Available to mentor
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Center MemberPrecision Health Initiative
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Center Membere-Health and Artificial Intelligence Initiative
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Center MemberRogel Cancer Center
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Center MemberInstitute for Healthcare Policy and Innovation
Research theme: my group’s research has developed methodologies for the analysis and integrative interpretation of spatially-based, multi-modal, omics datasets (e.g: imaging, genomics, spatial profiling) for improved disease understanding and clinical decision making. Our work spans machine learning and statistical modeling for radiomics, digital pathology, predictive modeling, genomic data integration, and most recently spatial immunoprofiling and spatial transcriptomics.
Research:
a. Biomedical Image Informatics & Spatial Biology: In order to quantify the phenotypic aspects of disease, their relationships with outcome, and their genetic context, we have developed methods for the analysis of histopathology and radiology images, focusing on tumor heterogeneity. One direction of my group is to develop image analysis tools to delineate tumor image features from radiology data and, along with underlying genomic measurements, to develop AI-based predictive models to relate them to outcomes in low grade gliomas. Further, we have also investigated methodologies to link tumor imaging, genetics, and immune status in disease. Along these lines, we have embarked on measuring immune contexture in the tumor microenvironment, developing methods for the inference of the spatial architecture and patterns of infiltration of immune cells, based on multiplex-IHC and spatial transcriptomics technologies. Further, we have also developed methods for the analysis of multiparametric magnetic resonance imaging (MR) datasets in radiation oncology
b. Artificial Intelligence (AI) methods for Medicine: Our expertise is evidenced by two streams of work: (1) Developing statistical and machine learning (ML) methods to analyze and interpret multi-modal image/genomic data; (2) application of AI/ML formalisms for predictive models based on genomics, radiology and pathology imaging. These are used to assess disease stage, suitability for specific drug targets, molecular therapies & immunotherapies. More recently, we have been working on problems of bias, uncertainty quantification as well as auditing of AI solutions (in radiology and pathology image informatics) in healthcare.
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Shankar S, Ravikumar V, Tripathy A, Ji S, Loper J, Hassan Z, Fehmi Z, Haydin Y, Huang D-L, Bhadury S, Kulkarni R, Regier J, Wahl D, Rao A, Rehemtulla A, Al-Holou WN. Cancer Research, 2024 Mar 4; 84 (5_Supplement_1): b001 - b001.Journal ArticleAbstract B001: Glioblastoma evolution and resistance is mediated by a shift in cell state and tumor microenvironmental interactions
DOI:10.1158/1538-7445.brain23-b001 -
Saldarriaga OA, Wanninger TG, Arroyave E, Gosnell J, Krishnan S, Oneka M, Bao D, Millian DE, Kueht ML, Moghe A, Jiao J, Sanchez JI, Spratt H, Beretta L, Rao A, Burks JK, Stevenson HL. JHEP Rep, 2024 Jan; 6 (1): 100958Journal ArticleHeterogeneity in intrahepatic macrophage populations and druggable target expression in patients with steatotic liver disease-related fibrosis.
DOI:10.1016/j.jhepr.2023.100958 PMID: 38162144 -
Zhang Q, Jiang L, Wang W, Huber AK, Valvo VM, Jungles KM, Holcomb EA, Pearson AN, The S, Wang Z, Parsels LA, Parsels JD, Wahl DR, Rao A, Sahai V, Lawrence TS, Green MD, Morgan MA. JCI Insight, 2024 Feb 20; 9 (6):Journal ArticlePotentiating the radiation-induced type I interferon antitumoral immune response by ATM inhibition in pancreatic cancer.
DOI:10.1172/jci.insight.168824 PMID: 38376927 -
Malgulwar PB, Danussi C, Dharmaiah S, Johnson W, Singh A, Rai K, Rao A, Huse JT. Neuro Oncol, 2024 Jan 5; 26 (1): 55 - 67.Journal ArticleSirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma.
DOI:10.1093/neuonc/noad155 PMID: 37625115 -
Masotti M, Osher N, Eliason J, Rao A, Baladandayuthapani V. Patterns (N Y), 2023 Dec 8; 4 (12): 100879Journal ArticleDIMPLE: An R package to quantify, visualize, and model spatial cellular interactions from multiplex imaging with distance matrices.
DOI:10.1016/j.patter.2023.100879 PMID: 38106614 -
Chekouo T, Stingo FC, Mohammed S, Rao A, Baladandayuthapani V. Annals of Applied Statistics, 2023 Dec 1; 17 (4): 3013 - 3034.Journal ArticleA BAYESIAN GROUP SELECTION WITH COMPOSITIONAL RESPONSES FOR ANALYSIS OF RADIOLOGIC TUMOR PROPORTIONS AND THEIR GENOMIC DETERMINANTS
DOI:10.1214/23-AOAS1749 -
Lee J, Narang S, Martinez J, Rao G, Rao A. Sci Rep, 2023 Oct 9; 13 (1): 17046Journal ArticleAssociation of graph-based spatial features with overall survival status of glioblastoma patients.
