Stefano Monti | Profiles RNS

Stefano Monti, PhD

Associate Professor

Boston University School of Medicine

Dept of Medicine

Computational Biomedicine

PhD, University of Pittsburgh
MS, University of Pittsburgh
MS, University of Houston

Websites

Department of Medicine Faculty

ORCID : 0000-0002-9376-0660

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.

Associate Professor
Boston University School of Public Health
Biostatistics

Member
Boston University
Bioinformatics Graduate Program

BU Sponsored Research

Metabolic Pathways of Increased Cardiovascular risk in type 2 Diabetes
04/01/2016 - 02/29/2020 (PI)
Joslin Diabetes Center NIH NHLBI
5R01HL132254-03

Novel genomic models to predict breast carcinogenicity of environmental chemicals
10/01/2014 - 09/30/2016 (PI)
Art beCAUSE

Lymphoma Target Testing Center
07/01/2013 - 06/30/2016 (PI)
Dana-Farber Cancer Institute Paul E. Singer Fdn

Receptor-based Developmental and Reproductive Toxicity of Superfund Chemicals
09/20/2012 - 03/31/2016 (Co-PI)
PI: David H. Sherr, PhD
NIH/National Institute of Environmental Health Sciences
5P42ES007381-19

Targeting Genetically-driven p53 and Cell Cycle Deregulation in DLBCL
10/01/2012 - 09/30/2015 (PI)
Dana-Farber Cancer Institute Leukemia & Lymph Soc

Yr	Title	Project-Sub Proj	Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

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 Apr; 127(4):47002.View Related Profiles.
Sherr, David
Monti, Stefano
PMID: 30964323.
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.
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.View Related Profiles.
Kern, Joseph
Sebastiani, Paola
Monti, Stefano
Varelas, Xaralabos
PMID: 30838036.
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 Jan 08.View Related Profiles.
Sebastiani, Paola
Andersen, Stacy
Monti, Stefano
Perls, Thomas
PMID: 30624692.
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.
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. Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1290-1291. PMID: 29955182.
Kartha VK, Alamoud KA, Sadykov K, Nguyen BC, Laroche F, Feng H, Lee J, Pai SI, Varelas X, Egloff AM, Snyder-Cappione JE, Belkina AC, Bais MV, Monti S, Kukuruzinska MA. Functional and genomic analyses reveal therapeutic potential of targeting ß-catenin/CBP activity in head and neck cancer. Genome Med. 2018 07 20; 10(1):54.View Related Profiles.
Belkina, Anna
Feng, Hui
Snyder-Cappione , Jennifer
Bais, Manish
Kukuruzinska, Maria
Monti, Stefano
Varelas, Xaralabos
PMID: 30029671.
Kim S, Li A, Monti S, Schlezinger JJ. Tributyltin induces a transcriptional response without a brite adipocyte signature in adipocyte models. Arch Toxicol. 2018 Sep; 92(9):2859-2874.View Related Profiles.
Schlezinger, Jennifer
Monti, Stefano
PMID: 30027469.
Narasimhan S, Stanford Zulick E, Novikov O, Parks AJ, Schlezinger JJ, Wang Z, Laroche F, Feng H, Mulas F, Monti S, Sherr DH. Towards Resolving the Pro- and Anti-Tumor Effects of the Aryl Hydrocarbon Receptor. Int J Mol Sci. 2018 May 07; 19(5).View Related Profiles.
Sherr, David
Feng, Hui
Schlezinger, Jennifer
Novikov, Olga
Monti, Stefano
Wang, Zhongyan
PMID: 29735912.
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. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 05; 24(5):679-690. PMID: 29713087.

