Oncometabolite D-2-Hydroxyglutarate Inhibits ALKBH DNA Repair Enzymes and Sensitizes IDH Mutant Cells to Alkylating Agents von Wang, Pu, Wu, Jing, Ma, Shenghong, Zhang, Lei, Yao, Jun, Hoadley, Katherine A., Wilkerson, Matthew D., Perou, Charles M., Guan, Kun-Liang, Ye, Dan, Xiong, Yue

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Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation von Wilkerson, Matthew D, Yin, Xiaoying, Walter, Vonn, Zhao, Ni, Cabanski, Christopher R, Hayward, Michele C, Miller, C Ryan, Socinski, Mark A, Parsons, Alden M, Thorne, Leigh B, Haithcock, Benjamin E, Veeramachaneni, Nirmal K, Funkhouser, William K, Randell, Scott H, Bernard, Philip S, Perou, Charles M, Hayes, D Neil

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Activation of the PD-1 pathway contributes to immune escape in EGFR-driven lung tumors von Akbay, Esra A, Koyama, Shohei, Carretero, Julian, Altabef, Abigail, Tchaicha, Jeremy H, Christensen, Camilla L, Mikse, Oliver R, Cherniack, Andrew D, Beauchamp, Ellen M, Pugh, Trevor J, Wilkerson, Matthew D, Fecci, Peter E, Butaney, Mohit, Reibel, Jacob B, Soucheray, Margaret, Cohoon, Travis J, Janne, Pasi A, Meyerson, Matthew, Hayes, D Neil, Shapiro, Geoffrey I, Shimamura, Takeshi, Sholl, Lynette M, Rodig, Scott J, Freeman, Gordon J, Hammerman, Peter S, Dranoff, Glenn, Wong, Kwok-Kin

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ABRA: improved coding indel detection via assembly-based realignment von Mose, Lisle E, Wilkerson, Matthew D, Hayes, D Neil, Perou, Charles M, Parker, Joel S

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Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1 von Verhaak, Roel G.W., Hoadley, Katherine A., Purdom, Elizabeth, Wang, Victoria, Qi, Yuan, Wilkerson, Matthew D., Miller, C. Ryan, Ding, Li, Golub, Todd, Mesirov, Jill P., Alexe, Gabriele, Lawrence, Michael, O'Kelly, Michael, Tamayo, Pablo, Weir, Barbara A., Gabriel, Stacey, Winckler, Wendy, Gupta, Supriya, Jakkula, Lakshmi, Feiler, Heidi S., Hodgson, J. Graeme, James, C. David, Sarkaria, Jann N., Brennan, Cameron, Kahn, Ari, Spellman, Paul T., Wilson, Richard K., Speed, Terence P., Gray, Joe W., Meyerson, Matthew, Getz, Gad, Perou, Charles M., Hayes, D. Neil

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BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization von Orvis, Tess, Hepperla, Austin, Walter, Vonn, Song, Shujie, Simon, Jeremy, Parker, Joel, Wilkerson, Matthew D, Desai, Nisarg, Major, Michael B, Hayes, D Neil, Davis, Ian J, Weissman, Bernard

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Inhibitor-Sensitive FGFR2 and FGFR3 Mutations in Lung Squamous Cell Carcinoma von LIAO, Rachel G, JUNG, Joonil, GRAY, Nathanael S, GETZ, Gad, WONG, Kwok-Kin, HADDAD, Robert I, MEYERSON, Matthew, HAMMERMAN, Peter S, TCHAICHA, Jeremy, WILKERSON, Matthew D, SIVACHENKO, Andrey, BEAUCHAMP, Ellen M, QINGSONG LIU, PUGH, Trevor J, PEDAMALLUL, Chandra Sekhar, HAYES, D. Neil

