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Marina Sirota, PhD

Title(s)Assistant Professor, Pediatrics
SchoolSchool of Medicine
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

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Featured Videos

    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.
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    1. Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B, Sirota M, Wiita AP. Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis. Leukemia. 2020 Mar 02. PMID: 32123307.
      View in: PubMed
    2. 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. Author Correction: A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Nat Commun. 2020 Feb 27; 11(1):1164. PMID: 32109229.
      View in: PubMed
    3. Le BL, Iwatani S, Wong RJ, Stevenson DK, Sirota M. Computational discovery of therapeutic candidates for preventing preterm birth. JCI Insight. 2020 Feb 13; 5(3). PMID: 32051340.
      View in: PubMed
    4. Vora B, Green EAE, Khuri N, Ballgren F, Sirota M, Giacomini KM. Drug-nutrient interactions: discovering prescription drug inhibitors of the thiamine transporter ThTR-2 (SLC19A3). Am J Clin Nutr. 2020 Jan 01; 111(1):110-121. PMID: 31764942.
      View in: PubMed
    5. Jessica Neely, Dmitry Rychkov, Manish Paranjpe, Michael Waterfield, Susan Kim, Marina Sirota. Gene Expression Meta-Analysis Reveals Concordance in Gene Activation, Pathway, and Cell-Type Enrichment in Dermatomyositis Target Tissues. ACR Open Rheumatology. 2019 Nov 9.
      View in: Publisher Site
    6. Neely J, Rychkov D, Paranjpe M, Waterfield M, Kim S, Sirota M. Gene Expression Meta-Analysis Reveals Concordance in Gene Activation, Pathway, and Cell-Type Enrichment in Dermatomyositis Target Tissues. ACR Open Rheumatol. 2019 Dec; 1(10):657-666. PMID: 31872188.
      View in: PubMed
    7. Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ. Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia. Sci Data. 2019 10 15; 6(1):201. PMID: 31615985.
      View in: PubMed
    8. Tsur A, Batsry L, Toussia-Cohen S, Rosenstein MG, Barak O, Brezinov Y, Yoeli-Ullman R, Sivan E, Sirota M, Druzin ML, Stevenson DK, Blumenfeld YJ, Aran D. Development and validation of a machine learning model for prediction of shoulder dystocia. Ultrasound Obstet Gynecol. 2019 Oct 06. PMID: 31587401.
      View in: PubMed
    9. Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M, Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Criswell LA. A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Nat Commun. 2019 08 29; 10(1):3902. PMID: 31467281.
      View in: PubMed
    10. Ashouri JF, Hsu LY, Yu S, Rychkov D, Chen Y, Cheng DA, Sirota M, Hansen E, Lattanza L, Zikherman J, Weiss A. Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis. Proc Natl Acad Sci U S A. 2019 Sep 10; 116(37):18517-18527. PMID: 31455730.
      View in: PubMed
    11. Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types. Nat Commun. 2019 08 08; 10(1):3574. PMID: 31395879.
      View in: PubMed
    12. Paranjpe MD, Taubes A, Sirota M. Insights into Computational Drug Repurposing for Neurodegenerative Disease. Trends Pharmacol Sci. 2019 Aug; 40(8):565-576. PMID: 31326236.
      View in: PubMed
    13. Manish Paranjpe, Min Liu, Yun Zhou, Marina Sirota. 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.
      View in: Publisher Site
    14. Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM. Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing. Nat Commun. 2019 04 23; 10(1):1906. PMID: 31015506.
      View in: PubMed
    15. Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ. Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets. JAMA Netw Open. 2019 04 05; 2(4):e191851. PMID: 30977847.
      View in: PubMed
    16. Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M. A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm. J Reprod Immunol. 2019 04; 132:16-20. PMID: 30852461.
      View in: PubMed
    17. 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. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics. 2019 01 01; 35(1):95-103. PMID: 30561547.
      View in: PubMed
    18. 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. Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Sci Data. 2018 12 18; 5(1):3. PMID: 30563979.
      View in: PubMed
    19. 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. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Sci Data. 2018 11 06; 5:180219. PMID: 30398470.