Showing 10 of 96 results. Show More

Yang CS, Stampouloglou E, Kingston NM, Zhang L, Monti S, Varelas X. Glutamine-utilizing transaminases are a metabolic vulnerability of TAZ/YAP-activated cancer cells. EMBO Rep. 2018 06; 19(6).View Related Profiles.
Stampouloglou, Eleni
Monti, Stefano
Varelas, Xaralabos
PMID: 29661856; DOI: 10.15252/embr.201643577;.
Alsaqer SF, Tashkandi MM, Kartha VK, Yang YT, Alkheriji Y, Salama A, Varelas X, Kukuruzinska M, Monti S, Bais MV. Inhibition of LSD1 epigenetically attenuates oral cancer growth and metastasis. Oncotarget. 2017 Sep 26; 8(43):73372-73386.View Related Profiles.
Salama, Andrew
Bais, Manish
Kukuruzinska, Maria
Monti, Stefano
Varelas, Xaralabos
PMID: 29088714.
Zhang L, Sement FM, Suematsu T, Yu T, Monti S, Huang L, Aphasizhev R, Aphasizheva I. PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes. EMBO J. 2017 Aug 15; 36(16):2435-2454.View Related Profiles.
Zhang, Liye
Afasizhev, Ruslan
Monti, Stefano
Suematsu, Takuma
PMID: 28684539.
Mulas F, Li A, Sherr DH, Monti S. Network-based analysis of transcriptional profiles from chemical perturbations experiments. BMC Bioinformatics. 2017 Mar 23; 18(Suppl 5):130.View Related Profiles.
Sherr, David
Monti, Stefano
PMID: 28361664; DOI: 10.1186/s12859-017-1536-9;.
Dame K, Cincotta S, Lang AH, Sanghrajka RM, Zhang L, Choi J, Kwok L, Wilson T, Kandula MM, Monti S, Hollenberg AN, Mehta P, Kotton DN, Ikonomou L. Thyroid Progenitors Are Robustly Derived from Embryonic Stem Cells through Transient, Developmental Stage-Specific Overexpression of Nkx2-1. Stem Cell Reports. 2017 Feb 14; 8(2):216-225.View Related Profiles.
Kotton, Darrell
Dame, Keri
Oikonomou, Laertis
Zhang, Liye
Monti, Stefano
PMID: 28162994; DOI: 10.1016/j.stemcr.2016.12.024;.
Alamoud K, Sadykov K, Kartha VK, Monti S, Belkina AC, Snyder-Cappione JE, Pai S, Kukuruzinska M. Cancer Research. Abstract 803: Targeting ß-catenin/CBP signaling in OSCC. 2017; 77(13 Suppl):803-803. View Publication
Monti et al. Cancer Research. Abstract 3259: The genomic landscape of premalignant lung squamous cell carcinoma lesions. 2017; 77(13 Suppl):3259. View Publication
Wang Z, Monti S, Sherr DH. The Diverse and Important Contributions of the AHR to Cancer and Cancer Immunity. 2017. View Publication
Lentucci C, Belkina AC, Cederquist CT, Chan M, Johnson HE, Prasad S, Lopacinski A, Nikolajczyk BS, Monti S, Snyder-Cappione J, Tanasa B, Cardamone MD, Perissi V. Inhibition of Ubc13-mediated Ubiquitination by GPS2 Regulates Multiple Stages of B Cell Development. J Biol Chem. 2017 Feb 17; 292(7):2754-2772.View Related Profiles.
Belkina, Anna
Nikolajczyk, Barbara
Cederquist, Carly
Snyder-Cappione , Jennifer
Cardamone, Maria
Monti, Stefano
Perissi, Valentina
PMID: 28039360; DOI: 10.1074/jbc.M116.755132;.
Novikov O, Wang Z, Stanford EA, Parks AJ, Ramirez-Cardenas A, Landesman E, Laklouk I, Sarita-Reyes C, Gusenleitner D, Li A, Monti S, Manteiga S, Lee K, Sherr DH. An Aryl Hydrocarbon Receptor-Mediated Amplification Loop That Enforces Cell Migration in ER-/PR-/Her2- Human Breast Cancer Cells. Mol Pharmacol. 2016 Nov; 90(5):674-688.View Related Profiles.
Sarita-Reyes, Carmen
Sherr, David
Stanford, Elizabeth
Landesman, Esther
Novikov, Olga
Monti, Stefano
Wang, Zhongyan
PMID: 27573671.
Voena C, Varesio LM, Zhang L, Menotti M, Poggio T, Panizza E, Wang Q, Minero VG, Fagoonee S, Compagno M, Altruda F, Monti S, Chiarle R. Oncogenic ALK regulates EMT in non-small cell lung carcinoma through repression of the epithelial splicing regulatory protein 1. Oncotarget. 2016 May 31; 7(22):33316-30.View Related Profiles.
Zhang, Liye
Monti, Stefano
PMID: 27119231; DOI: 10.18632/oncotarget.8955;.
Bae H, Monti S, Montano M, Steinberg MH, Perls TT, Sebastiani P. Learning Bayesian Networks from Correlated Data. Sci Rep. 2016 05 05; 6:25156.View Related Profiles.
