Research Profiles

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UCSF Profiles


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.

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.

Wu M, Sirota M, Butte AJ, Chen B. Characteristics of drug combination therapy in oncology by analyzing clinical trial data on Pac Symp Biocomput. 2015.

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.

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.

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.
Press Relese:

Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012.

Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet. 2012.

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.

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.
Press Relese:

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.
Press Relese:

Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol. 2011.

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.

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.

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.

Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune Disease Classification by Inverse Association with SNP Alleles. PLoS Genet. 2009.
Press Relese:

Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics. 2009.

Gross SS, Do CB, Sirota M, Batzoglou S. Contrast: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biology. 2007.

Wadia P, Coram M, Sirota M, Miklos DB, Butte A. Global Assessment of B Cell Alloimmunity Using Human Protein Microarrays, Clinical ImmunologyVolume 123, Supplement 1, FOCIS 2007 Abstract Supplement - 7th Annual Meeting, S68, 2007.

Drosophila Comparative Genome Sequencing and Analysis Consortium. Evolution of genes and genomes in the context of the Drosophila phylogeny. Nature 450: 203-218, 2007.

Conference Presentations

Elucidating the Genetic Determinants of Pre-Term Birth. PAS, April 2015.

How Bioinformatics Will Affect Transplantation Practice. World Transplant Summit, July 2014.

Computational Drug Repurposing in Scleroderma Scleroderma Foundation Scientific Workshop, April 2014.

Keynote Speaker: Advances in Autoimmune Informatics. Advances in Bioinformatics and Genomics Symposium, February 19th, 2010.

Late Breaking Session: Autoimmune Disease Classification by Inverse Association with SNP Alleles. 2010 AMIA Summit on Translational Bioinformatics, March 11, 2010.

Paper Presentation: Discovery and Validation of Novel Drug Indications Using Public Gene Expression Data. 2010 NLM Informatics Training Conference, June 15, 2010. Best Paper Award (First Day)

Selected Poster Presentation: Autoimmune Disease Classification by Inverse Association with SNP Alleles. RECOMB 2010, August 13, 2010.