Pre-Prints
Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA,
Sirota M..
Exposure to autoimmune disorders increases Alzheimer’s disease risk in a multi-site electronic health record analysis.
medRxiv. 2024.
10.1101/2024.05.02.24306649
Sur S, Kerwin M, Pineda S, Sansanwal P, Sigdel TK,
Sirota M., Sarwal MM.
Novel Mechanism for Tubular Injury in Nephropathic Cystinosis.
bioRxiv. 2024.
10.1101/2022.05.13.491826
Woldemariam S, Xie F, Roldan A, Roger J, Tang AS, Oskotsky TT, Stevenson DK, Lathi R, Rajkovic A, Aghaeepour N, Eisenberg M,
Sirota M..
Leveraging Electronic Medical Records from Two Hospital Systems Identifies Male Infertility Associated Comorbidities Across Time.
Research Square. 2023.
10.21203/rs.3.rs-3706493/v1
Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T,
Sirota M., Capra JA.
Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.
medRxiv. 2023.
10.1101/2023.11.29.23299216
Kodama L, Woldemariam S, Tang A, Li Y, Oskotsky T, Raphael E,
Sirota M.
Sex-stratified phenotyping of comorbidities associated with an inpatient delirium diagnosis using real world data.
medRxiv. 2023. DOI Name:
10.1101/2023.11.02.23297925
Kouznetsov RC, Belonwu S, Li Y, Andreolett G, Oskotsky TT, Kodama L,
Sirota M.
Identifying Age-Specific Transcriptomic and Metabolomic Changes Induced by
apoE Genotype in Mice.
SSRN. 2023. DOI Name:
10.2139/ssrn.4465497
Roger J, Xie F, Costello J, Tang A, Liu J, Oskotsky T, Woldemariam S, Kosti I, Le B, Snyder M, Giudice L, Torgerson D, Shaw G,
Stevenson D, Rajkovic A, Aghaeepour N, Glymour M, Cakmak H, Lathi R,
Sirota M.
Leveraging electronic health records to identify risk factors for recurrent pregnancy loss across two medical centers: a case-control study.
Research Square. 2023. DOI Name:
10.21203/rs.3.rs-2631220/v1
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
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
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
2024
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.
Physical inactivity exacerbates pathologic inflammatory signalling at the single cell level in patients with systemic lupus. EBioMedicine. 2024
PMID:
39531917
Ji X, Lakuleswaran M, Cowell W, Kahn LG,
Sirota M, Abrahamsson D. Insights into the Chemical Exposome during Pregnancy:
A Non-Targeted Analysis of Preterm and Term Births. Environ Sci Technol. 2024.
PMID:
39526929
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.
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 Sci. 2024.
PMID:
39345789
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.VMAP: Vaginal Microbiome Atlas during Pregnancy. JAMIA Open. 2024.
PMID:
39345789
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.
Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.
ACR Open Rheumatology. 2024. PMID:
39143499
Tang AS, Woldemariam SR, Miramontes S, Norgeot B, Oskotsky TT,
Sirota M.
Harnessing EHR data for health research.
Nat Med. 2024. PMID:
38965433
Binvignat M, Miao B, Wibrand C, Yang M, Rychkov D, Flynn E, Nititham J, Tamaki W, Khan U, Carvidi A, Krueger M,
Niemi E, Sun Y, Fragiadakis GK, Sellam J, Mariotti-Ferrandiz E, Klatzmann D, Gross A, Ye CJ, Butte AJ, Criswell L, Nakamura M,
Sirota M..
Deciphering Cell-types and Gene Signatures Associated with Disease Activity in Rheumatoid Arthritis using Single Cell RNA-sequencing.
JCI Insight. 2023. PMID:
38954480
Miramontes S, Pereda Serras C, Woldemariam SR, Khan U, Li Y, Tang AS, Tsoy E, Oskotsky TT,
Sirota M.
Alzheimer's disease as a women's health challenge: a call for action on integrative precision medicine approaches.
npj Womens Health. 2024. PMID:
38778871
Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Madubata C, Fragiadakis GK, Ye J, Kim S, Gartner ZJ,
Sirota M, Neely J.
Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics.
JCI Insight. 2024. PMID:
38743491.
Oskotsky TT, Yin O, Khan U, Arnaout L,
Sirota M.
Data-driven insights can transform women's reproductive health.
npj Womens Health. 2024. PMID:
38770215.
Oskotsky TT*, Bhoja A*, Bunis D*, Le BL, Kosti I, Li C, Houshdaran S, Sen S, Vallvé-Juanico J, Wang W, Arthurs E,
Mahoney L, Lang L, Gaudilliere B, Stevenson DK, Irwin JC, Giudice LC, McAllister S,
Sirota M.
Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach.
iScience. 2024. PMID:
38510116.
Tang AS,
Sirota M.
Disease insights from medical data using interpretable risk prediction models.
Nature Aging. 2024. PMID:
38383859
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 T, Miller Z, Allen I, Sanders SJ, Baranzini S,
Sirota M.
Leveraging Electronic Medical Records and Knowledge Networks to Predict Disease Onset and Gain Biological Insight Into
Alzheimer's Disease.
Nature Aging. 2024. PMID:
38383858
Amit G, Yanover C, Bivas-Benita M, Girshovitz I, Helbitz T, Sudry T, Bar V, Tang A, Le B, Roger J, Woldemariam S, Kosti I, Oskotsky TT, Akiva P,
Sirota M.
Antidepressant use during pregnancy and the risk of preterm birth – a cohort study.
npj Womens Health. 2024. DOI Name:
10.21203/rs.3.rs-3058509/v1
Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB,
Sirota M, Snyder M, Yatsenko SA, Rajkovic A.
Miscarriage risk assessment: a bioinformatic approach to identifying candidate lethal genes and variants.
Hum Genet. 2024. PMID:
38302665
Yang MM, Lee S, Neely J, Hinchcliff M, Wolters PJ,
Sirota M..
Gene Expression Meta-Analysis Reveals Aging and Cellular Senescence Signatures in Scleroderma-associated Interstitial Lung Disease.
Frontiers in Immunology. 2024.
PMID:
38348044
Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M,
Gillard J, Amar J, Cambriel A, Oskotsky TT, Roldan A, Golob JL, Sirota M, Bonham TA, Sato M, Diop M, Durand X, Angst MS, Stevenson DK,
Aghaeepour N, Montanari A, Gaudillière B.
Discovery of sparse, reliable omic biomarkers with Stabl.
Nat Biotechnol. 2024. PMID:
38168992
2023
Bland GD, Abrahamsson D, Wang M, Zlatnik M, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ.
Exploring applications of non-targeted analysis in the characterization of the prenatal exposome.
Science of The Total Environment. 2023. PMID:
38142008
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, Angelis MD, Bellotti R,
Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G,
Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC,
Sirota M.
Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.
Cell Reports Medicine. 2023. PMID:
38134931
Minot SS, Garb B, Roldan A, Tang A, Oskotsky TT, Rosenthal C, Hoffman NG,
Sirota M, Golob JL.
MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies.
Cell Reports Methods. 2023. PMID:
37939711
Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A,
Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M,
Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA.
Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib
through a Genome-Targeted Approach.
Clinical Cancer Research. 2023. PMID:
37703185
Giudice LC, Oskotsky TT, Falako S, Opoku-Anane J,
Sirota M.
Endometriosis in the era of precision medicine and impact on sexual and reproductive health across the lifespan and in diverse populations.
FASEB J. 2023. PMID:
37641572.
Mortlock S, Houshdaran S, Kosti I, Rahmioglu N, Nezhat C, Vitonis AF, Andrews SV, Grosjean P, Paranjpe M, Horne AW, Jacoby A,
Lager J, Opoku-Anane J, Vo KC, Manvelyan E, Sen S, Ghukasyan Z, Collins F, Santamaria X, Saunders P, Kober K, McRae AF, Terry KL, Vallvé-Juanico J,
Becker C, Rogers PAW, Irwin JC, Zondervan K, Montgomery GW, Missmer S,
Sirota M, Giudice L.
Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function.
Commun Biol. 2023. PMID:
37587191.