Steinberg, Martin
Sebastiani, Paola
Monti, Stefano
Perls, Thomas
PMID: 27146517; PMCID: PMC4857179; DOI: 10.1038/srep25156;.
Kartha VK, Stawski L, Han R, Haines P, Gallagher G, Noonan V, Kukuruzinska M, Monti S, Trojanowska M. PDGFRß Is a Novel Marker of Stromal Activation in Oral Squamous Cell Carcinomas. PLoS One. 2016; 11(4):e0154645.View Related Profiles.
Gallagher, George
Stawski, Lukasz
Kukuruzinska, Maria
Trojanowska, Maria
Han, Rong
Monti, Stefano
Noonan, Vikki
PMID: 27128408; PMCID: PMC4851360; DOI: 10.1371/journal.pone.0154645;.
Stanford EA, Ramirez-Cardenas A, Wang Z, Novikov O, Alamoud K, Koutrakis P, Mizgerd JP, Genco CA, Kukuruzinska M, Monti S, Bais MV, Sherr DH. Role for the Aryl Hydrocarbon Receptor and Diverse Ligands in Oral Squamous Cell Carcinoma Migration and Tumorigenesis. Mol Cancer Res. 2016 Aug; 14(8):696-706.View Related Profiles.
Sherr, David
Stanford, Elizabeth
Mizgerd, Joseph
Bais, Manish
Kukuruzinska, Maria
Novikov, Olga
Monti, Stefano
Wang, Zhongyan
PMID: 27130942; PMCID: PMC4987205; DOI: 10.1158/1541-7786.MCR-16-0069;.
Zhang L, Yang CS, Varelas X, Monti S. Altered RNA editing in 3' UTR perturbs microRNA-mediated regulation of oncogenes and tumor-suppressors. Sci Rep. 2016 Mar 16; 6:23226.View Related Profiles.
Zhang, Liye
Monti, Stefano
Varelas, Xaralabos
PMID: 26980570; PMCID: PMC4793219; DOI: 10.1038/srep23226;.
Stanford EA, Wang Z, Novikov O, Mulas F, Landesman-Bollag E, Monti S, Smith BW, Seldin DC, Murphy GJ, Sherr DH. The role of the aryl hydrocarbon receptor in the development of cells with the molecular and functional characteristics of cancer stem-like cells. BMC Biol. 2016 Mar 16; 14:20.View Related Profiles.
Sherr, David
Stanford, Elizabeth
Landesman, Esther
Murphy, George
Novikov, Olga
Monti, Stefano
Wang, Zhongyan
PMID: 26984638; PMCID: PMC4794823; DOI: 10.1186/s12915-016-0240-y;.
Suematsu T, Zhang L, Aphasizheva I, Monti S, Huang L, Wang Q, Costello CE, Aphasizhev R. Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs. Mol Cell. 2016 Feb 4; 61(3):364-78.View Related Profiles.
Costello, Catherine
Zhang, Liye
Wang, Qi
Afasizhev, Ruslan
Monti, Stefano
Suematsu, Takuma
PMID: 26833087; PMCID: PMC4744118; DOI: 10.1016/j.molcel.2016.01.004;.
Chapuy B, Cheng H, Watahiki A, Ducar MD, Tan Y, Chen L, Roemer MG, Ouyang J, Christie AL, Zhang L, Gusenleitner D, Abo RP, Farinha P, von Bonin F, Thorner AR, Sun HH, Gascoyne RD, Pinkus GS, van Hummelen P, Wulf GG, Aster JC, Weinstock DM, Monti S, Rodig SJ, Wang Y, Shipp MA. Diffuse large B-cell lymphoma patient-derived xenograft models capture the molecular and biological heterogeneity of the disease. Blood. 2016 May 05; 127(18):2203-13.View Related Profiles.
Zhang, Liye
Monti, Stefano
PMID: 26773040; PMCID: PMC4859195; DOI: 10.1182/blood-2015-09-672352;.
Tan Y, Tambouret Y, Monti S. SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq) Data. Biomed Res Int. 2015; 2015:780519. PMID: 26839886; PMCID: PMC4709598; DOI: 10.1155/2015/780519;.
Chapuy B, Roemer MG, Stewart C, Tan Y, Abo RP, Zhang L, Dunford AJ, Meredith DM, Thorner AR, Jordanova ES, Liu G, Feuerhake F, Ducar MD, Illerhaus G, Gusenleitner D, Linden EA, Sun HH, Homer H, Aono M, Pinkus GS, Ligon AH, Ligon KL, Ferry JA, Freeman GJ, van Hummelen P, Golub TR, Getz G, Rodig SJ, de Jong D, Monti S, Shipp MA. Targetable genetic features of primary testicular and primary central nervous system lymphomas. Blood. 2016 Feb 18; 127(7):869-81.View Related Profiles.
Liu, Gang
Zhang, Liye
Monti, Stefano
PMID: 26702065; PMCID: PMC4760091; DOI: 10.1182/blood-2015-10-673236;.
Hiemer SE, Zhang L, Kartha VK, Packer TS, Almershed M, Noonan V, Kukuruzinska M, Bais MV, Monti S, Varelas X. A YAP/TAZ-Regulated Molecular Signature Is Associated with Oral Squamous Cell Carcinoma. Mol Cancer Res. 2015 Jun; 13(6):957-68.View Related Profiles.
