Marina Sirota, PhD

Title(s)Associate Professor, Pediatrics
SchoolSchool of Medicine
Address490 Illinois Street, #21U
San Francisco CA 94158
ORCID ORCID Icon0000-0002-7246-6083 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Stanford UniversityB.S.2006Biomedical Computation
    Stanford UniversityM.S.2006Biomedical Informatics
    Stanford UniversityPh.D.2010Biomedical Informatics

    Collapse Overview 
    Collapse Overview
    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.
    Collapse In The News

    Collapse Research 
    Collapse Research Activities and Funding
    UCSF Stanford Endometriosis Center for Discovery, Innovation, Training and Community Engagement
    NIH P01HD106414Aug 1, 2021 - Jul 31, 2026
    Role: Co-Principal Investigator
    Trio Analysis of Recurrent Pregnancy Loss Integrated Bioinformatics Genomics Study (TRIOS)
    NIH R01HD105256May 15, 2021 - Mar 31, 2026
    Role: Co-Principal Investigator
    An Integrative Multi-Omics Approach to Elucidate Sex-Specific Differences in Alzheimers Disease
    NIH R01AG060393Sep 1, 2018 - May 31, 2023
    Role: Principal Investigator
    ApoE Genotype-Directed Drug Repositioning and Combination Therapy for Alzheimer's Disease
    NIH R01AG057683Sep 15, 2017 - May 31, 2022
    Role: Co-Principal Investigator
    A Precision Medicine Approach to Detect Dysbiosis and Immune Activation in Preterm Labor
    Burroughs Wellcome Fund Jul 1, 2017 - Jul 1, 2020
    Role: Co-Principal Investigator
    Discovery of novel environmental chemicals in a diverse population of maternal-infant pairs
    NIH R01ES027051Sep 30, 2016 - Aug 31, 2021
    Role: Co-Investigator
    Integrative Analysis of Genomic, Epigenomic and Phenotypic Data for Disease Stratification of Endometriosis
    NIH R01HD089511Sep 26, 2016 - Apr 30, 2021
    Role: Co-Investigator
    RESOURCE-BASED CENTER FOR THE ADVANCEMENT OF PRECISION MEDICINE IN RHEUMATOLOGY
    NIH P30AR070155Sep 21, 2016 - Aug 31, 2026
    Role: Co-Investigator, Bioinformatics Core Director
    Elucidating the Role of the Genetic and Environmental Determinants of Preterm Birth Using Integrative Computational Approaches
    NIH K01LM012381Aug 1, 2016 - Oct 31, 2019
    Role: Principal Investigator
    Towards an Integrated Data Repository for Preterm Birth
    March of Dimes 60982053-50185
    Role: Co-Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Data-driven insights can transform women’s reproductive health. npj Women's Health. 2024 May 14; 2(1):14. Oskotsky OT, Yin YO, Khan KU, Arnaout AL, Sirota SM. .
      View in: Publisher Site   Mentions:
    2. Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach. iScience. 2024 Apr 19; 27(4):109388. 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. PMID: 38510116; PMCID: PMC10952035.
      View in: PubMed   Mentions:
    3. Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights. Nat Aging. 2024 Mar; 4(3):379-395. 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. PMID: 38383858; PMCID: PMC10950787.
      View in: PubMed   Mentions: Translation:Humans
    4. Antidepressant use during pregnancy and the risk of preterm birth – a cohort study. npj Women's Health. 2024 Feb 20; 2(1):5. Amit AG, Yanover YC, Bivas-Benita BM, Girshovitz GI, Helbitz HT, Sudry ST, Bar BV, Tang TA, Le LB, Roger RJ, Woldemariam WS, Kosti KI, Oskotsky OT, Akiva AP, Sirota SM. .
      View in: Publisher Site   Mentions:
    5. Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach. Clin Cancer Res. 2024 02 16; 30(4):849-864. 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. PMID: 37703185; PMCID: PMC10870121.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    6. Miscarriage risk assessment: a bioinformatic approach to identifying candidate lethal genes and variants. Hum Genet. 2024 Feb; 143(2):185-195. Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A. PMID: 38302665; PMCID: PMC10881709.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    7. Gene expression meta-analysis reveals aging and cellular senescence signatures in scleroderma-associated interstitial lung disease. Front Immunol. 2024; 15:1326922. Yang MM, Lee S, Neely J, Hinchcliff M, Wolters PJ, Sirota M. PMID: 38348044; PMCID: PMC10859856.
      View in: PubMed   Mentions:    Fields:    
    8. Discovery of sparse, reliable omic biomarkers with Stabl. Nat Biotechnol. 2024 Jan 02. 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. PMID: 38168992.
      View in: PubMed   Mentions: 2     Fields:    
    9. Predictive Modeling Leveraging Electronic Health Records Identifies Early Predictors of Alzheimer’s Disease. Alzheimer's & Dementia. 2023 Dec 25; 19(S15). Tang TA, Rankin RK, Cerano CG, Miramontes MS, Mills MH, Oskotsky OT, Zeng ZB, Nelson NC, Soman SK, Woldemariam WS, Li LY, Lee LA, Miller MZ, Allen AI, Sanders SS, Baranzini BS, Sirota SM. .
      View in: Publisher Site   Mentions:
    10. Transcriptomic Profiling Across Age, APOE and Sex for Models of Alzheimer’s Disease at a Single Cell Resolution. Alzheimer's & Dementia. 2023 Dec 25; 19(S13). Li LY, Hao HY, Yoon YS, Grone GB, Ding DL, Blumenfeld BJ, Oskotsky OT, Huang HY, Sirota SM. .
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    11. Exploring applications of non-targeted analysis in the characterization of the prenatal exposome. Sci Total Environ. 2024 Feb 20; 912:169458. Bland GD, Abrahamsson D, Wang M, Zlatnik MG, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. PMID: 38142008; PMCID: PMC10947484.
