Stefano Monti, Ph.D.

Associate Professor of Medicine and Biostatistics

Affiliate faculty, Bioinformatics Program
Affiliate member, Broad Institute of MIT & Harvard
Affiliate member, Hariri Institute for Computing and Computational Science & Engineering


B.S., Computer Science, University of Udine, Italy, 1991
M.S., Computer Science/AI, Intelligent Systems Program, University of Pittsburgh, 1996
Ph.D., Computer Science/AI, Intelligent Systems Program, University of Pittsburgh, 1999
Postdoctoral Fellow, Machine Learning/AI, Robotics Institute, Carnegie Mellon, 2000

Contact Information

Office: E611
Phone:  617-358-7087

Research Interests

Computational Biology, Cancer Genomics, Statistics and Machine Learning (see lab page).

Selected Publications

[complete list; *co-first author; ✝co-senior author]

Federico A, Kern J, Varelas X, and Monti S (2023). Structure Learning for Hierarchical Regulatory Networks. PLoS Comp. Bio. (In press).

Karagiannis T*, Dowrey TW*, Villacorta-Martin C, Montano M, Reed E, Andersen SL, Perls TT, Monti S✝, Murphy GJ✝, Sebastiani S✝ (2023). Multi-modal profiling of peripheral blood cells across the human lifespan reveals distinct immune cell signatures of aging and longevity. Lancet eBiomedicine 90:104514. PMID: 37005201. PMCID: PMC10114155.

Kern J, Tilston-Lunel A, Federico A, Ning B, Mueller A, Peppler G, Stampouloglou E, Cheng N, Johnson, R, Lenburg M, Beane J, Monti S, Varelas X (2022). Inactivation of LATS1/2 drives luminal-basal plasticity to initiate basal-like mammary carcinomas. Nature Communications 13(1):7198. PMID: 36443313. PMCID: PMC9705439

Karagiannis T, Monti S, Sebastiani P (2022). Cell Type Diversity Statistic: An entropy-based metric to compare overall cell type composition across samples. Frontiers in Genetics 13:855076. PMID: 35464841.

Federico A, Monti S (2021). Contextualized Protein-Protein Interactions. Patterns (NY), 2(1):100153. PMID: 33511361. PMCID: PMC7815950.

Reed E, Monti S. (2021). Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data. Nucleic Acids Research, 49(17):e98, PMID: 34226941.

Kim S*, Reed E*, Monti S✝, Schlezinger J✝ (2021) A Data-Driven Transcriptional Taxonomy of Adipogenic Chemicals to Identify Emerging Metabolic Health Threats. Environmental Health Perspectives 129(7):077006. PMID: 34323617.

Federico A, Monti S (2020). hypeR: An R Package for Geneset Enrichment Workflows. Bioinformatics 36(4):1307. PMID: 31498385. PMCID: PMC7998712

Li A, Chapuy B, Varelas X, Sebastiani P, Monti S (2019). Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis. Scientific Reports 9(1):16904. PMID: 31729402. PMCID: PMC6858347.

Li AJ, Lu X, Natoli T, Bittker J, Sipes N, Subramanian A, Auerbach S, Sherr DH, Monti S (2019). The Carcinogenome Project: High-Throughput In-vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity. Environmental Health Perspectives 127(4):47002. PMCID: PMC6785232. PMID: 30964323.

Kartha VK, Sebastiani P, Kern J, Zang L, Varelas X, Monti S (2019). CaDrA: A computational framework for performing candidate driver analyses using genomic features. Frontiers in Genetics 10:121. PMID: 30838036. PMCID: PMC6390206

Kartha VK*, Alamoud KA*, Sadykov K, Laroche F, Feng H, Pai S, Varelas X, Egloff AM, Snyder-Cappione JE, Belkina AC, Bais MV, Monti S✝, Kukuruzinska MA✝ (2018). Functional and genomic analyses reveal therapeutic potential of targeting β-catenin/CBP activity in Head and Neck cancers. Genome Medicine 10(1):54. PMCID: PMC6053793. PMID: 30029671

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.

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.

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.

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.

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.

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]

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]

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

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 (2012) Metabolic Signatures Uncover Novel Targets in Molecular Subsets of Diffuse Large B Cell Lymphoma. Cancer Cell, 22(4) 547-560. [Cancer Cell review]

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 (2012) 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.

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 (2011) Genome-Wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells. Cell, 147:(1):107-119.

Green M, Monti S, et al. (2011) Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program. PNAS, 108(7): 2873-2878.

Chapman M, et al. (2011) Initial genome sequencing and analysis of multiple myeloma. Nature, 471(7339):467–472.

Green M, Monti S, et al. (2010) 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.

The Cancer Genome Atlas (TCGA) Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216):1061-8.

Takeyama K, Monti S, et al. (2008) Integrative Analysis Reveals 53BP1 Copy Loss and Decreased Expression in a Subset of Human Diffuse Large B-cell Lymphomas. Oncogene, 27(3): 318-322.

Polo JM, Juszczynski P, Monti S, et al. (2007) A transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B-cell lymphomas. PNAS, 104(9): 3207-3212.

Hayes DN, Monti S, et al. (2006) Gene Expression Profiling Reveals Reproducible Human Lung Adenocarcinoma Subtypes in Multiple Independent DNA Microarray Cohorts. J Clinical Oncology, 24(31): 5079-5090.

Monti, S., Savage, K.J., et al. (2005) Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood, 105(5): p. 1851-1861.

Monti, S., et al. (2003) Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data. Machine Learning, 52(1-2): p. 91-118.