Trowbridge J, Abrahamsson D, Bland GD, Jiang T, Wang M, Park JS, Morello-Frosch R,
Sirota M, Lee H, Goin DE, Zlatnik MG, Woodruff TJ.
Extending Nontargeted Discovery of Environmental Chemical Exposures during Pregnancy and Their Association with Pregnancy Complications-A Cross-Sectional Study.
Environ Health Perspect. 2023. PMID:
37466315.
Yu K, Basu A, Yau C, Wolf DM, Goodarzi H, Bandyopadhyay S, Korkola JE, Hirst GL, Asare S, Demichele A,
Hylton N, Yee D, Esserman L, Van't Veer L,
Sirota M.
Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments
and receptor subtypes.
Front. Oncol. Sec. Cancer Molecular Targets and Therapeutics. 2023. PMID:
37384294
Baglaenko Y, Wagner C, Bhoj VG, Brodin P, Gershwin ME, Graham D, Invernizzi P, Kidd KK, Korunsky I, Levy M, Mammen AL, Nizet V, Ramirez-Valle F, Stites EC,
Williams MS, Wilson M, Rose NR, Ladd V,
Sirota M.
Making inroads to precision medicine for the treatment of autoimmune diseases: harnessing genomic studies to better diagnose and treat complex disorders.
Cambridge Prisms: Precision Medicine. 2023.
DOI name:
10.1017/pcm.2023.14
Vora B, Wen A, Yee SW, Trinh K, Azimi M, Green EAE,
Sirota M, Greenberg AS, Newman JW, Giacomini KM.
The Effect of Trimethoprim on Thiamine Absorption: A Transporter-Mediated Drug-Nutrient Interaction.
Clin Pharmacol Ther. 2023.
PMID:
37151050
Sperry MM*, Oskotsky TT*, 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**.
Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased
survival in COVID-19 patients. PLoS Comput Biol. 2023.
PMID:
37146076
Laurent SA, Strauli NB, Eggers EL, Wu H, Michel B, Demuth S, Palanichamy A,
Wilson MR,
Sirota M, Hernandez RD, Cree BAC, Herman AE, von Büdingen HC.
Effect of Ocrelizumab on B- and T-Cell Receptor Repertoire Diversity in Patients With Relapsing
Multiple Sclerosis From the Randomized Phase III OPERA Trial.
Neurol Neuroimmunol Neuroinflamm. 2023
PMID:
37094998
Woldemariam SR, Tang AS, Oskotsky TT, Yaffe K,
Sirota M.
Similarities and differences in Alzheimer's dementia comorbidities in racialized populations identified from electronic medical records.
Commun Med. 2023 PMID:
37031271
Rahmioglu N, Mortlock S, Ghiasi M, Møller PL, Stefansdottir L, Galarneau G, Turman C, Danning R, Law MH, Sapkota Y, Christofidou P, Skarp S,
Giri A, Banasik K, Krassowski M, Lepamets M, Marciniak B, Nõukas 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-Górska A, Słomka M, Smith BH, Smolarz B, Szaflik T, Szyłło 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, Mägi R, Stefansson K, Becker CM, Yurttas-Beim P, Steinthorsdottir V, Nyegaard M,
Missmer SA, Montgomery GW, Morris AP, Zondervan KT.
The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions.
Nat Genet. 2023. PMID:
36914876
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, 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.
Data-driven longitudinal characterization of neonatal health and morbidity. Sci Transl Med. 2023.
PMID:
36791208
Benítez R, Yu K,
Sirota M, Malats N, Pineda S.
Characterization of the tumor-infiltrating immune repertoire in muscle invasive bladder cancer.
Front Immunol. 2023. DOI name:
10.3389/fimmu.2023.986598
Maïer B, Tsai AS, Einhaus JF, Desilles JP, Ho-Tin-Noé B, Gory B,
Sirota M, Leigh R, Lemmens R, Albers G,
Olivot JM, Mazighi M, Gaudillière B.
Neuroimaging is the new "spatial omic": multi-omic approaches to neuro-inflammation and immuno-thrombosis in acute ischemic stroke.
Semin Immunopathol. 2023. PMID:
36786929
2022
Tang A, Woldemariam S, Roger J, Sirota M.