      View in: PubMed   Mentions:    Fields:    Translation:HumansPHPublic Health
    12. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Rep Med. 2024 01 16; 5(1):101350. 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. PMID: 38134931; PMCID: PMC10829755.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    13. Identification d’une signature en Single Cell transcriptomique associée à l’activité de la maladie dans la polyarthrite rhumatoïde. Revue du Rhumatisme. 2023 Dec 1; 90:a26. Binvignat BM, Miao MB, Wibrand WC, Yang YM, Rychkov RD, Flynn FE, Nititham NJ, Tamaki TW, Khan KU, Carvidi CA, Krueger KM, Niemi NE, Sun SY, Fragiadakis FG, Sellam SJ, Mariotti-Ferrandiz ME, Klatzmann KD, Gross GA, Ye YJ, Butte BA, Criswell CL, Nakamura NM, Sirota SM. .
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    14. Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort. medRxiv. 2023 Nov 30. Costello JM, Takasuka H, Roger J, Yin O, Tang A, Oskotsky T, Sirota M, Capra JA. PMID: 38077057; PMCID: PMC10705634.
      View in: PubMed   Mentions:
    15. Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. bioRxiv. 2023 Nov 28. 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. PMID: 38076936; PMCID: PMC10705239.
      View in: PubMed   Mentions:
    16. Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics. bioRxiv. 2023 Nov 10. Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J. PMID: 37986917; PMCID: PMC10659396.
      View in: PubMed   Mentions:
    17. MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies. Cell Rep Methods. 2023 Nov 20; 3(11):100639. Minot SS, Garb B, Roldan A, Tang AS, Oskotsky TT, Rosenthal C, Hoffman NG, Sirota M, Golob JL. PMID: 37939711; PMCID: PMC10694490.
      View in: PubMed   Mentions: 2  
    18. Gene Expression Meta-Analysis Reveals Aging and Cellular Senescence Signatures in Scleroderma-associated Interstitial Lung Disease. bioRxiv. 2023 Nov 07. Yang MM, Lee S, Neely J, Hinchcliff M, Wolters PJ, Sirota M. PMID: 37986995; PMCID: PMC10659335.
      View in: PubMed   Mentions:
    19. Sex-stratified phenotyping of comorbidities associated with an inpatient delirium diagnosis using real world data. medRxiv. 2023 Nov 04. Kodama L, Woldemariam S, Tang A, Li Y, Oskotsky T, Raphael E, Sirota M. PMID: 37961487; PMCID: PMC10635265.
      View in: PubMed   Mentions:
    20. 10456 Endometriosis or Chronic Pelvic Pain —Disparities in Inpatient Surgical Care on the National Level. Journal of Minimally Invasive Gynecology. 2023 Nov 1; 30(11):s123. Okorie OC, Meghan MA, Bejerano BS, Rodriguez RA, Sirota SM, Oskotsky OT, Giudice GL, Opoku-Anane OJ. .
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    21. ENDOMETRIAL SUBCELLULAR ALTERATIONS IN ENDOMETRIOSIS IDENTIFIED BY SINGLE-CELL ANALYSIS ACROSS THE MENSTRUAL CYCLE. Fertility and Sterility. 2023 Oct 1; 120(4):e61-e62. Almonte AA, Wang WW, Flynn FE, Houshdaran HS, Vallvé-Juanico VJ, Irwin IJ, Kushnoor KD, Combes CA, Fragiadakis FG, Sirota SM, Giudice GL. .
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    22. MALE FIRSTBORN AND SUBSEQUENT PREGNANCY LOSS – A REAPPRAISAL USING REAL-WORLD DATA. Fertility and Sterility. 2023 Oct 1; 120(4):e81-e82. Roger RJ, Costello CJ, Rosenstein RM, Rajkovic RA, Cakmak CH, Shaw SG, Stevenson SD, Glymour GM, Lathi LR, Sirota SM. .
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    23. LEVERAGING ELECTRONIC MEDICAL RECORDS REVEALS COMORBIDITIES SIGNIFICANTLY ASSOCIATED WITH MALE INFERTILITY. Fertility and Sterility. 2023 Oct 1; 120(4):e53-e54. Woldemariam WS, Xie XF, Roldan RA, Roger RJ, Tang TA, Oskotsky OT, Aghaeepour AN, Eisenberg EM, Sirota SM. .
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    24. Endometriosis in the era of precision medicine and impact on sexual and reproductive health across the lifespan and in diverse populations. FASEB J. 2023 09; 37(9):e23130. Giudice LC, Oskotsky TT, Falako S, Opoku-Anane J, Sirota M. PMID: 37641572; PMCID: PMC10503213.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    25. Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function. Commun Biol. 2023 08 16; 6(1):780. 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. PMID: 37587191; PMCID: PMC10432557.
      View in: PubMed   Mentions: 2  Translation:HumansCells
    26. 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]. J Pediatr. 2023 Oct; 261:113345. Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N. PMID: 37495478.
      View in: PubMed   Mentions:    Fields:    
    27. Extending Nontargeted Discovery of Environmental Chemical Exposures during Pregnancy and Their Association with Pregnancy Complications-A Cross-Sectional Study. Environ Health Perspect. 2023 07; 131(7):77003. 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. PMID: 37466315; PMCID: PMC10355149.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    28. Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes. Front Oncol. 2023; 13:1192208. 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. PMID: 37384294; PMCID: PMC10294228.
      View in: PubMed   Mentions:
    29. Preconception Genetic Carrier Screening for Miscarriage Risk Assessment: A Bioinformatic Approach to Identifying Candidate Lethal Genes and Variants. medRxiv. 2023 Jun 03. Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A. PMID: 37398382; PMCID: PMC10312874.
      View in: PubMed   Mentions:
    30. POS1044 SINGLE CELL TRANSCRIPTOMICS ANALYSIS OF BLOOD IMMUNE CELLS IDENTIFIES GENE SIGNATURES AND CELL SUBSETS ASSOCIATED WITH DISEASE ACTIVITY IN A DIVERSE POPULATION OF RHEUMATOID ARTHRITIS PATIENTS. Annals of the Rheumatic Diseases. 2023 May 30; 82(Suppl 1):839.2-840. Binvignat BM, Miao MB, Wibrand WC, Yang YM, Rychkov RD, Flynn FE, Nititham NJ, Carvidi CA, Krueger KM, Niemi NE, Sun SY, Mariotti-Ferrandiz ME, Sellam SJ, Ye YC, Butte BA, Criswell CL, Nakamura NM, Sirota SM. .
