Monti Lab

Mission Statement

Monti’s research centers on the development and application of computational approaches for the study of the molecular mechanisms of tumor initiation and progression and of the role played in it by environmental exposure, with the goals of advancing prevention and care.  This multidisciplinary effort relies on the generation, analysis, and integration of high-throughput genomics data, and it is aimed at the identification of novel therapeutic targets and the development of diagnostic and prognostic markers.


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 multiple human malignancies: genome, transcriptome, epi-genome, and their cross-talk.
  • Computational genomics models of environmental and chemical carcinogenesis.

Principal Investigator
Stefano Monti

Postdoctoral Fellows

Graduate Students
Eric Reed
Anthony Federico

Past Trainees
Daniel Gusenleitner
Francesca Mulas
Yuxiang Tan
Anastasia Gurinovich
Stephanie Kim
Liye Zhang
Vinay Kartha
Amy Li

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
Scott Auerbach, Ph.D., National Toxicology Program/NIEHS

Recent Publications

  1. Kartha VK*, Stawski L*, Han R, Haines P, Gallagher G, Noonan V, Kukuruzinska M, Monti S, Trojanowska T (2016). PDGFRβ is a novel marker of stromal activation in oral squamous cell carcinomas. PLoS One 11(4): e0154645. PMCID: PMC4851360.
  2. Zhang L, Yang CS, Varelas X, Monti S (2016). Altered RNA editing in 3’ UTR perturbs microRNA-mediated regulation of oncogenes and tumor-suppressors. Nature Scientific Reports 6:23226. PMCID: PMC4793219.
  3. Chapuy B, Roemer MGM, Stewart C, Tan Y, Abo R, Zhang L, Dunford AJ, Meredith D, Thorner A, Jordanova ES, Liu G, Feuerhake F, Ducar M, Illerhaus G, Gusenleitner D, Linden E, Sun HH, Homer H, Aono M, Pinkus G, Ligon A, Ligon K, Ferry J, Freeman GJ, van Hummelen P, Golub TR, Getz G, Rodig SJ, de Jong D, Monti S, Shipp MA (2015). Targetable Genetic Features of Primary Testicular and Primary Central Nervous System Lymphomas. Blood 127(7):869-881. PMCID: PMC4760091.
  4. Hiemer SE, Zhang L, Kartha VK, Packer TS, Almershed M, Noonan V, Kukuruzinska M, Bais MV, Monti S, Varelas X (2015). A YAP/TAZ-Regulated Molecular Signature is Associated with Oral Squamous Cell Carcinoma. Molecular Cancer Research 13(6):957-68. PMCID: PMC4470857.
  5. Carey C, Gusenleitner D, Chapuy B, Kovach AE, Kluk MJ, Sun HH, Crossland RE, Bacon CM, Rand V, Dal Cin P, Le LP, Neuberg D, Sohani AR, Monti S, Rodig S (2015). Molecular Classification of MYC-Driven B-cell Lymphomas by Targeted Gene Expression Profiling of Fixed Biopsy Specimens. Journal of Molecular Diagnostics 17(1):19-30. PMCID: PMC4279427.
  6. Gusenleitner D, Auerbach S, Meila T, Gómez H, Sherr DH, Monti S (2014). Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action. PLoS ONE 9(7):e102579 [Chemical watch review; Voice of America report]
  7. Chapuy B, McKeown MR, Lin C, Monti S, Roemer MGM, Qi J, Rahl P, Sun H, Yeda KT, Kung AJ, Rodig SJ, Young RA, Shipp MA, and Bradner JE (2013). Disruption of Super Enhancer Driven Cancer Dependencies in Diffuse Large B-Cell Lymphoma. Cancer Cell 24(6):777-790. PMCID: PMC4018722
  8. 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]
  9. 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
  10. 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]
  11. 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.
  12. 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.
  13. 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.
  14. Chapman M, et al. Initial genome sequencing and analysis of multiple myeloma. Nature, 471(7339):467–472, 2011.
  15. 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.
  16. The Cancer Genome Atlas (TCGA) Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216):1061-8, 2008.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.