      View in: PubMed
    20. Baer RJ, McLemore MR, Adler N, Oltman SP, Chambers BD, Kuppermann M, Pantell MS, Rogers EE, Ryckman KK, Sirota M, Rand L, Jelliffe-Pawlowski LL. Pre-pregnancy or first-trimester risk scoring to identify women at high risk of preterm birth. Eur J Obstet Gynecol Reprod Biol. 2018 Dec; 231:235-240. PMID: 30439652.
      View in: PubMed
    21. Pineda S, Sirota M. Determining Significance in the New Era for P Values. J Pediatr Gastroenterol Nutr. 2018 11; 67(5):547-548. PMID: 30052572.
      View in: PubMed
    22. Kosti I, Sirota M. Electronic Medical Records Enable Precision Medicine Approaches for Celiac Disease. J Pediatr Gastroenterol Nutr. 2018 10; 67(4):434-435. PMID: 29746345.
      View in: PubMed
    23. Hongtai Huang, Aolin Wang, Rachel Morello-Frosch, Juleen Lam, Marina Sirota, Amy M. Padula, Tracey Woodruff. Cumulative Risk and Impacts Modeling on Environmental/Chemical and Social Stressors. ISEE Conference Abstracts. 2018 Sep 24; 2018(1).
      View in: Publisher Site
    24. Aolin Wang, Jackie M. Schwartz, Roy Gerona, Thomas Lin, Rachel Morello-Frosch, Marina Sirota, Tracey Woodruff. 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).
      View in: Publisher Site
    25. Padula AM, Huang H, Baer RJ, August LM, Jankowska MM, Jellife-Pawlowski LL, Sirota M, Woodruff TJ. Environmental pollution and social factors as contributors to preterm birth in Fresno County. Environ Health. 2018 08 29; 17(1):70. PMID: 30157858.
      View in: PubMed
    26. Huang H, Woodruff TJ, Baer RJ, Bangia K, August LM, Jellife-Palowski LL, Padula AM, Sirota M. Investigation of association between environmental and socioeconomic factors and preterm birth in California. Environ Int. 2018 12; 121(Pt 2):1066-1078. PMID: 30075861.
      View in: PubMed
    27. Wang A, Gerona RR, Schwartz JM, Lin T, Sirota M, Morello-Frosch R, Woodruff TJ. A Suspect Screening Method for Characterizing Multiple Chemical Exposures among a Demographically Diverse Population of Pregnant Women in San Francisco. Environ Health Perspect. 2018 07; 126(7):077009. PMID: 30044231.
      View in: PubMed
    28. Silvia Pineda, Tara K Sigdel, Jieming Chen, Annette M Jackson, Marina Sirota, Minnie M Sarwal. Pre-Transplant Assessment of AMR Risk by Novel Donor/Recipient Non-HLA Variants. Transplantation Journal. 2018 Jul 1; 102(&NA;):s165.
      View in: Publisher Site
    29. Silvia Pineda, Tara K Sigdel, Juliane Liberto, Krishna Roskin, Scott Boyd, Marina Sirota, Minnie M Sarwal. B Cell Immune Repertoire Sequencing Identifies Pre-transplant Rejection Risk. Transplantation Journal. 2018 Jul 1; 102(&NA;):s36.
      View in: Publisher Site
    30. Vora B, Wang A, Kosti I, Huang H, Paranjpe I, Woodruff TJ, MacKenzie T, Sirota M. Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. Front Immunol. 2018; 9:993. PMID: 29867970.
      View in: PubMed
    31. Huang H, Wang A, Morello-Frosch R, Lam J, Sirota M, Padula A, Woodruff TJ. Cumulative Risk and Impact Modeling on Environmental Chemical and Social Stressors. Curr Environ Health Rep. 2018 03; 5(1):88-99. PMID: 29441463.
      View in: PubMed
    32. Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Dudley RA, Yazdany J. Correction to: Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Rheumatol Int. 2018 02; 38(2):319. PMID: 29273937.
      View in: PubMed
    33. Pineda S, Sigdel TK, Chen J, Jackson AM, Sirota M, Sarwal MM. Corrigendum: Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant. Front Immunol. 2018; 9:107. PMID: 29406538.