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    31. The Effect of Trimethoprim on Thiamine Absorption: A Transporter-Mediated Drug-Nutrient Interaction. Clin Pharmacol Ther. 2023 08; 114(2):381-392. Vora B, Wen A, Yee SW, Trinh K, Azimi M, Green EAE, Sirota M, Greenberg AS, Newman JW, Giacomini KM. PMID: 37151050.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    32. Making inroads to precision medicine for the treatment of autoimmune diseases: Harnessing genomic studies to better diagnose and treat complex disorders. Camb Prism Precis Med. 2023; 1:e25. 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. PMID: 38550937; PMCID: PMC10953750.
      View in: PubMed   Mentions:
    33. 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 05; 19(5):e1011050. 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. PMID: 37146076; PMCID: PMC10191356.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    34. 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 07; 10(4). 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. PMID: 37094998; PMCID: PMC10136682.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCTClinical Trials
    35. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv. 2023 Apr 11. 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, 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 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. PMID: 36945505; PMCID: PMC10029035.
      View in: PubMed   Mentions:
    36. Similarities and differences in Alzheimer's dementia comorbidities in racialized populations identified from electronic medical records. Commun Med (Lond). 2023 Apr 08; 3(1):50. Woldemariam SR, Tang AS, Oskotsky TT, Yaffe K, Sirota M. PMID: 37031271; PMCID: PMC10082816.
      View in: PubMed   Mentions:
    37. VMAP: Vaginal Microbiome Atlas During Pregnancy. medRxiv. 2023 Apr 05. Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M. PMID: 36993193; PMCID: PMC10055588.
      View in: PubMed   Mentions:
    38. Leveraging electronic health records to identify risk factors for recurrent pregnancy loss across two medical centers: a case-control study. Res Sq. 2023 Mar 31. Roger J, Xie F, Costello J, Tang A, Liu J, Oskotsky T, Woldemariam S, Kosti I, Le B, Snyder MP, Giudice LC, Torgerson D, Shaw GM, Stevenson DK, Rajkovic A, Glymour MM, Aghaeepour N, Cakmak H, Lathi RB, Sirota M. PMID: 36993325; PMCID: PMC10055527.
      View in: PubMed   Mentions:
    39. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions. Nat Genet. 2023 03; 55(3):423-436. 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, 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, Mägi R, Stefansson K, Becker CM, Yurttas-Beim P, Steinthorsdottir V, Nyegaard M, Missmer SA, Montgomery GW, Morris AP, Zondervan KT. PMID: 36914876; PMCID: PMC10042257.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    40. Data-driven longitudinal characterization of neonatal health and morbidity. Sci Transl Med. 2023 02 15; 15(683):eadc9854. 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. PMID: 36791208; PMCID: PMC10197092.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    41. Characterization of the tumor-infiltrating immune repertoire in muscle invasive bladder cancer. Front Immunol. 2023; 14:986598. Benítez R, Yu K, Sirota M, Malats N, Pineda S. PMID: 36817478; PMCID: PMC9936234.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    42. Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities. bioRxiv. 2023 Jan 20. 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. PMID: 36711882; PMCID: PMC9882347.
      View in: PubMed   Mentions:
    43. Translational Bioinformatics to Enable Precision Medicine for All: Elevating Equity across Molecular, Clinical, and Digital Realms. Yearb Med Inform. 2022 Aug; 31(1):106-115. Tang A, Woldemariam S, Roger J, Sirota M. PMID: 36463867; PMCID: PMC9719766.
      View in: PubMed   Mentions: 2     Fields:    
    44. Perturbations of the T-cell immune repertoire in kidney transplant rejection. Front Immunol. 2022; 13:1012042. Sigdel TK, Fields PA, Liberto J, Damm I, Kerwin M, Hood J, Towfighi P, Sirota M, Robins HS, Sarwal MM. PMID: 36466928; PMCID: PMC9709472.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    45. Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth. BMC Med. 2022 09 28; 20(1):333. 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. PMID: 36167547; PMCID: PMC9516830.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    46. Extending non-targeted exposure discovery of environmental chemical exposures during pregnancy and their association with pregnancy complications. ISEE Conference Abstracts. 2022 Sep 18; 2022(1). Trowbridge TJ, Abrahamsson AD, Jiang JT, Wang WM, Park PJ, Morello-Frosch MR, Sirota SM, Going GD, Zlatnick ZM, Woodruff WT. .
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    47. Dynamics of Methylation of CpG Sites Associated With Systemic Lupus Erythematosus Subtypes in a Longitudinal Cohort. Arthritis Rheumatol. 2022 10; 74(10):1676-1686. 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. PMID: 35635730; PMCID: PMC9529797.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    48. Disparities in chemical exposures among pregnant women and neonates by socioeconomic and demographic characteristics: A nontargeted approach. Environ Res. 2022 12; 215(Pt 1):114158. Goin DE, Abrahamsson D, Wang M, Jiang T, Park JS, Sirota M, Morello-Frosch R, DeMicco E, Zlatnik MG, Woodruff TJ. PMID: 36049512; PMCID: PMC10016233.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    49. Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients. medRxiv. 2022 Jul 22. Sperry MM, Oskotsky T, MariÄ I, Kaushal S, Takeda T, Horvath V, Powers RK, Rodas M, Furlong B, Soong M, Prabhala P, Goyal G, Carlson KE, Wong RJ, Kosti I, Le BL, Logue J, Hammond H, Frieman M, Stevenson DK, Ingber DE, Sirota M, Novak R. PMID: 35441166; PMCID: PMC9016655.
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    50. Physical Activity Associates With Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis. J Rheumatol. 2022 12; 49(12):1320-1327. Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier CR, Sirota M. PMID: 35777820; PMCID: PMC9722583.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    51. Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity. Front Immunol. 2022; 13:902232. Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota M. PMID: 35799782; PMCID: PMC9254730.
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    52. Large-scale placenta DNA methylation integrated analysis reveals fetal sex-specific differentially methylated CpG sites and regions. Sci Rep. 2022 06 07; 12(1):9396. Andrews SV, Yang IJ, Froehlich K, Oskotsky T, Sirota M. PMID: 35672357; PMCID: PMC9174475.
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    53. In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures. J Am Soc Mass Spectrom. 2022 Jul 06; 33(7):1134-1147. Abrahamsson D, Siddharth A, Young TM, Sirota M, Park JS, Martin JW, Woodruff TJ. PMID: 35649165; PMCID: PMC9365522.