Zhang, Liye
Bais, Manish
Kukuruzinska, Maria
Hiemer, Samantha
Monti, Stefano
Noonan, Vikki
Varelas, Xaralabos
PMID: 25794680; PMCID: PMC4470857; DOI: 10.1158/1541-7786.MCR-14-0580;.
Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE. ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. Bioinformatics. 2015 Jun 1; 31(11):1745-53.View Related Profiles.
Monti, Stefano
Piccolo, Stephen
Johnson, William
PMID: 25617415; PMCID: PMC4443674; DOI: 10.1093/bioinformatics/btv031;.
Monti S, et al. Cancer Research. Abstract 2878: Development of the pre-cancer genome atlas (PCGA) for squamous cell lung carcinoma. 2015; 75(15 Suppl):2878. View Publication
Voena C, Varesio L, Zhang L, Menotti M, Poggio T, Di Giacomo F, Panizza E, Mastini C, Compagno M, Monti S, Chiarle R. Cancer Research. Abstract 131: ALK oncogene regulates epithelial-mesenchymal transition (EMT) in ALK-rearranged non-small cell lung carcinoma through repression of the epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2). 2015; 75(15 Suppl):131. View Publication
Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, Johnson WE, Monti S, Spira A, Beane J, Lenburg ME. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA. 2015 Feb; 21(2):164-71.View Related Profiles.
Spira, Avrum
Liu, Gang
Beane-Ebel, Jennifer
Campbell, Joshua
Luo, Lingqi
Lenburg, Marc
Monti, Stefano
Johnson, William
Alekseyev, Yuriy
PMID: 25519487; PMCID: PMC4338344; DOI: 10.1261/rna.046060.114;.
Carey CD, 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, Shipp MA, Monti S, Rodig SJ. Molecular classification of MYC-driven B-cell lymphomas by targeted gene expression profiling of fixed biopsy specimens. J Mol Diagn. 2015 Jan; 17(1):19-30. PMID: 25468432; PMCID: PMC4279427; DOI: 10.1016/j.jmoldx.2014.08.006;.
Aphasizheva I, Zhang L, Wang X, Kaake RM, Huang L, Monti S, Aphasizhev R. RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol Cell Biol. 2014 Dec 1; 34(23):4329-42.View Related Profiles.
Afasizheva, Inna
Zhang, Liye
Afasizhev, Ruslan
Monti, Stefano
PMID: 25225332; PMCID: PMC4248751; DOI: 10.1128/MCB.01075-14;.
Gusenleitner D, Auerbach SS, Melia T, Gómez HF, Sherr DH, Monti S. Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action. PLoS One. 2014; 9(7):e102579.View Related Profiles.
Sherr, David
Monti, Stefano
PMID: 25058030; PMCID: PMC4109923; DOI: 10.1371/journal.pone.0102579;.
Hao Y, Chapuy B, Monti S, Sun HH, Rodig SJ, Shipp MA. Selective JAK2 inhibition specifically decreases Hodgkin lymphoma and mediastinal large B-cell lymphoma growth in vitro and in vivo. Clin Cancer Res. 2014 May 15; 20(10):2674-83. PMID: 24610827; PMCID: PMC4084704; DOI: 10.1158/1078-0432.CCR-13-3007;.
Carey C, Gusenleitner D, Chapuy B, Sun H, Ligon A, Kovach AE, Phi Le L, Sohani AR, Shipp M, Monti S, Rodig SJ. Cancer Research. Abstract 5582: A targeted molecular classifier of MYC activity and BCL-2 expression in aggressive B-cell lymphomas, designed for clinical practice. 2014; 74(19 Suppl):5582. View Publication
Chapuy B, McKeown MR, Lin CY, Monti S, Roemer MG, Qi J, Rahl PB, Sun HH, Yeda KT, Doench JG, Reichert E, Kung AL, Rodig SJ, Young RA, Shipp MA, Bradner JE. Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. Cancer Cell. 2013 Dec 9; 24(6):777-90. PMID: 24332044; PMCID: PMC4018722; DOI: 10.1016/j.ccr.2013.11.003;.
Leung A, Nah SK, Reid W, Ebata A, Koch CM, Monti S, Genereux JC, Wiseman RL, Wolozin B, Connors LH, Berk JL, Seldin DC, Mostoslavsky G, Kotton DN, Murphy GJ. Induced pluripotent stem cell modeling of multisystemic, hereditary transthyretin amyloidosis. Stem Cell Reports. 2013; 1(5):451-63.View Related Profiles.
Leung, Amy
Ebata, Atsushi
