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 in January 2011 in the section of Computational Biomedicine, with joint appointments in the Biostatistics Department and 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.

Dr. Monti's laboratory integrates systems biology, machine learning, and bioinformatics approaches to investigate the molecular drivers of human disease, with the goals of advancing prevention and care. This multidisciplinary effort relies on the development of novel computational methodologies, and on the design of experiments based on the generation and integrative analysis of high-throughput multi-omics data, with the goal of identifying novel therapeutic targets and developing accurate diagnostic and prognostic biomarkers. Specific areas of research include the study of the molecular mechanisms of tumor initiation and progression and of the role played in it by environmental exposure, as well as the study of the biological factors contributing to healthy aging and extreme longevity.

Associate Professor
Boston University School of Public Health
Biostatistics

Member
Boston University
BU-BMC Cancer Center

Member
Boston University
Evans Center for Interdisciplinary Biomedical Research

Member
Boston University
Bioinformatics Graduate Program

Member
Boston University
Genome Science Institute

Graduate Faculty (Primary Mentor of Grad Students)
Boston University School of Medicine, Graduate Medical Sciences

BU Research

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

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 (Subcontract 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 (Subcontract PI)
Dana-Farber Cancer Institute Leukemia & Lymph Soc

Title

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.

iCite Analysis Copy PMIDs To Clipboard

Chandler KB, Alamoud KA, Stahl VL, Nguyen BC, Kartha VK, Bais MV, Nomoto K, Owa T, Monti S, Kukuruzinska MA, Costello CE. ß-Catenin/CBP inhibition alters epidermal growth factor receptor fucosylation status in oral squamous cell carcinoma. Mol Omics. 2020 06 01; 16(3):195-209.View Related Profiles.

Costello, Catherine
Chandler, Kevin
Bais, Manish
Kukuruzinska, Maria
Monti, Stefano

PMID: 32203567

Federico A, Monti S. hypeR: an R package for geneset enrichment workflows. Bioinformatics. 2020 02 15; 36(4):1307-1308. PMID: 31498385

Stampouloglou E, Cheng N, Federico A, Slaby E, Monti S, Szeto GL, Varelas X. Yap suppresses T-cell function and infiltration in the tumor microenvironment. PLoS Biol. 2020 01; 18(1):e3000591.View Related Profiles.

Stampouloglou, Eleni
Monti, Stefano
Varelas, Xaralabos

PMID: 31929526

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 11 15; 9(1):16904.View Related Profiles.

Sebastiani, Paola
Monti, Stefano
Varelas, Xaralabos

PMID: 31729402

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 09 01; 35(17):3046-3054.View Related Profiles.

Sebastiani, Paola
Andersen, Stacy
Monti, Stefano
Perls, Thomas

PMID: 30624692

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. 2020 May; 105(5):1361-1368. PMID: 31471373

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 12; 18(6):e13023.View Related Profiles.

Sebastiani, Paola
Andersen, Stacy
Monti, Stefano
Perls, Thomas

PMID: 31385390

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

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.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

Showing 10 of 103 results. Show More

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

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 09; 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

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
Ikonomou, 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

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 Artificial Intelligence and Statistics. "A Latent Variable Model for Multivariate Discretization". 1999; 249-254. View Publication
Monti S, Cooper GF. Proceedings of 15th Conference of Uncertainty in Artificial Intelligence. "A Bayesian Network Classifier that Combines a Naive-Bayes model and a Finite-Mixture Model". Morgan Kaufmann Publishers Inc. San Francisco, CA, USA. 1999; 447-456. View Publication
Monti S, Cooper GF. Proceedings of 14th Conference of Uncertainty in Artificial Intelligence . "A Multivariate Discretization Method for Learning Bayesian Networks from Mixed Data". Morgan Kaufmann Publishers Inc. San Francisco, CA, USA. 1998; 404-413. View Publication

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; 9:578-584. View Publication
Monti S, Cooper GF. Learning Hybrid Bayesian Networks from Data. Learning in Graphical Models. Springer, Dordrecht. 1997; 89:521-540. 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 99 publications over 26 distinct years, with a maximum of 10 publications in 2016