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    54. Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions. Front Aging Neurosci. 2022; 14:749991. Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M. PMID: 35572130; PMCID: PMC9093608.
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    55. Investigating geographic differences in environmental chemical exposures in maternal and cord sera using non-targeted screening and silicone wristbands in California. J Expo Sci Environ Epidemiol. 2023 07; 33(4):548-557. 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. PMID: 35449448; PMCID: PMC9585116.
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    56. Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates. Sci Transl Med. 2022 03 09; 14(635):eabm8646. 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. PMID: 35263147; PMCID: PMC9487170.
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    57. Deep phenotyping of Alzheimer's disease leveraging electronic medical records identifies sex-specific clinical associations. Nat Commun. 2022 02 03; 13(1):675. 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. PMID: 35115528; PMCID: PMC8814236.
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    58. Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students. PLoS Comput Biol. 2022 01; 18(1):e1009719. 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. PMID: 35100256; PMCID: PMC8830787.
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    59. Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis. Front Immunol. 2021; 12:788315. Bunis DG, Wang W, Vallvé-Juanico J, Houshdaran S, Sen S, Ben Soltane I, Kosti I, Vo KC, Irwin JC, Giudice LC, Sirota M. PMID: 35069565; PMCID: PMC8766492.
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    60. A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires. Front Immunol. 2021; 12:790119. Yu K, Ravoor A, Malats N, Pineda S, Sirota M. PMID: 35069569; PMCID: PMC8767103.
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    61. Author Correction: Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease. Nat Aging. 2021 Dec; 1(12):1202. 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. PMID: 37117528.
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    62. Mortality Risk Among Patients With COVID-19 Prescribed Selective Serotonin Reuptake Inhibitor Antidepressants. JAMA Netw Open. 2021 11 01; 4(11):e2133090. Oskotsky T, Maric I, Tang A, Oskotsky B, Wong RJ, Aghaeepour N, Sirota M, Stevenson DK. PMID: 34779847; PMCID: PMC8593759.
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    63. 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. 2022 Jan; 59(1):276-293. Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M. PMID: 34669146; PMCID: PMC8786804.
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    64. Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development in Term and Preterm Infants. J Immunol. 2021 11 15; 207(10):2445-2455. Le BL, Sper R, Nielsen SCA, Pineda S, Nguyen QH, Lee JY, Boyd SD, MacKenzie TC, Sirota M. PMID: 34654689; PMCID: PMC8578401.
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    65. Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease. Nat Aging. 2021 10; 1(10):932-947. 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. PMID: 36172600; PMCID: PMC9514594.
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    66. Sex-Specific Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease. JAMA Neurol. 2021 10 01; 78(10):1249-1254. Davis EJ, Solsberg CW, White CC, Miñones-Moyano E, Sirota M, Chibnik L, Bennett DA, De Jager PL, Yokoyama JS, Dubal DB. PMID: 34424272; PMCID: PMC8383157.
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    67. Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer's Disease. Front Aging Neurosci. 2021; 13:735611. Paranjpe MD, Belonwu S, Wang JK, Oskotsky T, Gupta A, Taubes A, Zalocusky KA, Paranjpe I, Glicksberg BS, Huang Y, Sirota M. PMID: 34658838; PMCID: PMC8515049.
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    68. Tumor-Infiltrating B- and T-Cell Repertoire in Pancreatic Cancer Associated With Host and Tumor Features. Front Immunol. 2021; 12:730746. Pineda S, López de Maturana E, Yu K, Ravoor A, Wood I, Malats N, Sirota M. PMID: 34630409; PMCID: PMC8495220.
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    69. A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons. Elife. 2021 09 22; 10. 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. PMID: 34550070; PMCID: PMC8457844.
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    70. Personalizing routine lab tests with machine learning. Nat Med. 2021 09; 27(9):1514-1515. Tang A, Oskotsky T, Sirota M. PMID: 34518677.
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    71. Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS. Nat Commun. 2021 08 26; 12(1):5152. 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. PMID: 34446707; PMCID: PMC8390461.
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    72. Using non-targeted screening and silicone wristbands to investigate geographic differences in pollution exposures among maternal and cord sera. ISEE Conference Abstracts. 2021 Aug 23; 2021(1). Goin GD, Abrahamsson AD, Wang WM, Park PJ, Sirota SM, Morello Frosch MR, DeMicco DE, Trowbridge TJ, August AL, O’Connell OS, Ladella LS, Woodruff WT. .
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    73. “Where do these chemicals come from?” Tracing-back chemical exposures to consumer products. ISEE Conference Abstracts. 2021 Aug 23; 2021(1). Abrahamsson AD, Jiang JT, Wang WM, Park PJ, Morello Frosch MR, Sirota SM, Woodruff WT. .
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    74. Extrathymic Aire-expressing cells support maternal-fetal tolerance. Sci Immunol. 2021 07 16; 6(61). Gillis-Buck E, Miller H, Sirota M, Sanders SJ, Ntranos V, Anderson MS, Gardner JM, MacKenzie TC. PMID: 34272228; PMCID: PMC9363019.
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    75. A Comprehensive Non-targeted Analysis Study of the Prenatal Exposome. Environ Sci Technol. 2021 08 03; 55(15):10542-10557. Panagopoulos Abrahamsson D, Wang A, Jiang T, Wang M, Siddharth A, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. PMID: 34260856; PMCID: PMC8338910.
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    76. Abstract 2787: Landscape of tumor-infiltrating B and T cell repertoire in pancreatic cancer. Cancer Research. 2021 Jul 1; 81(13_Supplement):2787-2787. Pineda PS, Yu YK, Malats MN, Sirota SM. .
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    77. Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. Cell Rep Med. 2021 06 15; 2(6):100323. 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. PMID: 34195686; PMCID: PMC8233692.
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    78. Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. Sci Rep. 2021 06 10; 11(1):12310. 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. PMID: 34112877; PMCID: PMC8192542.
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    79. Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. Front Immunol. 2021; 12:638066. Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M. PMID: 34177888; PMCID: PMC8223752.
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    80. P0467 Characterization of the tumor-infiltrating immune repertoire in Muscle Invasive Bladder Cancer. European Urology. 2021 Jun 1; 79:s641. Dorta DR, Yu YK, Sirota SM, Malats MN, Pineda PS. .