Wolozin, Benjamin
Koch, Clarissa
Kotton, Darrell
Seldin, David
Murphy, George
Mostoslavsky, Gustavo
Berk, John
Connors, Lawreen
Monti, Stefano
PMID: 24286032.
Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, Brennan R, Crofton KM, Gordon B, Fornace AJ, Gaido K, Gerhold D, Haw R, Henney A, Ma'ayan A, McBride M, Monti S, Ochs MF, Pandey A, Sharan R, Stierum R, Tugendreich S, Willett C, Wittwehr C, Xia J, Patton GW, Arvidson K, Bouhifd M, Hogberg HT, Luechtefeld T, Smirnova L, Zhao L, Adeleye Y, Kanehisa M, Carmichael P, Andersen ME, Hartung T. t4 workshop report: Pathways of Toxicity. ALTEX. 2014; 31(1):53-61. PMID: 24127042; PMCID: PMC4041485; DOI: 10.14573/altex.1309261;.
Sherr DH, Monti S. The role of the aryl hydrocarbon receptor in normal and malignant B cell development. Semin Immunopathol. 2013 Nov; 35(6):705-16.View Related Profiles.
Sherr, David
Monti, Stefano
PMID: 23942720; PMCID: PMC3824572; DOI: 10.1007/s00281-013-0390-8;.
Chen L, Monti S, Juszczynski P, Ouyang J, Chapuy B, Neuberg D, Doench JG, Bogusz AM, Habermann TM, Dogan A, Witzig TE, Kutok JL, Rodig SJ, Golub T, Shipp MA. SYK inhibition modulates distinct PI3K/AKT- dependent survival pathways and cholesterol biosynthesis in diffuse large B cell lymphomas. Cancer Cell. 2013 Jun 10; 23(6):826-38. PMID: 23764004; PMCID: PMC3700321; DOI: 10.1016/j.ccr.2013.05.002;.
Smith BW, Rozelle SS, Leung A, Ubellacker J, Parks A, Nah SK, French D, Gadue P, Monti S, Chui DH, Steinberg MH, Frelinger AL, Michelson AD, Theberge R, McComb ME, Costello CE, Kotton DN, Mostoslavsky G, Sherr DH, Murphy GJ. The aryl hydrocarbon receptor directs hematopoietic progenitor cell expansion and differentiation. Blood. 2013 Jul 18; 122(3):376-85.View Related Profiles.
Leung, Amy
Costello, Catherine
Kotton, Darrell
Sherr, David
Murphy, George
Mostoslavsky, Gustavo
McComb, Mark
Steinberg, Martin
Theberge, Roger
Monti, Stefano
PMID: 23723449; PMCID: PMC3716202; DOI: 10.1182/blood-2012-11-466722;.
Friedman R, Kudesia V, Sebastiani P, Monti S, Misquitta D, Peterson K, Whinfield J, Stoeckle R. Educating translational researchers in research informatics principles and methods: an evaluation of a model online course and plans for its dissemination. AMIA Summits Transl Sci Proc. 2013; 2013:59.View Related Profiles.
Sebastiani, Paola
Friedman, Robert
Monti, Stefano
Kudesia, Valmeek
PMID: 24303298.
Monti S, Cooper GF. A Bayesian Network Classifier that Combines a Finite Mixture Model and a Naive Bayes Model. 2013.
Monti S, Cooper GF. A Multivariate Discretization Method for Learning Bayesian Networks from Mixed Data. 2013.
Caro P, Kishan AU, Norberg E, Stanley IA, 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 NN. Metabolic signatures uncover distinct targets in molecular subsets of diffuse large B cell lymphoma. Cancer Cell. 2012 Oct 16; 22(4):547-60. PMID: 23079663; PMCID: PMC3479446; DOI: 10.1016/j.ccr.2012.08.014;.
Hartley SW, Monti S, Liu CT, Steinberg MH, Sebastiani P. Bayesian methods for multivariate modeling of pleiotropic SNP associations and genetic risk prediction. Front Genet. 2012; 3:176.View Related Profiles.
Liu, Ching-Ti
Steinberg, Martin
Sebastiani, Paola
Monti, Stefano
PMID: 22973300; PMCID: PMC3438684; DOI: 10.3389/fgene.2012.00176;.
Monti S, Chapuy B, Takeyama K, Rodig SJ, Hao Y, Yeda KT, Inguilizian H, Mermel C, Currie T, Dogan A, Kutok JL, Beroukhim R, Neuberg D, Habermann TM, 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. 2012 Sep 11; 22(3):359-72. PMID: 22975378; PMCID: PMC3778921; DOI: 10.1016/j.ccr.2012.07.014;.
Kluk MJ, Chapuy B, Sinha P, Roy A, Dal Cin P, Neuberg DS, Monti S, Pinkus GS, Shipp MA, Rodig SJ. Immunohistochemical detection of MYC-driven diffuse large B-cell lymphomas. PLoS One. 2012; 7(4):e33813. PMID: 22511926; PMCID: PMC3325231; DOI: 10.1371/journal.pone.0033813;.
