Publications

Deep-Learning Integrates Histopathology and Proteogenomics at a Pan-cancer Level
We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive …
Joshua M. Wang, Hong R*, Lazar AJ, Demicco EG, Tan J, Moreira AL, Razavian N, Schraink T, Gillette MA, Omenn G, An E, Rodriguez H, Tsirigos A, Ruggles KV, Ding L, Robles AI, Mani DR, Rodland KD, Liu W, Fenyö D
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Proteogenomic characterization of pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying …
Liwei Cao, Chen Huang, Daniel Cui Zhou, Yingwei Hu, T Mamie Lih, Sara R Savage, Karsten Krug, David J Clark, Michael Schnaubelt, Lijun Chen, Felipe da Veiga Leprevost, Rodrigo Vargas Eguez, Weiming Yang, Jianbo Pan, Bo Wen, Yongchao Dou, Wen Jiang, Yuxing Liao, Zhiao Shi, Nadezhda V Terekhanova, Song Cao, Rita Jui-Hsien Lu, Yize Li, Ruiyang Liu, Houxiang Zhu, Peter Ronning, Yige Wu, Matthew A Wyczalkowski, Hariharan Easwaran, Ludmila Danilova, Arvind Singh Mer, Seungyeul Yoo, Joshua M. Wang, Wenke Liu, Benjamin Haibe-Kains, Mathangi Thiagarajan, Scott D Jewell, Galen Hostetter, Chelsea J Newton, Qing Kay Li, Michael H Roehrl, David Fenyö, Pei Wang, Alexey I Nesvizhskii, DR Mani, Gilbert S Omenn, Emily S Boja, Mehdi Mesri, Ana I Robles, Henry Rodriguez, Oliver F Bathe, Daniel W Chan, Ralph H Hruban, Li Ding, Bing Zhang, Hui Zhang, Mitual Amin, Eunkyung An, Christina Ayad, Thomas Bauer, Chet Birger, Michael J Birrer, Simina M Boca, William Bocik, Melissa Borucki, Shuang Cai, Steven A Carr, Sandra Cerda, Huan Chen, Steven Chen, David Chesla, Arul M Chinnaiyan, Antonio Colaprico, Sandra Cottingham, Magdalena Derejska, Saravana M Dhanasekaran, Marcin J Domagalski, Brian J Druker, Elizabeth Duffy, Maureen A Dyer, Nathan J Edwards, Matthew J Ellis, Jennifer Eschbacher, Alicia Francis, Jesse Francis, Stacey Gabriel, Nikolay Gabrovski, Johanna Gardner, Gad Getz, Michael A Gillette, Charles A Goldthwaite, Pamela Grady, Shuai Guo, Pushpa Hariharan, Tara Hiltke, Barbara Hindenach, Katherine A Hoadley, Jasmine Huang, Corbin D Jones, Karen A Ketchum, Christopher R Kinsinger, Jennifer M Koziak, Katarzyna Kusnierz, Tao Liu, Jiang Long, David Mallery, Sailaja Mareedu, Ronald Matteotti, Nicollette Maunganidze, Peter B McGarvey, Parham Minoo, Oxana V Paklina, Amanda G Paulovich, Samuel H Payne, Olga Potapova, Barbara Pruetz, Liqun Qi, Nancy Roche, Karin D Rodland, Daniel C Rohrer, Eric E Schadt, Alexey V Shabunin, Troy Shelton, Yvonne Shutack, Shilpi Singh, Michael Smith, Richard D Smith, Lori J Sokoll, James Suh, Ratna R Thangudu, Shirley X Tsang, Ki Sung Um, Dana R Valley, Negin Vatanian, Wenyi Wang, George D Wilson, Maciej Wiznerowicz, Zhen Zhang, Grace Zhao
DOI
Proteogenomic characterization of pancreatic ductal adenocarcinoma
Predictive modeling of morbidity and mortality in patients hospitalized with COVID-19 and its clinical implications: algorithm development and interpretation
Background: The COVID-19 pandemic began in early 2021 and placed significant strains on health care systems worldwide. There remains a compelling need to analyze factors that are predictive for patients at elevated risk of morbidity and mortality.