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    81. Drugs in COVID-19 Clinical Trials: Predicting Transporter-Mediated Drug-Drug Interactions Using In Vitro Assays and Real-World Data. Clin Pharmacol Ther. 2021 07; 110(1):108-122. Yee SW, Vora B, Oskotsky T, Zou L, Jakobsen S, Enogieru OJ, Koleske ML, Kosti I, Rödin M, Sirota M, Giacomini KM. PMID: 33759449; PMCID: PMC8217266.
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    82. Oxypurinol pharmacokinetics and pharmacodynamics in healthy volunteers: Influence of BCRP Q141K polymorphism and patient characteristics. Clin Transl Sci. 2021 07; 14(4):1431-1443. Vora B, Brackman DJ, Zou L, Garcia-Cremades M, Sirota M, Savic RM, Giacomini KM. PMID: 33931953; PMCID: PMC8301548.
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    83. Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures. Commun Biol. 2021 04 21; 4(1):488. 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. PMID: 33883687; PMCID: PMC8060402.
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    84. dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit. Bioinformatics. 2021 Apr 01; 36(22-23):5535-5536. Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M. PMID: 33313640; PMCID: PMC8016464.
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    85. Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. Res Sq. 2021 Mar 30. 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. PMID: 33821262; PMCID: PMC8020993.
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    86. The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury. Blood. 2021 03 25; 137(12):1679-1689. Zinter MS, Lindemans CA, Versluys BA, Mayday MY, Sunshine S, Reyes G, Sirota M, Sapru A, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL. PMID: 33512420; PMCID: PMC7995292.
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    87. Suspect Screening, Prioritization, and Confirmation of Environmental Chemicals in Maternal-Newborn Pairs from San Francisco. Environ Sci Technol. 2021 04 20; 55(8):5037-5049. Wang A, Abrahamsson DP, Jiang T, Wang M, Morello-Frosch R, Park JS, Sirota M, Woodruff TJ. PMID: 33726493; PMCID: PMC8114949.
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    88. The Effects of Genetic Mutations and Drugs on the Activity of the Thiamine Transporter, SLC19A2. AAPS J. 2021 03 01; 23(2):35. Enogieru OJ, Koleske ML, Vora B, Ngo H, Yee SW, Chatad D, Sirota M, Giacomini KM. PMID: 33649974; PMCID: PMC7921063.
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    89. Abstract PS11-04: Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatment arms and molecular subtypes. Cancer Research. 2021 Feb 15; 81(4_Supplement):ps11-04-ps11-04. Yu YK, Basu BA, Yau YC, Wolf WD, Hirst HG, Sit SL, O’Grady ON, Brown BT, DeMichele DA, Berry BD, Hylton HN, Yee YD, Esserman EL, van 't Veer vL, Sirota SM. .
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    90. Decreased Mortality Rate Among COVID-19 Patients Prescribed Statins: Data From Electronic Health Records in the US. Front Med (Lausanne). 2021; 8:639804. Maric I, Oskotsky T, Kosti I, Le B, Wong RJ, Shaw GM, Sirota M, Stevenson DK. PMID: 33614688; PMCID: PMC7887302.
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    91. COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone. Res Sq. 2021 Jan 14. Sarma A, Christenson SA, Mick E, DeVoe C, Deiss T, Pisco AO, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha BS, Neff N, Tan M, Serpa PH, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, COMET Consortium, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. PMID: 33469573; PMCID: PMC7814832.
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    92. Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. Cell Rep. 2021 01 05; 34(1):108573. 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. PMID: 33406429; PMCID: PMC10263444.
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    93. Molecular Diversity of Clinically Stable Human Kidney Allografts. JAMA Netw Open. 2021 01 04; 4(1):e2035048. Rychkov D, Sur S, Sirota M, Sarwal MM. PMID: 33492376; PMCID: PMC7835722.
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    94. 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. Res Sq. 2020 Nov 04. 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. PMID: 33173861; PMCID: PMC7654875.
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    95. A method for comprehensively characterizing chemical exposures of pregnant women in San Francisco using non-targeted analysis. ISEE Conference Abstracts. 2020 Oct 26; 2020(1). Abrahamsson AD, Wang WA, Jiang JT, Wang WM, Morello-Frosch MR, Park PJ, Sirota SM, Woodruff WT. .
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    96. Peripheral Blood RNA Sequencing Unravels a Differential Signature of Coding and Noncoding Genes by Types of Kidney Allograft Rejection. Kidney Int Rep. 2020 Oct; 5(10):1706-1721. Pineda S, Sur S, Sigdel T, Nguyen M, Crespo E, Torija A, Meneghini M, Gomà M, Sirota M, Bestard O, Sarwal MM. PMID: 33102963; PMCID: PMC7569686.
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    97. Data Integration for Immunology. Annual Review of Biomedical Data Science. 2020 Jul 20; 3(1):1-24. Pineda PS, Bunis BD, Kosti KI, Sirota SM. .
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    98. Towards personalized medicine in maternal and child health: integrating biologic and social determinants. Pediatr Res. 2021 01; 89(2):252-258. 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. PMID: 32454518; PMCID: PMC8061757.
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    99. Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards. J Chem Inf Model. 2020 06 22; 60(6):2718-2727. Panagopoulos Abrahamsson D, Park JS, Singh RR, Sirota M, Woodruff TJ. PMID: 32379974; PMCID: PMC7328371.
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    100. Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. NPJ Digit Med. 2020; 3:57. 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. PMID: 32337372; PMCID: PMC7156708.
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    101. Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Front Microbiol. 2020; 11:476. Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M. PMID: 32322240; PMCID: PMC7156768.
      View in: PubMed   Mentions: 23  
    102. Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis. Leukemia. 2020 10; 34(10):2754-2765. Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B, Sirota M, Wiita AP. PMID: 32123307; PMCID: PMC7483300.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    103. Author Correction: A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Nat Commun. 2020 02 27; 11(1):1164. 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. PMID: 32109229; PMCID: PMC7046614.
