Dennis Jay Montoya, Ph.D.
Assistant Researcher
Oak Park Research Building
Sacramento Campus
email
Research Interests
Dennis Montoya is a wet-lab immunologist turned computational immunologist. His research focuses on developing methods to parse the tissue cellular microenvironment through integration of genomic, transcriptomic, and epigenomic data. He has developed a suite of computational tools for the estimation of cellular frequency or immune activation pathways from whole tissue functional genomic data. His computational tools have been used in many settings, in particular for biomarker discovery from observational research studies. His research approach strives leverage patient and tissue heterogeneity to elucidate underlying genomic-phenotype associations. He is currently focusing on cancer therapy resistance.
Full list of publications can be seen at: PubMed or Google Scholar »
Oien DB, Ray U, Pathoulas CL, Jin L, Thirusangu P, Jung D, Kumka JE, Xiao Y, Sarkar Bhattacharya S, Montoya D, Chien J, Shridhar V. “Quinacrine Induces Nucleolar Stress in Treatment-Refractory Ovarian Cancer Cell Lines”. Cancers (Basel). (2021) Sep 16;13(18):4645.
De Souza C, Madden J, Koestler DC, Minn D, Montoya DJ, Minn K, Raetz AG, Zhu Z, Xiao WW, Tahmassebi N, Reddy H, Nelson N, Karnezis AN, Chien J. “Effect of the p53 P72R Polymorphism on Mutant TP53 Allele Selection in Human Cancer.” J Natl Cancer Inst. (2021) Sep 4;113(9):1246-1257.
Nadel BB, Oliva M, Shou BL, Mitchell K, Ma F, Montoya DJ, Mouton A, Kim-Hellmuth S, Stranger BE, Pellegrini M, Mangul S. “Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples.” Brief Bioinform. (2021) Aug 3:bbab265
Chang YL, Rossetti M, Gjertson DW, Rubbi L, Thompson M, Montoya DJ, Morselli M, Ruffin F, Hoffmann A, Pellegrini M, Fowler VG Jr, Yeaman MR, Reed EF; with the MRSA Systems Immunology Group. “Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia.” Proc Natl Acad Sci U S A. (2021) Mar 9;118(10):e2000663118.
Nadel BB, Lopez D, Montoya DJ, Ma F, Waddel H, Khan MM, Mangul S, Pellegrini M. “The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data.” Gigascience. (2021) Feb 16;10(2):giab002.
Sharma NK, Comeau ME, Montoya D, Pellegrini M, Howard TD, Langefeld CD, Das SK. “Integrative Analysis of Glucometabolic Traits, Adipose Tissue DNA Methylation and Gene Expression Identifies Epigenetic Regulatory Mechanisms of Insulin Resistance and Obesity in African Americans.” Diabetes. (2020). Dec;69(12):2779-2793.
Mandric I, Yang HT, Strauli N, Montoya D, Rotman J, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V, Zelikovsky A, Spreafico R, Shifman S, Zaitlen N, Rossetti M, Ansel KM, Eskin E, Mangul S. “Profiling immunoglobulin repertoires across multiple human tissues using RNA Sequencing.” Nature Communications. (2020) Jun 19;11(1):3126.
Montoya DJ, Andrade P, Silva BJA, Teles RMB, Ma F, Bryson B, Sadanand S, Noel T, Lu J, Sarno E, Arnvig KB, Young D, Lahiri R, Williams DL, Fortune S, Bloom BR, Pellegrini M, Modlin RL. “Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response.” Cell Reports (2019) Mar 26, 3574–3585.e3.
Montoya D, Mehta M, Ferguson BG, Teles RM, Kruzik SR, Cruz D, Pellegrini M, Modlin RL. “Plasticity of antimicrobial and phagocytic programs in human macrophages.” Immunology. (2018) Oct 24.
Orozco LD, Farrell C, Hale C, Rubbi L, Rinaldi A, Civelek M, Pan C, Lam L, Montoya D, Edillor C, Seldin M, Boehnke M, Mohlke KL, Jacobsen S, Kuusisto J, Laakso M, Lusis AJ, Pellegrini M. “Epigenome-wide association in adipose tissue from the METSIM cohort.” Human Molecular Genetics. (2018) May 15; 7(10):1830-1846.
Grasso C, Giannakis M, Wells D, Hamada T, Mu XJ, Quist M, Nowak J, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels M, Grady W, Hsu L, Hu-Lieskovan S, Huyghe J, Kim YJ, Krystofinski P, Leiserson M, Montoya DJ, Nadel B, Pellegrini M, Pritchard C, Puig-Saus C, Quist E, Raphael B, Salipante S, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford J, Sun W, Ts:oi J, Upfill-Brown A, Wheeler D, Wu C, Yu M, Zaidi S, Zaretsky J, Gabriel S, Lander E, Garraway L, Hudson T, Fuchs C, Ribas A, Ogino S, Peter U. “Genetic mechanisms of immune evasion in colorectal cancer.” Cancer Discovery. (2018) Mar 6.
Lopez D, Montoya D, Ambrose M, Lam L, Briscoe L, Adams C, Modlin RL, Pellegrini M. “SaVanT: A web-based tool for the sample-level visualization of molecular signatures in gene expression profiles”. (2017) BMC Genomics. Oct 25;18(1):824.
Montoya D, Inkeles MS, Liu PT, Realegeno S, Teles RM, Vaidya P, Munoz MA, Schenk M, Swindell WR, Chun R, Zavala K, Hewison M, Adams JS, Horvath S, Pellegrini M, Bloom BR, Modlin RL. (2014) “IL-32 is a molecular marker of a host defense network in human tuberculosis.” Science Translational Medicine. 6(250):250ra114.
Montoya D, Cruz D, Teles RM, Lee DJ, Ochoa MT, Krutzik SR, Chun R, Schenk M, Zhang X, Ferguson BG, Burdick AE, Sarno EN, Rea TH, Hewison M, Adams JS, Cheng G, Modlin RL. (2009) “Divergence of macrophage phagocytic and antimicrobial programs in leprosy.” Cell Host & Microbe.” Oct 22;6(4):343-53.