Chiarle R, Zhang Y, Frock RL, Lewis SM, Molinie B, Ho YJ, Myers DR, Choi VW, Compagno M, Malkin DJ, Neuberg D, Monti S, Giallourakis CC, Gostissa M, Alt FW. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell. 2011 Sep 30; 147(1):107-19. PMID: 21962511; PMCID: PMC3186939; DOI: 10.1016/j.cell.2011.07.049;.
Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, Siegel DS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T, Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, Golub TR. Initial genome sequencing and analysis of multiple myeloma. Nature. 2011 Mar 24; 471(7339):467-72. PMID: 21430775; PMCID: PMC3560292; DOI: 10.1038/nature09837;.
Ouyang J, Juszczynski P, Rodig SJ, Green MR, O'Donnell E, Currie T, Armant M, Takeyama K, Monti S, Rabinovich GA, Ritz J, Kutok JL, Shipp MA. Viral induction and targeted inhibition of galectin-1 in EBV+ posttransplant lymphoproliferative disorders. Blood. 2011 Apr 21; 117(16):4315-22. PMID: 21300977; DOI: 10.1182/blood-2010-11-320481;.
Green MR, Monti S, Dalla-Favera R, Pasqualucci L, Walsh NC, Schmidt-Supprian M, Kutok JL, Rodig SJ, Neuberg DS, Rajewsky K, Golub TR, Alt FW, Shipp MA, Manis JP. Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program. Proc Natl Acad Sci U S A. 2011 Feb 15; 108(7):2873-8. PMID: 21282644; PMCID: PMC3041080; DOI: 10.1073/pnas.1019537108;.
Chapuy B, Green MR, Lu J, Monti S, Hao Y, Yeda K, Curie T, Takeyama K, Golub T, Kutok J, Shipp M. Annals of Oncology. IDENTIFICATION OF A "DELETION BLOCK'' AT 13Q14 THAT PERTURBS MULTIPLE SIGNALING AND SURVIVAL PATHWAYS IN PRIMARY CLASSICAL HODGKIN LYMPHOMA. 11th International Conference on Malignant Lymphoma. 2011; 22.
Green MR, Monti S, Rodig SJ, Juszczynski P, Currie T, O'Donnell E, Chapuy B, Takeyama K, Neuberg D, Golub TR, Kutok JL, Shipp MA. 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. 2010 Oct 28; 116(17):3268-77. PMID: 20628145; PMCID: PMC2995356; DOI: 10.1182/blood-2010-05-282780;.
Tadigotla V, Alexe G, Sethi N, Bilal E, Huang C, Monti S, Tamayo P, DeLisi C, Bhanot GV, Ganesan S. NF- B Activation in Breast Cancer Occurs Via Different Mechanisms in Triple Negative and HER2+ Tumors with Lymphocytic Infiltrate. Cancer Research. 2010; 69(24 Suppl):1164. View Publication
Ouyang J, Jusczynski P, O'Donnell E, Armant M, Rodig SJ, Takeyama K, Monti S, Rabinovich G, Kutok JL, Ritz J, Ship MA. Blood. Expression and Targeted Inhibition of the Immunoregulatory Carbohydrate-Binding Lectin, Galectin 1, in EBV-Driven Post-Transplant Lymphoproliferative Disorders. 1st Annual Meeting of the American-Society-of-Hematology. 2009; 114.
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23; 455(7216):1061-8. PMID: 18772890; DOI: 10.1038/nature07385;.
Huang G, Eisenberg R, Yan M, Monti S, Lawrence E, Fu P, Walbroehl J, Löwenberg E, Golub T, Merchan J, Tenen DG, Markowitz SD, Halmos B. 15-Hydroxyprostaglandin dehydrogenase is a target of hepatocyte nuclear factor 3beta and a tumor suppressor in lung cancer. Cancer Res. 2008 Jul 1; 68(13):5040-8. PMID: 18593902; PMCID: PMC2762106; DOI: 10.1158/0008-5472.CAN-07-6575;.
Tam WF, Gu TL, Chen J, Lee BH, Bullinger L, Fröhling S, Wang A, Monti S, Golub TR, Gilliland DG. Id1 is a common downstream target of oncogenic tyrosine kinases in leukemic cells. Blood. 2008 Sep 1; 112(5):1981-92. PMID: 18559972; PMCID: PMC2518899; DOI: 10.1182/blood-2007-07-103010;.
Chen L, Monti S, Juszczynski P, Daley J, Chen W, Witzig TE, Habermann TM, Kutok JL, Shipp MA. SYK-dependent tonic B-cell receptor signaling is a rational treatment target in diffuse large B-cell lymphoma. Blood. 2008 Feb 15; 111(4):2230-7. PMID: 18006696; PMCID: PMC2234057.
