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Marina Sirota, PhD

Title(s)Associate Professor, Pediatrics
SchoolSchool of Medicine
Address490 Illinois Street
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 Institute for Computational Health Sciences 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.

    Collapse Research 
    Collapse Research Activities and Funding
    An Integrative Multi-Omics Approach to Elucidate Sex-Specific Differences in Alzheimers Disease
    NIH/NIA R01AG060393Sep 1, 2018 - May 31, 2023
    Role: Principal Investigator
    ApoE Genotype-Directed Drug Repositioning and Combination Therapy for Alzheimer's Disease
    NIH/NIA 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/NIEHS R01ES027051Sep 30, 2016 - Aug 31, 2021
    Role: Co-Investigator
    Integrative Analysis of Genomic, Epigenomic and Phenotypic Data for Disease Stratification of Endometriosis
    NIH/NICHD R01HD089511Sep 26, 2016 - Apr 30, 2021
    Role: Co-Investigator
    Resource-based Center for the Advancement of Precision Medicine in Rheumatology
    NIH/NIAMS P30AR070155Sep 21, 2016 - Aug 31, 2021
    Role: Co-Investigator, Bioinformatics Core Director
    Elucidating the Role of the Genetic and Environmental Determinants of Preterm Birth Using Integrative Computational Approaches
    NIH/NLM K01LM012381Aug 1, 2016 - Jul 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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. 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.
      View in: PubMed   Mentions:
    2. Data Integration for Immunology. Annual Review of Biomedical Data Science. 2020 Jul 20; 3(1):1-24. Silvia Pineda, Daniel G. Bunis, Idit Kosti, Marina Sirota. .
      View in: Publisher Site   Mentions:
    3. Towards personalized medicine in maternal and child health: integrating biologic and social determinants. Pediatr Res. 2020 May 26. 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.
      View in: PubMed   Mentions: 1     Fields:    
    4. Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards. J Chem Inf Model. 2020 Jun 22; 60(6):2718-2727. Panagopoulos Abrahamsson D, Park JS, Singh RR, Sirota M, Woodruff TJ. PMID: 32379974.
      View in: PubMed   Mentions:    Fields:    
    5. 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.
      View in: PubMed   Mentions:
    6. 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.
      View in: PubMed   Mentions:
    7. Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis. Leukemia. 2020 Oct; 34(10):2754-2765. Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B, Sirota M, Wiita AP. PMID: 32123307.
      View in: PubMed   Mentions: 1     Fields:    
    8. 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.
      View in: PubMed   Mentions:    Fields:    
    9. 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.
      View in: PubMed   Mentions: 1     Fields:    
    10. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    11. 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.
      View in: PubMed   Mentions:    Fields:    
    12. 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.
      View in: PubMed   Mentions:
    13. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. 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. Vishesh Sarin, Katharine Yu, Marina Sirota, Arun Wiita. .
      View in: Publisher Site   Mentions:
    15. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    16. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    17. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    18. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    19. 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. Manish Paranjpe, Min Liu, Yun Zhou, Marina Sirota. .
      View in: Publisher Site   Mentions:
    20. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    21. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    22. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    23. 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.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    24. 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. PMID: 30563979.
      View in: PubMed   Mentions:    Fields:    
    25. 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. PMID: 30398470.
      View in: PubMed   Mentions: 1     Fields:    
    26. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    27. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    28. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    29. Cumulative Risk and Impacts Modeling on Environmental/Chemical and Social Stressors. ISEE Conference Abstracts. 2018 Sep 24; 2018(1). Hongtai Huang, Aolin Wang, Rachel Morello-Frosch, Juleen Lam, Marina Sirota, Amy M. Padula, Tracey Woodruff. .
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    30. 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). Aolin Wang, Jackie M. Schwartz, Roy Gerona, Thomas Lin, Rachel Morello-Frosch, Marina Sirota, Tracey Woodruff. .
