Monti Lab

Mission Statement

Monti’s research centers on the development and application of computational approaches for the dissection and characterization of the molecular machinery of human malignancies and their response to environmental insults. This multidisciplinary effort relies on the generation, analysis, and integration of high-throughput genomic data, and it is aimed at the identification of novel therapeutic targets and the development of diagnostic and prognostic markers.

Background

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.

Ongoing Projects

  • Development of gene expression-based clinical classifiers for prognosis and clinical trial patient stratification.
  • Molecular Characterization of lymphoma malignancies: genome, transcriptome, epi-genome, and their cross-talk.
  • Molecular characterization of the transcriptional program in lung cancer based on high-throughput RNA-sequencing.
  • Computational genomic models of environmental and chemical carcinogenesis.

Principal Investigator
Stefano Monti

Postdoctoral Fellows
Liye Zhang

Graduate Students
Daniel Gusenleitner
Yuxiang Tan
Yu Fu
Adam Labadorf
Brenda LaBarre
Ana Brandusa Pavel
Heather Selby
Arjan van der Velde

Collaborators (outside of BU medical center)
Margaret Shipp, M.D, Dana Farber Cancer Institute, Boston, MA
Todd R. Golub, M.D., Broad Institute, Cambridge, MA
Frederick Alt,  Ph.D., Children Hospital, Boston, MA
Nika Danial, Ph.D., Dana Farber Cancer Institute, Boston, MA
Scott J. Rodig, M.D. Ph.D., Brigham & Women’s Hospital, Boston, MA
Roberto Chiarle, M.D., Children Hospital, Boston, MA

Recent Publications

  1. Chen L, Monti S, Juszczynski P, Ouyang J, Chapuy B, Neuberg D, Doench JG, et al. (2013). SYK Inhibition Modulates Distinct PI3K/AKT- Dependent Survival Pathways and Cholesterol Biosynthesis in Diffuse Large B Cell Lymphomas. Cancer Cell, 23(6), 826–838. [Cancer Discovery review]
  2. Hartley SW, Monti S, Liu CT, Steinberg MH, and Sebastiani P (2012) Bayesian methods for multivariate modeling of pleiotropic SNP associations and genetic risk prediction, Frontiers in Genetics, 3:176
  3. Caro P, Kishan  AU, Norberg E, Stanley I, Chapuy B, Ficarro SB, Polak K, Tondera D, Gounarides J, Yin H, Zhou F, Green MR, Chen L, Monti S, Marto JA, Shipp MA, Danial N. Metabolic Signatures Uncover Novel Targets in Molecular Subsets of Diffuse Large B Cell Lymphoma. Cancer Cell, 22(4) 547-560. 2012. [Cancer Cell review]
  4. Monti S, Chapuy B, Takeyama K, Rodig SJ, Hao Y, T. Yeda KT, Inguilizian H, Mermel C, Curie T, Dogan A, Kutok JL, Beroukim R, Neuberg D, Habermann T, Getz G, Kung AL, Golub TR, Shipp MA. Integrative Analysis Reveals an Outcome-associated and Targetable Pattern of p53 and Cell Cycle Deregulation in Diffuse Large B-cell Lymphoma, Cancer Cell, 22(3):359-372, 2012.
  5. Chiarle R, Zhang Y, Frock RL, Lewis SM, Molinie B, Ho Y, Myers DR,  Choi VW, Compagno M, Malkin DJ, Neuberg D, Monti S, Giallourakis CC, Gostissa M,  and Alt FW. Genome-Wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells. Cell, 147:(1):107-119, 2011.
  6. Green M, Monti S, et al., Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program. PNAS, 108(7): 2873-2878, 2011.
  7. Chapman M, et al. Initial genome sequencing and analysis of multiple myeloma. Nature, 471(7339):467–472, 2011.
  8. Green M, Monti S, et al. Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular Sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma. Blood, 116(17): 3268-3277, 2010.
  9. The Cancer Genome Atlas (TCGA) Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216):1061-8, 2008.
  10. Takeyama K, Monti S, et al., Integrative Analysis Reveals 53BP1 Copy Loss and Decreased Expression in a Subset of Human Diffuse Large B-cell Lymphomas. Oncogene, 27(3): 318-322, 2008.
  11. Polo JM, Juszczynski P, Monti S, et al. A transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B-cell lymphomas. PNAS, 104(9): 3207-3212, 2007.
  12. Hayes DN, Monti S, et al., Gene Expression Profiling Reveals Reproducible Human Lung Adenocarcinoma Subtypes in Multiple Independent DNA Microarray Cohorts. J Clinical Oncology, 24(31): 5079-5090, 2006.
  13. Monti, S., Savage, K.J., et al., Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood, 2005. 105(5): p. 1851-1861.
  14. Monti, S., et al., Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data. Machine Learning, 2003. 52(1-2): p. 91-118.