Juszczynski P, Ouyang J, Monti S, Rodig SJ, Takeyama K, Abramson J, Chen W, Kutok JL, Rabinovich GA, Shipp MA. The AP1-dependent secretion of galectin-1 by Reed Sternberg cells fosters immune privilege in classical Hodgkin lymphoma. Proc Natl Acad Sci U S A. 2007 Aug 7; 104(32):13134-9. PMID: 17670934; PMCID: PMC1936978.
Shin J, Monti S, Aires DJ, Duvic M, Golub T, Jones DA, Kupper TS. Lesional gene expression profiling in cutaneous T-cell lymphoma reveals natural clusters associated with disease outcome. Blood. 2007 Oct 15; 110(8):3015-27. PMID: 17638852; PMCID: PMC2018675.
Takeyama K, Monti S, Manis JP, Dal Cin P, Getz G, Beroukhim R, Dutt S, Aster JC, Alt FW, Golub TR, Shipp MA. Integrative analysis reveals 53BP1 copy loss and decreased expression in a subset of human diffuse large B-cell lymphomas. Oncogene. 2008 Jan 10; 27(3):318-22. PMID: 17637749; DOI: 10.1038/sj.onc.1210650;.
Polo JM, Juszczynski P, Monti S, Cerchietti L, Ye K, Greally JM, Shipp M, Melnick A. Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas. Proc Natl Acad Sci U S A. 2007 Feb 27; 104(9):3207-12. PMID: 17360630; PMCID: PMC1805543.
Juszczynski P, Ouyang J, Monti S, Rodig S. Takeyama K, Abramson J, Chen W, Kutok JL, Rabinovich GA, Ship MA. Haematologica. Galectin 1 mediates tumor escape in HL. 7th International Symposium on Hodgkin Lymphoma. 2007; 92.
Kobayashi S, Shimamura T, Monti S, Steidl U, Hetherington CJ, Lowell AM, Golub T, Meyerson M, Tenen DG, Shapiro GI, Halmos B. Transcriptional profiling identifies cyclin D1 as a critical downstream effector of mutant epidermal growth factor receptor signaling. Cancer Res. 2006 Dec 1; 66(23):11389-98. PMID: 17145885.
Hayes DN, Monti S, Parmigiani G, Gilks CB, Naoki K, Bhattacharjee A, Socinski MA, Perou C, Meyerson M. Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol. 2006 Nov 1; 24(31):5079-90. PMID: 17075127.
Takahashi H, Feuerhake F, Kutok JL, Monti S, Dal Cin P, Neuberg D, Aster JC, Shipp MA. FAS death domain deletions and cellular FADD-like interleukin 1beta converting enzyme inhibitory protein (long) overexpression: alternative mechanisms for deregulating the extrinsic apoptotic pathway in diffuse large B-cell lymphoma subtypes. Clin Cancer Res. 2006 Jun 1; 12(11 Pt 1):3265-71. PMID: 16740746.
Gould J, Getz G, Monti S, Reich M, Mesirov JP. Comparative gene marker selection suite. Bioinformatics. 2006 Aug 1; 22(15):1924-5. PMID: 16709585.
Pasqualucci L, Compagno M, Houldsworth J, Monti S, Grunn A, Nandula SV, Aster JC, Murty VV, Shipp MA, Dalla-Favera R. Inactivation of the PRDM1/BLIMP1 gene in diffuse large B cell lymphoma. J Exp Med. 2006 Feb 20; 203(2):311-7. PMID: 16492805; PMCID: PMC2118216.
Bassères DS, Levantini E, Ji H, Monti S, Elf S, Dayaram T, Fenyus M, Kocher O, Golub T, Wong KK, Halmos B, Tenen DG. Respiratory failure due to differentiation arrest and expansion of alveolar cells following lung-specific loss of the transcription factor C/EBPalpha in mice. Mol Cell Biol. 2006 Feb; 26(3):1109-23. PMID: 16428462; PMCID: PMC1347037.
Takahashi H, Feuerhake F, Monti S, Kutok JL, Aster JC, Shipp MA. Lack of IKBA coding region mutations in primary mediastinal large B-cell lymphoma and the host response subtype of diffuse large B-cell lymphoma. Blood. 2006 Jan 15; 107(2):844-5. PMID: 16401828.
Feuerhake F, Kutok JL, Monti S, Chen W, LaCasce AS, Cattoretti G, Kurtin P, Pinkus GS, de Leval L, Harris NL, Savage KJ, Neuberg D, Habermann TM, Dalla-Favera R, Golub TR, Aster JC, Shipp MA. NFkappaB activity, function, and target-gene signatures in primary mediastinal large B-cell lymphoma and diffuse large B-cell lymphoma subtypes. Blood. 2005 Aug 15; 106(4):1392-9. PMID: 15870177.
Cooper GF, Abraham V, Aliferis CF, Aronis JM, Buchanan BG, Caruana R, Fine MJ, Janosky JE, Livingston G, Mitchell T, Monti S, Spirtes P. Predicting dire outcomes of patients with community acquired pneumonia. J Biomed Inform. 2005 Oct; 38(5):347-66. PMID: 16198995.