      View in: PubMed   Mentions:    Fields:    
    104. Computational discovery of therapeutic candidates for preventing preterm birth. JCI Insight. 2020 02 13; 5(3). Le BL, Iwatani S, Wong RJ, Stevenson DK, Sirota M. PMID: 32051340; PMCID: PMC7098786.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    105. Drug-nutrient interactions: discovering prescription drug inhibitors of the thiamine transporter ThTR-2 (SLC19A3). Am J Clin Nutr. 2020 01 01; 111(1):110-121. Vora B, Green EAE, Khuri N, Ballgren F, Sirota M, Giacomini KM. PMID: 31764942; PMCID: PMC6944527.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    106. 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. Mol Pain. 2020 Jan-Dec; 16:1744806920936502. Kober KM, Lee MC, Olshen A, Conley YP, Sirota M, Keiser M, Hammer MJ, Abrams G, Schumacher M, Levine JD, Miaskowski C. PMID: 32586194; PMCID: PMC7322824.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    107. Molecular Characterization of Familial Hypercholesterolemia in a North American Cohort. J Endocr Soc. 2020 Jan 01; 4(1):bvz015. 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. PMID: 31993549; PMCID: PMC6977948.
      View in: PubMed   Mentions: 4  
    108. Gene Expression Meta-Analysis Reveals Concordance in Gene Activation, Pathway, and Cell-Type Enrichment in Dermatomyositis Target Tissues. ACR Open Rheumatol. 2019 Dec; 1(10):657-666. Neely J, Rychkov D, Paranjpe M, Waterfield M, Kim S, Sirota M. PMID: 31872188; PMCID: PMC6917332.
      View in: PubMed   Mentions: 12  
    109. Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia. Sci Data. 2019 10 15; 6(1):201. Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ. PMID: 31615985; PMCID: PMC6794302.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    110. Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis. Clinical Lymphoma Myeloma & Leukemia. 2019 Oct 1; 19(10):e76. Sarin SV, Yu YK, Sirota SM, Wiita WA. .
      View in: Publisher Site   Mentions:
    111. A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Nat Commun. 2019 08 29; 10(1):3902. 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. PMID: 31467281; PMCID: PMC6715644.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    112. Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis. Proc Natl Acad Sci U S A. 2019 09 10; 116(37):18517-18527. Ashouri JF, Hsu LY, Yu S, Rychkov D, Chen Y, Cheng DA, Sirota M, Hansen E, Lattanza L, Zikherman J, Weiss A. PMID: 31455730; PMCID: PMC6744919.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    113. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types. Nat Commun. 2019 08 08; 10(1):3574. Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M. PMID: 31395879; PMCID: PMC6687785.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansCells
    114. Insights into Computational Drug Repurposing for Neurodegenerative Disease. Trends Pharmacol Sci. 2019 08; 40(8):565-576. Paranjpe MD, Taubes A, Sirota M. PMID: 31326236; PMCID: PMC6771436.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimals
    115. ASSOCIATION BETWEEN POLYGENIC RISK SCORE AND INCREASED BRAIN TAU DEPOSITION IN COGNITIVELY NORMAL AND MCI INDIVIDUALS. Alzheimer's & Dementia. 2019 Jul 1; 15(7):p404-p405. Paranjpe PM, Liu LM, Zhou ZY, Sirota SM. .
      View in: Publisher Site   Mentions:
    116. Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing. Nat Commun. 2019 04 23; 10(1):1906. Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM. PMID: 31015506; PMCID: PMC6479061.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    117. Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets. JAMA Netw Open. 2019 04 05; 2(4):e191851. Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ. PMID: 30977847; PMCID: PMC6481454.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    118. Metatranscriptomic Evaluation of Pulmonary Complications after Pediatric Hematopoietic Cell Transplantation Reveals Pathogenic Microbes Linked to Dysregulated Human Immunologic Gene Expression. Biology of Blood and Marrow Transplantation. 2019 Mar 1; 25(3):s45. Zinter ZM, Lindemans LC, Mayday MM, Versluys VB, Sirota SM, Dvorak DC, Boelens BJ, DeRisi DJ, Biohub BC. .
      View in: Publisher Site   Mentions:
    119. A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm. J Reprod Immunol. 2019 04; 132:16-20. Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M. PMID: 30852461; PMCID: PMC6456418.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    120. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics. 2019 01 01; 35(1):95-103. 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. PMID: 30561547; PMCID: PMC6298056.
      View in: PubMed   Mentions: 87     Fields:    Translation:HumansCells
    121. Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Sci Data. 2018 12 18; 5(1):3. 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. PMID: 30563979; PMCID: PMC6309114.
      View in: PubMed   Mentions:    Fields:    
    122. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Sci Data. 2018 11 06; 5:180219. 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. PMID: 30398470; PMCID: PMC6219406.
      View in: PubMed   Mentions: 6     Fields:    
    123. Pre-pregnancy or first-trimester risk scoring to identify women at high risk of preterm birth. Eur J Obstet Gynecol Reprod Biol. 2018 Dec; 231:235-240. 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. PMID: 30439652; PMCID: PMC6697157.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    124. Determining Significance in the New Era for P Values. J Pediatr Gastroenterol Nutr. 2018 11; 67(5):547-548. Pineda S, Sirota M. PMID: 30052572; PMCID: PMC7442122.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    125. Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease. J Pediatr Gastroenterol Nutr. 2018 10; 67(4):434-435. Kosti I, Sirota M. PMID: 29746345; PMCID: PMC6150815.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    126. Cumulative Risk and Impacts Modeling on Environmental/Chemical and Social Stressors. ISEE Conference Abstracts. 2018 Sep 24; 2018(1). Huang HH, Wang WA, Morello-Frosch MR, Lam LJ, Sirota SM, Padula PA, Woodruff WT. .
      View in: Publisher Site   Mentions:
    127. The Pregnancy Chemisome in Relation to Birth Outcomes and Consumer Product Use: Suspect Screening of Industrial Chemicals. ISEE Conference Abstracts. 2018 Sep 24; 2018(1). Wang WA, Schwartz SJ, Gerona GR, Lin LT, Morello-Frosch MR, Sirota SM, Woodruff WT. .