Joshua M. Wang, Wenke Liu, Xiaoshan Chen, Michael P McRae, John T McDevitt, David Fenyö
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Intraspecies transcriptional profiling reveals key regulators of Candida albicans pathogenic traits
The human commensal and opportunistic fungal pathogen Candida albicans displays extensive genetic and phenotypic variation across …
Joshua M. Wang, Andrew L Woodruff, Matthew J Dunn, Robert J Fillinger, Richard J Bennett, Matthew Z Anderson
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Integrated proteogenomic characterization across major histological types of pediatric brain cancer
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
Francesca Petralia, Nicole Tignor, Boris Reva, Mateusz Koptyra, Shrabanti Chowdhury, Dmitry Rykunov, Azra Krek, Weiping Ma, Yuankun Zhu, Jiayi Ji, Anna Calinawan, Jeffrey R Whiteaker, Antonio Colaprico, Vasileios Stathias, Tatiana Omelchenko, Xiaoyu Song, Pichai Raman, Yiran Guo, Miguel A Brown, Richard G Ivey, John Szpyt, Sanjukta Guha Thakurta, Marina A Gritsenko, Karl K Weitz, Gonzalo Lopez, Selim Kalayci, Zeynep H Gümüş, Seungyeul Yoo, Felipe da Veiga Leprevost, Hui-Yin Chang, Karsten Krug, Lizabeth Katsnelson, Ying Wang, Jacob J Kennedy, Uliana J Voytovich, Lei Zhao, Krutika S Gaonkar, Brian M Ennis, Bo Zhang, Valerie Baubet, Lamiya Tauhid, Jena V Lilly, Jennifer L Mason, Bailey Farrow, Nathan Young, Sarah Leary, Jamie Moon, Vladislav A Petyuk, Javad Nazarian, Nithin D Adappa, James N Palmer, Robert M Lober, Samuel Rivero-Hinojosa, Liang-Bo Wang, Joshua M. Wang, Matilda Broberg, Rosalie K Chu, Ronald J Moore, Matthew E Monroe, Rui Zhao, Richard D Smith, Jun Zhu, Ana I Robles, Mehdi Mesri, Emily Boja, Tara Hiltke, Henry Rodriguez, Bing Zhang, Eric E Schadt, DR Mani, Li Ding, Antonio Iavarone, Maciej Wiznerowicz, Stephan Schürer, Xi S Chen, Allison P Heath, Jo Lynne Rokita, Alexey I Nesvizhskii, David Fenyö, Karin D Rodland, Tao Liu, Steven P Gygi, Amanda G Paulovich, Adam C Resnick, Phillip B Storm, Brian R Rood, Pei Wang, Alicia Francis, Allison M Morgan, Angela J Waanders, Angela N Viaene, Anna Maria Buccoliero, Arul M Chinnaiyan, Carina A Leonard, Cassie N Kline, Chiara Caporalini, Christopher R Kinsinger, Chunde Li, David E Kram, Derek Hanson, Elizabeth Appert, Emily A Kawaler, Eric H Raabe, Eric M Jackson, Jeffrey P Greenfield, Gabrielle S Stone, Gad Getz, Gerald Grant, Guo Ci Teo, Ian F Pollack, Jason E Cain, Jessica B Foster, Joanna J Phillips, July E Palma, Karen A Ketchum, Kelly V Ruggles, Lili Blumenberg, Macintosh Cornwell, Mahdi Sarmady, Marcin J Domagalski, Marcin P Cieślik, Mariarita Santi, Marilyn M Li, Matthew J Ellis, Matthew A Wyczalkowski, Meghan Connors, Mirko Scagnet, Nalin Gupta, Nathan J Edwards, Nicholas A Vitanza, Olena M Vaske, Oren Becher, Peter B McGarvey, Ron Firestein, Sabine Mueller, Samuel G Winebrake, Saravana Mohan Dhanasekaran, Shuang Cai, Sonia Partap, Tatiana Patton, Toan Le, Travis D Lorentzen, Wenke Liu, William E Bocik
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Hemizygosity enables a mutational transition governing fungal virulence and commensalism
Shen-Huan Liang, Matthew Z Anderson, Matthew P Hirakawa, Joshua M. Wang, Corey Frazer, Leenah M Alaalm, Gregory J Thomson, Iuliana V Ene, Richard J Bennett
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The Genome of the Human Pathogen Candida albicans Is Shaped by Mutation and Cryptic Sexual Recombination
The opportunistic fungal pathogen Candida albicans lacks a conventional sexual program and is thought to evolve, at least primarily, …
Joshua M. Wang, Richard J Bennett, Matthew Z Anderson
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Genetic and phenotypic intra-species variation in Candida albicans
Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity …
Matthew P Hirakawa, Diego A Martinez, Sharadha Sakthikumar, Matthew Z Anderson, Aaron Berlin, Sharvari Gujja, Qiandong Zeng, Ethan Zisson, Joshua M. Wang, Joshua M Greenberg, Judith Berman, Richard J Bennett, Christina A Cuomo
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