DOI:10.1038/s41598-023-44353-7 PMID: 37813981 -
Pati S, Baid U, Edwards B, Sheller M, Wang S-H, Reina GA, Foley P, Gruzdev A, Karkada D, Davatzikos C, Sako C, Ghodasara S, Bilello M, Mohan S, Vollmuth P, Brugnara G, Preetha CJ, Sahm F, Maier-Hein K, Zenk M, Bendszus M, Wick W, Calabrese E, Rudie J, Villanueva-Meyer J, Cha S, Ingalhalikar M, Jadhav M, Pandey U, Saini J, Garrett J, Larson M, Jeraj R, Currie S, Frood R, Fatania K, Huang RY, Chang K, Balaña C, Capellades J, Puig J, Trenkler J, Pichler J, Necker G, Haunschmidt A, Meckel S, Shukla G, Liem S, Alexander GS, Lombardo J, Palmer JD, Flanders AE, Dicker AP, Sair HI, Jones CK, Venkataraman A, Jiang M, So TY, Chen C, Heng PA, Dou Q, Kozubek M, Lux F, Michálek J, Matula P, Keřkovský M, Kopřivová T, Dostál M, Vybíhal V, Vogelbaum MA, Mitchell JR, Farinhas J, Maldjian JA, Yogananda CGB, Pinho MC, Reddy D, Holcomb J, Wagner BC, Ellingson BM, Cloughesy TF, Raymond C, Oughourlian T, Hagiwara A, Wang C, To M-S, Bhardwaj S, Chong C, Agzarian M, Falcão AX, Martins SB, Teixeira BCA, Sprenger F, Menotti D, Lucio DR, LaMontagne P, Marcus D, Wiestler B, Kofler F, Ezhov I, Metz M, Jain R, Lee M, Lui YW, McKinley R, Slotboom J, Radojewski P, Meier R, Wiest R, Murcia D, Fu E, Haas R, Thompson J, Ormond DR, Badve C, Sloan AE, Vadmal V, Waite K, Colen RR, Pei L, Ak M, Srinivasan A, Bapuraj JR, Rao A, Wang N, Yoshiaki O, Moritani T, Turk S, Lee J, Prabhudesai S, Morón F, Mandel J, Kamnitsas K, Glocker B, Dixon LVM, Williams M, Zampakis P, Panagiotopoulos V, Tsiganos P, Alexiou S, Haliassos I, Zacharaki EI, Moustakas K, Kalogeropoulou C, Kardamakis DM, Choi YS, Lee S-K, Chang JH, Ahn SS, Luo B, Poisson L, Wen N, Tiwari P, Verma R, Bareja R, Yadav I, Chen J, Kumar N, Smits M, van der Voort SR, Alafandi A, Incekara F, Wijnenga MMJ, Kapsas G, Gahrmann R, Schouten JW, Dubbink HJ, Vincent AJPE, van den Bent MJ, French PJ, Klein S, Yuan Y, Sharma S, Tseng T-C, Adabi S, Niclou SP, Keunen O, Hau A-C, Vallières M, Fortin D, Lepage M, Landman B, Ramadass K, Xu K, Chotai S, Chambless LB, Mistry A, Thompson RC, Gusev Y, Bhuvaneshwar K, Sayah A, Bencheqroun C, Belouali A, Madhavan S, Booth TC, Chelliah A, Modat M, Shuaib H, Dragos C, Abayazeed A, Kolodziej K, Hill M, Abbassy A, Gamal S, Mekhaimar M, Qayati M, Reyes M, Park JE, Yun J, Kim HS, Mahajan A, Muzi M, Benson S, Beets-Tan RGH, Teuwen J, Herrera-Trujillo A, Trujillo M, Escobar W, Abello A, Bernal J, Gómez J, Choi J, Baek S, Kim Y, Ismael H, Allen B, Buatti JM, Kotrotsou A, Li H, Weiss T, Weller M, Bink A, Pouymayou B, Shaykh HF, Saltz J, Prasanna P, Shrestha S, Mani KM, Payne D, Kurc T, Pelaez E, Franco-Maldonado H, Loayza F, Quevedo S, Guevara P, Torche E, Mendoza C, Vera F, Ríos E, López E, Velastin SA, Ogbole G, Soneye M, Oyekunle D, Odafe-Oyibotha O, Osobu B, Shu'aibu M, Dorcas A, Dako F, Simpson AL, Hamghalam M, Peoples JJ, Hu R, Tran A, Cutler D, Moraes FY, Boss MA, Gimpel J, Veettil DK, Schmidt K, Bialecki B, Marella S, Price C, Cimino L, Apgar C, Shah P, Menze B, Barnholtz-Sloan JS, Martin J, Bakas S. Nat Commun, 2023 Jan 26; 14 (1): 436Journal ArticleAuthor Correction: Federated learning enables big data for rare cancer boundary detection.
DOI:10.1038/s41467-023-36188-7 PMID: 36702828