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    128. Environmental pollution and social factors as contributors to preterm birth in Fresno County. Environ Health. 2018 08 29; 17(1):70. Padula AM, Huang H, Baer RJ, August LM, Jankowska MM, Jellife-Pawlowski LL, Sirota M, Woodruff TJ. PMID: 30157858; PMCID: PMC6114053.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansPHPublic Health
    129. Investigation of association between environmental and socioeconomic factors and preterm birth in California. Environ Int. 2018 12; 121(Pt 2):1066-1078. Huang H, Woodruff TJ, Baer RJ, Bangia K, August LM, Jellife-Palowski LL, Padula AM, Sirota M. PMID: 30075861; PMCID: PMC6638551.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansPHPublic Health
    130. A Suspect Screening Method for Characterizing Multiple Chemical Exposures among a Demographically Diverse Population of Pregnant Women in San Francisco. Environ Health Perspect. 2018 07; 126(7):077009. Wang A, Gerona RR, Schwartz JM, Lin T, Sirota M, Morello-Frosch R, Woodruff TJ. PMID: 30044231; PMCID: PMC6108847.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansPHPublic Health
    131. Pre-Transplant Assessment of AMR Risk by Novel Donor/Recipient Non-HLA Variants. Transplantation Journal. 2018 Jul 1; 102(&NA;):s165. Pineda PS, Sigdel ST, Chen CJ, Jackson JA, Sirota SM, Sarwal SM. .
      View in: Publisher Site   Mentions:
    132. B Cell Immune Repertoire Sequencing Identifies Pre-transplant Rejection Risk. Transplantation Journal. 2018 Jul 1; 102(&NA;):s36. Pineda PS, Sigdel ST, Liberto LJ, Roskin RK, Boyd BS, Sirota SM, Sarwal SM. .
      View in: Publisher Site   Mentions:
    133. Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. Front Immunol. 2018; 9:993. Vora B, Wang A, Kosti I, Huang H, Paranjpe I, Woodruff TJ, MacKenzie T, Sirota M. PMID: 29867970; PMCID: PMC5954243.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    134. Cumulative Risk and Impact Modeling on Environmental Chemical and Social Stressors. Curr Environ Health Rep. 2018 03; 5(1):88-99. Huang H, Wang A, Morello-Frosch R, Lam J, Sirota M, Padula A, Woodruff TJ. PMID: 29441463; PMCID: PMC5876145.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansPHPublic Health
    135. Correction to: Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Rheumatol Int. 2018 02; 38(2):319. Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Dudley RA, Yazdany J. PMID: 29273937.
      View in: PubMed   Mentions:    Fields:    
    136. Corrigendum: Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant. Front Immunol. 2018; 9:107. Pineda S, Sigdel TK, Chen J, Jackson AM, Sirota M, Sarwal MM. PMID: 29406538; PMCID: PMC5797733.
      View in: PubMed   Mentions: 2     Fields:    
    137. Are minor alleles more likely to be risk alleles? BMC Med Genomics. 2018 01 19; 11(1):3. Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ. PMID: 29351777; PMCID: PMC5775585.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    138. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Sci Rep. 2018 01 09; 8(1):226. 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. PMID: 29317701; PMCID: PMC5760643.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    139. Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies. MAbs. 2018 Feb/Mar; 10(2):256-268. 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. PMID: 29227213; PMCID: PMC5825193.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    140. Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth. J Pediatr. 2018 03; 194:40-46.e4. Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N. PMID: 29249523; PMCID: PMC5987530.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    141. Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant. Front Immunol. 2017; 8:1687. Pineda S, Sigdel TK, Chen J, Jackson AM, Sirota M, Sarwal MM. PMID: 29259604; PMCID: PMC5723302.
      View in: PubMed   Mentions: 18     Fields:    
    142. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. JCI Insight. 2017 11 02; 2(21). 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. PMID: 29093271; PMCID: PMC5752280.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    143. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat Commun. 2017 10 20; 8(1):1077. Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ. PMID: 29057876; PMCID: PMC5651823.
      View in: PubMed   Mentions: 250     Fields:    Translation:HumansCells
    144. Precision annotation of digital samples in NCBI's gene expression omnibus. Sci Data. 2017 09 19; 4:170125. 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. PMID: 28925997; PMCID: PMC5604135.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    145. Transplantomics: Toward Precision Medicine in Transplantation Research. Transplantation. 2017 08; 101(8):1777-1782. Sirota M, Sarwal MM. PMID: 28121910.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    146. Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Rheumatol Int. 2017 10; 37(10):1611-1618. Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Yazdany J. PMID: 28748425; PMCID: PMC5693716.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    147. A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data. Sci Rep. 2017 07 13; 7(1):5338. Apeltsin L, Wang S, von Büdingen HC, Sirota M. PMID: 28706301; PMCID: PMC5509648.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    148. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun. 2017 07 12; 8:16022. Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. PMID: 28699633; PMCID: PMC5510182.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansAnimalsCells
    149. Synergistic drug combinations from electronic health records and gene expression. J Am Med Inform Assoc. 2017 May 01; 24(3):565-576. 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. PMID: 27940607; PMCID: PMC6080645.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    150. An Integrative Bioinformatics Approach Identifies In Vivo Validated Drug Candidates with Novel Mechanisms of Action in Rheumatoid Arthritis. The Journal of Immunology. 2017 May 1; 198(1_Supplement):72.4-72.4. Noblin NE, Daugherty DA, Farrington FC, Hakim HI, Radin RA, Chua CM, Rabe RM, Fernald FG, Ford FD, Sirota SM, Schaevitz SL, Radin RA. .
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    151. Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab. Medicine (Baltimore). 2017 Mar; 96(13):e6528. Schmajuk G, Tonner C, Trupin L, Li J, Sarkar U, Ludwig D, Shiboski S, Sirota M, Dudley RA, Murray S, Yazdany J. PMID: 28353614; PMCID: PMC5380298.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansPHPublic Health
    152. 313: Development of a first-trimester risk score to predict preterm birth for black women in California. American Journal of Obstetrics and Gynecology. 2017 Jan 1; 216(1):s191-s192. Baer BR, Oltman OS, Kuppermann KM, Pantell PM, Rogers RE, Ryckman RK, Sirota SM, Rand RL, Jelliffe-Pawlowski JL. .
      View in: Publisher Site   Mentions:
    153. Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Nat Commun. 2016 11 18; 7:13376. 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. PMID: 27857134; PMCID: PMC5120205.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    154. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol. 2016 11; 5(11):599-607. Paik H, Chen B, Sirota M, Hadley D, Butte AJ. PMID: 27860440; PMCID: PMC5192994.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    155. Novel Chemicals Identified in Pregnant Women in Northern California. ISEE Conference Abstracts. 2016 Aug 17; 2016(1). Wang* WA, Schwartz SJ, Gerona GR, Lin LT, Sirota SM, Woodruff WT. .
