Stefano Monti, PhD

Associate Professor, Medicine

Stefano Monti
617.414.7031
75 E. Newton St Evans Building

Biography

Stefano Monti is a Computational Biologist and joined the BU faculty as an associate professor in January 2011 in the section of Computational Biomedicine, with a joint appointment in the Bioinformatics program. Monti received his Ph.D. in Intelligent Systems and Artificial Intelligence from the University of Pittsburgh, and completed his training with a post-doctoral fellowship at the Robotics Institute at Carnegie Mellon. His doctoral and post-doctoral research focused on the development of machine learning and knowledge discovery methodologies, with a particular emphasis on probabilistic reasoning and Bayesian approaches to modeling biomedical data. Since 2001, he has worked in the field of Cancer Genomics, first as a Research Scientist at the Whitehead Institute’s Center for Genome Research, and later as a Computational Biologist in the Cancer Program at the Broad Institute, of which he remains an affiliate member.

Other Positions

  • Associate Professor, Biostatistics, Boston University School of Public Health
  • Member, Bioinformatics Graduate Program, Boston University

Education

  • University of Pittsburgh, PhD
  • University of Pittsburgh, MS
  • University of Houston, MS
  • Università degli Studi di Udine, BS

Publications

  • Published on 11/15/2019

    Li A, Chapuy B, Varelas X, Sebastiani P, Monti S. Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis. Sci Rep. 2019 Nov 15; 9(1):16904. PMID: 31729402.

    Read at: PubMed
  • Published on 9/9/2019

    Federico A, Monti S. hypeR: An R Package for Geneset Enrichment Workflows. Bioinformatics. 2019 Sep 09. PMID: 31498385.

    Read at: PubMed
  • Published on 9/1/2019

    Gurinovich A, Bae H, Farrell JJ, Andersen SL, Monti S, Puca A, Atzmon G, Barzilai N, Perls TT, Sebastiani P. PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects. Bioinformatics. 2019 Sep 01; 35(17):3046-3054. PMID: 30624692.

    Read at: PubMed
  • Published on 8/30/2019

    Chen L, Ouyang J, Wienand K, Bojarczuk K, Hao Y, Chapuy B, Neuberg D, Juszczynski P, Lawton LN, Rodig SJ, Monti S, Shipp MA. CXCR4 upregulation is an indicator of sensitivity to B-cell receptor/PI3K blockade and a potential resistance mechanism in B-cell receptor-dependent diffuse large B-cell lymphomas. Haematologica. 2019 Aug 30. PMID: 31471373.

    Read at: PubMed
  • Published on 8/5/2019

    Sebastiani P, Monti S, Morris M, Gurinovich A, Toshiko T, Andersen SL, Sweigart B, Ferrucci L, Jennings LL, Glass DJ, Perls TT. A serum protein signature of APOE genotypes in centenarians. Aging Cell. 2019 Dec; 18(6):e13023. PMID: 31385390.

    Read at: PubMed
  • Published on 6/28/2019

    Federico A, Karagiannis T, Karri K, Kishore D, Koga Y, Campbell JD, Monti S. Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines. Front Genet. 2019; 10:614. PMID: 31316552.

    Read at: PubMed
  • Published on 4/1/2019

    Li A, Lu X, Natoli T, Bittker J, Sipes NS, Subramanian A, Auerbach S, Sherr DH, Monti S. The Carcinogenome Project: In Vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity. Environ Health Perspect. 2019 04; 127(4):47002. PMID: 30964323.

    Read at: PubMed
  • Published on 3/5/2019

    Reed E, Moses E, Xiao X, Liu G, Campbell J, Perdomo C, Monti S. Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques. Front Genet. 2019; 10:150. PMID: 30891063.

    Read at: PubMed
  • Published on 2/19/2019

    Kartha VK, Sebastiani P, Kern JG, Zhang L, Varelas X, Monti S. CaDrA: A Computational Framework for Performing Candidate Driver Analyses Using Genomic Features. Front Genet. 2019; 10:121. PMID: 30838036.

    Read at: PubMed
  • Published on 8/1/2018

    Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1292. PMID: 29955181.

    Read at: PubMed

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