Translational Bioinformatics to Enable Precision Medicine for All:
Elevating Equity across Molecular, Clinical, and Digital Realms.
Yearb Med Inform. 2022. PMID:
36463867
Sigdel TK, Fields PA, Liberto J, Damm I, Kerwin M, Hood J, Towfighi P, Sirota M, Robins HS, Sarwal MM.
Perturbations of the T-cell immune repertoire in kidney transplant rejection.
Front Immunol. 2022 PMID:
36466928
Abraham A, Le B, Kosti I, Straub P, Velez-Edwards DR, Davis LK, Newton JM, Muglia LJ, Rokas A, Bejan CA,
Sirota M, Capra JA.
Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth.
BMC Med. 2022. PMID:
36167547
Goin DE, Abrahamsson D, Wang M, Jiang T, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Zlatnik MG, Woodruff TJ.
Disparities in chemical exposures among pregnant women and neonates by socioeconomic and demographic characteristics:
A nontargeted approach.
Environ Res. 2022. PMID:
36049512
Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier CR, Sirota M.
Physical Activity Associates with Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis.
J Rheumatol. 2022 PMID:
35777820
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.
Front. Immunol. 2022. PMID:
35799782
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.
Scientific Reports. 2022. PMID:
35672357
Abrahamsson D, Siddharth A, Young TM,
Sirota M, Park JS, Martin JW, Woodruff TJ.
In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures.
J Am Soc Mass Spectrom. 2022. PMID:
35649165
Lanata CM, Nititham J, Taylor KE, Solomon O, Chung SA, Blazer A, Trupin L, Katz P, Dall'Era M, Yazdany J,
Sirota M, Barcellos LF, Criswell LA.
The dynamics of methylation of CpG sites associated with SLE subtypes in a longitudinal cohort.
Arthritis Rheumatol. 2022. PMID:
35635730
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.
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.
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. 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. 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. 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. 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. 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. 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 PMID:
34867983
Oskotsky TT*, 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. 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. 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. 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. PMID:
36172600
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. 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.
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.
PMID:
34658838
Tang A, Oskotsky T,
Sirota M.
Personalizing routine lab tests with machine learning.
Nat Med. 2021. 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. 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. 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. 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. 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. 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.
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. 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. 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. 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. 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. 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. PMID:
33614688
Rychkov D, Sur S,
Sirota M, Sarwal MM.
Molecular Diversity of Clinically Stable Human Kidney Allografts.
JAMA Network Open. 2021. 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.
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.
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. 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. 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. 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. PMID:
32123307
Le BL, Iwatani S, Wong RJ, Stevenson DK,
Sirota M.
Computational discovery of therapeutic candidates for preventing preterm birth.
JCI Insight. 2020. 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. 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. 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. 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. 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. 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. 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. 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. PMID:
31395879.
Paranjpe MD, Taubes A,
Sirota M. Insights into Computational Drug Repurposing
for Neurodegenerative Disease. Trends Pharmacol Sci. 2019. 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. 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. 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. 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. 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. 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. 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. 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. PMID:
30075861.
Pineda S,
Sirota M . Determining Significance in the New Era for p-Values.
J Pediatr Gastroenterol Nutr. 2018. 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. 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. PMID:
29867970.
Kosti I,
Sirota M. Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease. J Pediatr Gastroenterol Nutr. 2018. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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.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. 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. 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.PMID:
28353614.
Sirota M, Sarwal M. Transplantomics: Towards Precision Medicine in Transplantation Research. Transplantation, 2017. 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. 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. 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. PMID:
27860440.
Wang A, Padula A,
Sirota M, Woodruff TJ. Environmental influences on reproductive health: the importance of chemical exposures. Fertil Steril, 2016. Review. 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. 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. 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. 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. 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. 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. 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. 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.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. 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.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. 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. 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. PMID:
22499789.
2012
Khatri P,
Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol, 2012. 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. 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. 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. 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. PMID:
21849664.
Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol, 2011. 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. 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. 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. 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. 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. 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. PMID:
18096039.
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature, 2007. PMID:
17994087.