      View in: PubMed
    34. Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ. Are minor alleles more likely to be risk alleles? BMC Med Genomics. 2018 01 19; 11(1):3. PMID: 29351777.
      View in: PubMed
    35. Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ, Sirota M. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Sci Rep. 2018 01 09; 8(1):226. PMID: 29317701.
      View in: PubMed
    36. 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. Productive common light chain libraries yield diverse panels of high affinity bispecific antibodies. MAbs. 2018 Feb/Mar; 10(2):256-268. PMID: 29227213.
      View in: PubMed
    37. Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N. Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth. J Pediatr. 2018 03; 194:40-46.e4. PMID: 29249523.
      View in: PubMed
    38. Pineda S, Sigdel TK, Chen J, Jackson AM, Sirota M, Sarwal MM. Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant. Front Immunol. 2017; 8:1687. PMID: 29259604.
      View in: PubMed
    39. Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, Chen B, Lee A, Brown AS, Aasi SZ, Hollmig T, Ator MA, Dorsey BD, Ruggeri BR, Zificsak CA, Sirota M, Tang JY, Butte A, Epstein E, Sarin KY, Oro AE. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. JCI Insight. 2017 11 02; 2(21). PMID: 29093271.
      View in: PubMed
    40. Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat Commun. 2017 10 20; 8(1):1077. PMID: 29057876.
      View in: PubMed
    41. Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, Bhattacharya S, Sirota M, Musen MA, Butte AJ. Precision annotation of digital samples in NCBI's gene expression omnibus. Sci Data. 2017 09 19; 4:170125. PMID: 28925997.
      View in: PubMed
    42. Sirota M, Sarwal MM. Transplantomics: Toward Precision Medicine in Transplantation Research. Transplantation. 2017 08; 101(8):1777-1782. PMID: 28121910.
      View in: PubMed
    43. Gianfrancesco MA, Schmajuk G, Haserodt S, Trupin L, Izadi Z, Jafri K, Shiboski S, Sirota M, Yazdany J. Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety. Rheumatol Int. 2017 10; 37(10):1611-1618. PMID: 28748425.
      View in: PubMed
    44. Apeltsin L, Wang S, von Büdingen HC, Sirota M. A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data. Sci Rep. 2017 07 13; 7(1):5338. PMID: 28706301.
      View in: PubMed
    45. Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun. 2017 07 12; 8:16022. PMID: 28699633.
      View in: PubMed
    46. 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. Synergistic drug combinations from electronic health records and gene expression. J Am Med Inform Assoc. 2017 May 01; 24(3):565-576. PMID: 27940607.
      View in: PubMed
    47. Schmajuk G, Tonner C, Trupin L, Li J, Sarkar U, Ludwig D, Shiboski S, Sirota M, Dudley RA, Murray S, Yazdany J. Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab. Medicine (Baltimore). 2017 Mar; 96(13):e6528. PMID: 28353614.
      View in: PubMed
    48. Rebecca J. Baer, Scott P. Oltman, Miriam Kuppermann, Matthew Pantell, Elizabeth E. Rogers, Kelli K. Ryckman, Marina Sirota, Larry Rand, Laura L. Jelliffe-Pawlowski. 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.
      View in: Publisher Site
    49. Yeung YA, Foletti D, Deng X, Abdiche Y, Strop P, Glanville J, Pitts S, Lindquist K, Sundar PD, Sirota M, Hasa-Moreno A, Pham A, Melton Witt J, Ni I, Pons J, Shelton D, Rajpal A, Chaparro-Riggers J. Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Nat Commun. 2016 11 18; 7:13376. PMID: 27857134.
      View in: PubMed
    50. Paik H, Chen B, Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol. 2016 11; 5(11):599-607. PMID: 27860440.
      View in: PubMed
    51. Aolin Wang*, Jackie Schwartz, Roy Gerona, Thomas Lin, Marina Sirota, Tracey Woodruff. Novel Chemicals Identified in Pregnant Women in Northern California. ISEE Conference Abstracts. 2016 Aug 17; 2016(1).