Monti S, Savage KJ, Kutok JL, Feuerhake F, Kurtin P, Mihm M, Wu B, Pasqualucci L, Neuberg D, Aguiar RC, Dal Cin P, Ladd C, Pinkus GS, Salles G, Harris NL, Dalla-Favera R, Habermann TM, Aster JC, Golub TR, Shipp MA. Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood. 2005 Mar 1; 105(5):1851-61. PMID: 15550490.
Halmos B, Bassères DS, Monti S, D'Aló F, Dayaram T, Ferenczi K, Wouters BJ, Huettner CS, Golub TR, Tenen DG. A transcriptional profiling study of CCAAT/enhancer binding protein targets identifies hepatocyte nuclear factor 3 beta as a novel tumor suppressor in lung cancer. Cancer Res. 2004 Jun 15; 64(12):4137-47. PMID: 15205324.
Savage KJ, Monti S, Kutok JL, Cattoretti G, Neuberg D, De Leval L, Kurtin P, Dal Cin P, Ladd C, Feuerhake F, Aguiar RC, Li S, Salles G, Berger F, Jing W, Pinkus GS, Habermann T, Dalla-Favera R, Harris NL, Aster JC, Golub TR, Shipp MA. The molecular signature of mediastinal large B-cell lymphoma differs from that of other diffuse large B-cell lymphomas and shares features with classical Hodgkin lymphoma. Blood. 2003 Dec 1; 102(12):3871-9. PMID: 12933571.
Monti S, Tamayo P, Mesirov JP, Golub TR. Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data. Machine Learning. 2003; 52(1-2):91-118. View Publication
Chen CZ, Li M, de Graaf D, Monti S, Göttgens B, Sanchez MJ, Lander ES, Golub TR, Green AR, Lodish HF. Identification of endoglin as a functional marker that defines long-term repopulating hematopoietic stem cells. Proc Natl Acad Sci U S A. 2002 Nov 26; 99(24):15468-73. PMID: 12438646; PMCID: PMC137740.
Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A. 2001 Nov 20; 98(24):13790-5. PMID: 11707567; DOI: 10.1073/pnas.191502998;.
Monti S, Carenini G. Dealing with the expert inconsistency in probability elicitation. IEEE Transactions on Knowledge and Data Engineering. 2000; 12(4):499-508. View Publication
Monti S, Cooper GF. 7-th International Workshop on AI and Statistics. A Latent Variable Model for Multivariate Discretization. 1999.
Monti S, Cooper GF. The impact of modeling the dependencies among patient findings on classification accuracy and calibration. Proc AMIA Symp. 1998; 592-6. PMID: 9929288.
Monti S, Cooper GF. Learning Bayesian belief networks with neural network estimators. Advances in neural information processing systems. 1997.
Monti S, Cooper GF. Learning Hybrid Bayesian Networks from Data. Learning in Graphical Models. 1997. View Publication
Monti S, Cooper GF. Bounded recursive decomposition: A search-based method for belief-network inference under limited resources. International Journal of Approximate Reasoning. 1996; 15(1):49-75. View Publication
Carenini G, Monti S, Banks G. Artificial Intelligence in Medicine: 5th Conference on Artificial Intelligence in Medicine Europe, AIME '95 Pavia, Italy, June 25–28, 1995 Proceedings. An Information-Based Bayesian Approach to History Taking. 1995; 129-138. View Publication
Monti S, Savage K, Kutok JL, Ladd C, Friedrich F, Kurtin PJ, Mihm MC, Wu B, Pasqualucci L, Neuberg D, Aguiar RCT, Dal Cin P. Supplementary information for Molecular profiling of diffuse large B-cell lymphoma reveals discrete clusters including one characterized by host inflammatory response.
Tam WF, Gu TL, Chen J, Lee BH, Bullinger L, Frohling S, Wang A, Monti S, Golub TR, Gilliland DG. Running Title: Oncogenic tyrosine kinases upregulate Id1.
Gould J, Liefeld T, Reich M, Thorvaldottir H, Ross K, Monti S. GenePattern Workshop.
Getz G, Gould J, Monti S. Boosting permutation tests for marker selection.

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 92 publications over 25 distinct years, with a maximum of 10 publications in 2016