      View in: Publisher Site   Mentions:
    156. Environmental influences on reproductive health: the importance of chemical exposures. Fertil Steril. 2016 09 15; 106(4):905-29. Wang A, Padula A, Sirota M, Woodruff TJ. PMID: 27513554; PMCID: PMC5158104.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansPHPublic Health
    157. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep. 2016 05 04; 6:24799. Kosti I, Jain N, Aran D, Butte AJ, Sirota M. PMID: 27142790; PMCID: PMC4855174.
      View in: PubMed   Mentions: 88     Fields:    Translation:Humans
    158. 251 Identification of alpha-adrenergic agonists as potential therapeutic agents for dermatomyositis through drug-repurposing using public expression datasets. Journal of Investigative Dermatology. 2016 May 1; 136(5):s44. Cho CH, Fiorentino FD, Lewis LM, Sirota SM, Sarin SK. .
      View in: Publisher Site   Mentions:
    159. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol. 2016 Apr; 12(4):e1004885. Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. PMID: 27115429; PMCID: PMC4846031.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    160. Identification of Alpha-Adrenergic Agonists as Potential Therapeutic Agents for Dermatomyositis through Drug-Repurposing Using Public Expression Datasets. J Invest Dermatol. 2016 07; 136(7):1517-1520. Cho HG, Fiorentino D, Lewis M, Sirota M, Sarin KY. PMID: 26975725; PMCID: PMC5399882.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    161. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015 Dec 04; 6:8971. Aran D, Sirota M, Butte AJ. PMID: 26634437; PMCID: PMC4671203.
      View in: PubMed   Mentions: 572     Fields:    Translation:Humans
    162. 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 Oct; 4(10):576-84. Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. PMID: 26535158; PMCID: PMC4625862.
      View in: PubMed   Mentions: 25     Fields:    
    163. Fighting disease with data. XRDS Crossroads The ACM Magazine for Students. 2015 Jul 27; 21(4):28-33. Sirota SM, Chen CB. .
      View in: Publisher Site   Mentions:
    164. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics. 2015; 8 Suppl 2:S5. Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ. PMID: 26043652; PMCID: PMC4460709.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    165. Effect of genome and environment on metabolic and inflammatory profiles. PLoS One. 2015; 10(4):e0120898. 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. PMID: 25853885; PMCID: PMC4390246.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    166. Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov. Pac Symp Biocomput. 2015; 68-79. Wu M, Sirota M, Butte AJ, Chen B. PMID: 25592569; PMCID: PMC4361221.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    167. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pac Symp Biocomput. 2015; 383-94. Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ. PMID: 25592598; PMCID: PMC4299914.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    168. Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis. Sci Transl Med. 2014 Aug 06; 6(248):248ra106. 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. PMID: 25100740; PMCID: PMC4176763.
      View in: PubMed   Mentions: 122     Fields:    Translation:HumansCells
    169. B cell exchange across the blood-brain barrier in multiple sclerosis. J Clin Invest. 2012 Dec; 122(12):4533-43. 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. PMID: 23160197; PMCID: PMC3533544.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansCells
    170. 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 May 01; 109(18):7049-54. 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. PMID: 22499789; PMCID: PMC3344989.
      View in: PubMed   Mentions: 91     Fields:    Translation:HumansAnimalsCells
    171. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012; 8(2):e1002375. Khatri P, Sirota M, Butte AJ. PMID: 22383865; PMCID: PMC3285573.
      View in: PubMed   Mentions: 709     Fields:    Translation:HumansAnimals
    172. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet. 2012 Mar; 131(3):353-64. Liu LY, Schaub MA, Sirota M, Butte AJ. PMID: 21858542; PMCID: PMC3260375.
      View in: PubMed   Mentions: 41     Fields:    Translation:Humans
    173. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011 Aug 17; 3(96):96ra77. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. PMID: 21849665; PMCID: PMC3502016.
      View in: PubMed   Mentions: 378     Fields:    Translation:HumansAnimals
    174. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med. 2011 Aug 17; 3(96):96ra76. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. PMID: 21849664; PMCID: PMC3479650.
      View in: PubMed   Mentions: 298     Fields:    Translation:Humans
    175. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol. 2011 06 21; 7(8):489-94. Sirota M, Butte AJ. PMID: 21691330.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    176. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Inflamm Bowel Dis. 2012 Feb; 18(2):312-22. Liu LY, Schaub MA, Sirota M, Butte AJ. PMID: 21618365; PMCID: PMC3165065.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    177. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010 Dec 02; 6(12):e1001025. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. PMID: 21152010; PMCID: PMC2996323.
      View in: PubMed   Mentions: 865     Fields:    Translation:HumansAnimals
    178. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One. 2010 Oct 22; 5(10):e13574. Chen R, Davydov EV, Sirota M, Butte AJ. PMID: 21042586; PMCID: PMC2962641.
      View in: PubMed   Mentions: 90     Fields:    Translation:Humans
    179. Drug discovery in a multidimensional world: systems, patterns, and networks. J Cardiovasc Transl Res. 2010 Oct; 3(5):438-47. Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. PMID: 20677029.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    180. Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet. 2009 Dec; 5(12):e1000792. Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. PMID: 20041220; PMCID: PMC2791168.
      View in: PubMed   Mentions: 92     Fields:    Translation:Humans
    181. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics. 2009 Jun 15; 25(12):i21-9. Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. PMID: 19477990; PMCID: PMC2687980.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    182. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. 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, et al. PMID: 17994087.
      View in: PubMed   Mentions: 1073     Fields:    Translation:AnimalsCells
    183. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 2007; 8(12):R269. Gross SS, Do CB, Sirota M, Batzoglou S. PMID: 18096039; PMCID: PMC2246271.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    184. Global Assessment of B Cell Alloimmunity Using Human Protein Microarrays. Clinical Immunology. 2007 Jan 1; 123:s68. Wadia WP, Coram CM, Sirota SM, Miklos MD, Butte BA. .
      View in: Publisher Site   Mentions:
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