      View in: Publisher Site
    52. Wang A, Padula A, Sirota M, Woodruff TJ. Environmental influences on reproductive health: the importance of chemical exposures. Fertil Steril. 2016 09 15; 106(4):905-29. PMID: 27513554.
      View in: PubMed
    53. Kosti I, Jain N, Aran D, Butte AJ, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep. 2016 05 04; 6:24799. PMID: 27142790.
      View in: PubMed
    54. H.G. Cho, D. Fiorentino, M. Lewis, M. Sirota, K. Sarin. 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.
      View in: Publisher Site
    55. Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol. 2016 Apr; 12(4):e1004885. PMID: 27115429.
      View in: PubMed
    56. Cho HG, Fiorentino D, Lewis M, Sirota M, Sarin KY. Identification of Alpha-Adrenergic Agonists as Potential Therapeutic Agents for Dermatomyositis through Drug-Repurposing Using Public Expression Datasets. J Invest Dermatol. 2016 07; 136(7):1517-1520. PMID: 26975725.
      View in: PubMed
    57. Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015 Dec 04; 6:8971. PMID: 26634437.
      View in: PubMed
    58. Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. CPT Pharmacometrics Syst Pharmacol. 2015 Oct; 4(10):576-84. PMID: 26535158.
      View in: PubMed
    59. Marina Sirota, Bin Chen. Fighting disease with data. XRDS Crossroads The ACM Magazine for Students. 2015 Jul 27; 21(4):28-33.
      View in: Publisher Site
    60. Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics. 2015; 8 Suppl 2:S5. PMID: 26043652.
      View in: PubMed
    61. Sirota M, Willemsen G, Sundar P, Pitts SJ, Potluri S, Prifti E, Kennedy S, Ehrlich SD, Neuteboom J, Kluft C, Malone KE, Cox DR, de Geus EJ, Boomsma DI. Effect of genome and environment on metabolic and inflammatory profiles. PLoS One. 2015; 10(4):e0120898. PMID: 25853885.
      View in: PubMed
    62. Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pac Symp Biocomput. 2015; 383-94. PMID: 25592598.
      View in: PubMed
    63. Wu M, Sirota M, Butte AJ, Chen B. Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov. Pac Symp Biocomput. 2015; 68-79. PMID: 25592569.
      View in: PubMed
    64. Palanichamy A, Apeltsin L, Kuo TC, Sirota M, Wang S, Pitts SJ, Sundar PD, Telman D, Zhao LZ, Derstine M, Abounasr A, Hauser SL, von Büdingen HC. Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis. Sci Transl Med. 2014 Aug 06; 6(248):248ra106. PMID: 25100740.
      View in: PubMed
    65. von Büdingen HC, Kuo TC, Sirota M, van Belle CJ, Apeltsin L, Glanville J, Cree BA, Gourraud PA, Schwartzburg A, Huerta G, Telman D, Sundar PD, Casey T, Cox DR, Hauser SL. B cell exchange across the blood-brain barrier in multiple sclerosis. J Clin Invest. 2012 Dec; 122(12):4533-43. PMID: 23160197.
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    66. Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A. 2012 May 01; 109(18):7049-54. PMID: 22499789.
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    67. Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012; 8(2):e1002375. PMID: 22383865.
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    68. Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet. 2012 Mar; 131(3):353-64. PMID: 21858542.
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    69. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011 Aug 17; 3(96):96ra77. PMID: 21849665.
      View in: PubMed
    70. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med. 2011 Aug 17; 3(96):96ra76. PMID: 21849664.
      View in: PubMed
    71. Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol. 2011 06 21; 7(8):489-94. PMID: 21691330.
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    72. Liu LY, Schaub MA, Sirota M, Butte AJ. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Inflamm Bowel Dis. 2012 Feb; 18(2):312-22. PMID: 21618365.
      View in: PubMed
    73. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010 Dec 02; 6(12):e1001025. PMID: 21152010.
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    74. Chen R, Davydov EV, Sirota M, Butte AJ. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One. 2010 Oct 22; 5(10):e13574. PMID: 21042586.
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    75. Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. J Cardiovasc Transl Res. 2010 Oct; 3(5):438-47. PMID: 20677029.
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