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    31. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansPHPublic Health
    32. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansPHPublic Health
    33. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansPHPublic Health
    34. Pre-Transplant Assessment of AMR Risk by Novel Donor/Recipient Non-HLA Variants. Transplantation Journal. 2018 Jul 1; 102(&NA;):s165. Silvia Pineda, Tara K Sigdel, Jieming Chen, Annette M Jackson, Marina Sirota, Minnie M Sarwal. .
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    35. B Cell Immune Repertoire Sequencing Identifies Pre-transplant Rejection Risk. Transplantation Journal. 2018 Jul 1; 102(&NA;):s36. Silvia Pineda, Tara K Sigdel, Juliane Liberto, Krishna Roskin, Scott Boyd, Marina Sirota, Minnie M Sarwal. .
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    36. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    37. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansPHPublic Health
    38. 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:    
    39. 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.
      View in: PubMed   Mentions:    Fields:    
    40. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    41. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    42. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    43. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    44. 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.
      View in: PubMed   Mentions: 6     Fields:    
    45. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    46. 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.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    47. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    48. Transplantomics: Toward Precision Medicine in Transplantation Research. Transplantation. 2017 08; 101(8):1777-1782. Sirota M, Sarwal MM. PMID: 28121910.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    49. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    50. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    51. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    52. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    53. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansPHPublic Health
    54. 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. Rebecca J. Baer, Scott P. Oltman, Miriam Kuppermann, Matthew Pantell, Elizabeth E. Rogers, Kelli K. Ryckman, Marina Sirota, Larry Rand, Laura L. Jelliffe-Pawlowski. .
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    55. 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.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    56. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    57. Novel Chemicals Identified in Pregnant Women in Northern California. ISEE Conference Abstracts. 2016 Aug 17; 2016(1). Aolin Wang*, Jackie Schwartz, Roy Gerona, Thomas Lin, Marina Sirota, Tracey Woodruff. .
      View in: Publisher Site   Mentions:
    58. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansPHPublic Health
    59. 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.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    60. 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. H.G. Cho, D. Fiorentino, M. Lewis, M. Sirota, K. Sarin. .
      View in: Publisher Site   Mentions:
    61. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    62. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    63. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015 Dec 04; 6:8971. Aran D, Sirota M, Butte AJ. PMID: 26634437.
      View in: PubMed   Mentions: 172     Fields:    Translation:Humans
    64. 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.
      View in: PubMed   Mentions: 13     Fields:    
    65. Fighting disease with data. XRDS Crossroads The ACM Magazine for Students. 2015 Jul 27; 21(4):28-33. Marina Sirota, Bin Chen. .
      View in: Publisher Site   Mentions:
    66. 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.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    67. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    68. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    69. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    70. 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.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    71. 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.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    72. 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.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    73. 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.
      View in: PubMed   Mentions: 451     Fields:    Translation:HumansAnimals
    74. 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.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    75. 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.
      View in: PubMed   Mentions: 252     Fields:    Translation:HumansAnimals
    76. 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.
      View in: PubMed   Mentions: 194     Fields:    Translation:Humans
    77. 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: 2     Fields:    Translation:Humans
    78. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    79. 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.
      View in: PubMed   Mentions: 487     Fields:    Translation:HumansAnimals
    80. 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.
      View in: PubMed   Mentions: 70     Fields:    Translation:Humans
    81. 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: 22     Fields:    Translation:HumansAnimals
    82. 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.
      View in: PubMed   Mentions: 77     Fields:    Translation:Humans
    83. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    84. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, et al. PMID: 17994087.
      View in: PubMed   Mentions: 880     Fields:    Translation:AnimalsCells
    85. 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.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    86. Global Assessment of B Cell Alloimmunity Using Human Protein Microarrays. Clinical Immunology. 2007 Jan 1; 123:s68. Persis P. Wadia, Marc Coram, Marina Sirota, David B. Miklos, Atul Butte. .
      View in: Publisher Site   Mentions:
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