota M, Tang JY, Butte A, Epstein E, Sarin KY, Oro AE. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. JCI Insight. 2017. PubMed PMID:
29093271.
Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A,
Sirota M, Butte AJ. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat Commun. 2017. PubMed PMID:
29057876.
Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, Bhattacharya S,
Sirota M, Musen MA, Butte AJ. Precision annotation of digital samples in NCBI's gene expression omnibus. Sci Data. 2017. PubMed PMID:
28925997.
Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S,
Sirota M, Adams Dudley R, Yazdany J. Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Rheumatol Int. 2017.PubMed PMID:
28748425.
Apeltsin L, Wang S, von Büdingen HC,
Sirota M. A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data. Sci Rep. 2017. PubMed PMID:
28706301.
Chen B, Ma L, Paik H,
Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun. 2017. PubMed PMID:
28699633.
Schmajuk G, Tonner C, Trupin L, Li J, Sarkar U, Ludwig D, Shiboski S,
Sirota M, Dudley RA, Murray S, Yazdany J. Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab. Medicine (Baltimore), 2017.PubMed PMID:
28353614.
Sirota M, Sarwal M. Transplantomics: Towards Precision Medicine in Transplantation Research. Transplantation, 2017. PubMed PMID:
28121910.
2016
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 Jr, Kurian AW, Shah NH. Synergistic drug combinations from electronic health records and gene expression. J Am Med Inform Assoc, 2016. PubMed PMID:
27940607.
Yeung YA, Foletti D, Deng X, Abdiche Y, Strop P, Glanville J, Pitts S, Lindquist K, Sundar PD,
Sirota M, Hasa-Moreno A, Pham A, Melton Witt J, Ni I, Pons J, Shelton D, Rajpal A, Chaparro-Riggers J. Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Nat Commun, 2016. PubMed PMID:
27857134.
Paik H, Chen B,
Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol, 2016. PubMed PMID:
27860440.
Wang A, Padula A,
Sirota M, Woodruff TJ. Environmental influences on reproductive health: the importance of chemical exposures. Fertil Steril, 2016. Review. PubMed PMID:
27513554.
Kosti I, Jain N, Aran D, Butte AJ,
Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep, 2016. PubMed PMID:
27142790.
Bagley SC*,
Sirota M*, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol, 2016. PubMed PMID:
27115429.
Cho HG, Fiorentino D, Lewis M,
Sirota M*, Sarin KY*. Identification of alpha-adrenergic agonists as potential therapeutic agents for dermatomyositis through drug-repurposing using public expression datasets. J Invest Dermatol, 2016. PubMed PMID:
26975725.
2015
Aran D,
Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015 Dec 4;6:8971. doi: 10.1038/ncomms9971. PubMed PMID:
26634437.
Chen B, Greenside P, Paik H,
Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. CPT Pharmacometrics Syst Pharmacol, 2015. PubMed PMID:
26535158.
Chen B,
Sirota M, Fan-Minogue H, Hadley D, Butte AJ. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics, 2015. PubMed PMID:
26043652.
Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS; ClinGen. ClinGen--the Clinical Genome Resource. N Engl J Med, 2015. PubMed PMID:
26014595.
Sirota M, Willemsen G, Sundar P, Pitts SJ, Potluri S, Prifti E, Kennedy S, Ehrlich SD, Neuteboom J, Kluft C, Malone KE, Cox DR, de Geus EJ, Boomsma DI. Effect of genome and environment on metabolic and inflammatory profiles. PLoS One, 2015.PubMed PMID:
25853885.
Fan-Minogue H, Chen B, Sikora-Wohlfeld W,
Sirota M, Butte AJ. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pac Symp Biocomput, 2015. PubMed PMID:
25592598.
Wu M,
Sirota M, Butte AJ, Chen B. Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov. Pac Symp Biocomput, 2015.PubMed PMID:
25592569.
2014
Palanichamy A*, Apeltsin L*, Kuo TC*,
Sirota M*, Wang S, Pitts SJ, Sundar PD, Telman D, Zhao LZ,
Derstine M, Abounasr A, Hauser SL, von Büdingen HC.
Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis.
Sci Transl Med, 2014. PubMed PMID:
25100740.
von Büdingen HC, Kuo TC,
Sirota M, van Belle CJ, Apeltsin L, Glanville J, Cree BA, Gourraud PA, Schwartzburg A, Huerta G, Telman D, Sundar PD, Casey T, Cox DR, Hauser SL. B cell exchange across the blood-brain barrier in multiple sclerosis. J Clin Invest, 2012. PubMed PMID:
23160197.
Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J,
Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A, 2012. PubMed PMID:
22499789.
2012
Khatri P,
Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol, 2012. PubMed PMID:
22383865.
Liu LY, Schaub MA,
Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet, 2012. PubMed PMID:
21858542.
Liu LY, Schaub MA,
Sirota M, Butte AJ. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Inflamm Bowel Dis, 2012. PubMed PMID:
21618365.
2011
Sirota M*, Dudley JT*, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med, 2011. PubMed PMID:
21849665.
Dudley JT*,
Sirota M*, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med, 2011. PubMed PMID:
21849664.
Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol, 2011. PubMed PMID:
21691330.
2010
Davydov EV, Goode DL,
Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol, 2010. PubMed PMID:
21152010.
Chen R, Davydov EV,
Sirota M, Butte AJ. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One, 2010. PubMed PMID:
21042586.
Dudley JT, Schadt E,
Sirota M, Butte AJ, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. J Cardiovasc Transl Res, 2010. PubMed PMID:
20677029.
2009
Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet, 2009. PubMed PMID:
20041220.
Schaub MA, Kaplow IM,
Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics, 2009. PubMed PMID:
19477990.
2007
Gross SS, Do CB,
Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol, 2007. PubMed PMID:
18096039.
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature, 2007. PubMed PMID:
17994087.