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Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes von Walter, Vonn, Yin, Xiaoying, Wilkerson, Matthew D, Cabanski, Christopher R, Zhao, Ni, Du, Ying, Ang, Mei Kim, Hayward, Michele C, Salazar, Ashley H, Hoadley, Katherine A, Fritchie, Karen, Sailey, Charles J, Sailey, Charles G, Weissler, Mark C, Shockley, William W, Zanation, Adam M, Hackman, Trevor, Thorne, Leigh B, Funkhouser, William D, Muldrew, Kenneth L, Olshan, Andrew F, Randell, Scott H, Wright, Fred A, Shores, Carol G, Hayes, D Neil

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Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking von Porrello, Alessandro, Leslie, Patrick L., Harrison, Emily B., Gorentla, Balachandra K., Kattula, Sravya, Ghosh, Subrata K., Azam, Salma H., Holtzhausen, Alisha, Chao, Yvonne L., Hayward, Michele C., Waugh, Trent A., Bae, Sanggyu, Godfrey, Virginia, Randell, Scott H., Oderup, Cecilia, Makowski, Liza, Weiss, Jared, Wilkerson, Matthew D., Hayes, D. Neil, Earp, H. Shelton, Baldwin, Albert S., Wolberg, Alisa S., Pecot, Chad V.

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Integrative and Comparative Genomic Analysis of Lung Squamous Cell Carcinomas in East Asian Patients von YOUNGWOOK KIM, HAMMERMAN, Peter S, LAWRENCE, Michael S, STOJANOV, Petar, CARTER, Scott L, McKENNA, Aaron, STEWART, Chip, SIVACHENKO, Andrey Y, OH, In-Jae, HONG KWAN KIM, YONG SOO CHOI, KWHANMIEN KIM, JAEGIL KIM, YOUNG MOG SHIM, KIM, Kyu-Sik, SONG, Sang-Yun, NA, Kook-Joo, CHOI, Yoon-La, HAYES, D. Neil, JHINGOOK KIM, SUKKI CHO, KIM, Young-Chul, JIN SEOK AHN, YOON, Ji-Ae, AHN, Myung-Ju, GETZ, Gad, MEYERSON, Matthew, KEUNCHIL PARK, YOOMI LEE, SUN, Jong-Mu, WILKERSON, Matthew D, CHANDRA SEKHAR PEDAMALLU, CIBULSKIS, Kristian, YEONG KYUNG YOO

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MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes von Soltis, Anthony R., Dalgard, Clifton L., Pollard, Harvey B., Wilkerson, Matthew D.

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Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors von Wong, Kwong-Kwok, Bateman, Nicholas W, Ng, Chun Wai, Tsang, Yvonne T M, Sun, Charlotte S, Celestino, Joseph, Nguyen, Tri V, Malpica, Anais, Hillman, R Tyler, Zhang, Jianhua, Futreal, P Andrew, Rojas, Christine, Conrads, Kelly A, Hood, Brian L, Dalgard, Clifton L, Wilkerson, Matthew D, Phippen, Neil T, Conrads, Thomas P, Maxwell, George L, Sood, Anil K, Gershenson, David M

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Lung Squamous Cell Carcinoma mRNA Expression Subtypes Are Reproducible, Clinically Important, and Correspond to Normal Cell Types von WILKERSON, Matthew D, XIAOYING YIN, PARSONS, Alden M, FUNKHOUSER, William K, LEE, Carrie B, ROBERTS, Patrick J, THORNE, Leigh, BERNARD, Philip S, PEROU, Charles M, HAYS, D. Neil, HOADLEY, Katherine A, YUFENG LIU, HAYWARD, Michele C, CABANSKI, Christopher R, MULDREW, Kenneth, MILLER, C. Ryan, RANDELL, Scott H, SOCINSKI, Mark A

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Integrated RNA and DNA sequencing improves mutation detection in low purity tumors von Wilkerson, Matthew D, Cabanski, Christopher R, Sun, Wei, Hoadley, Katherine A, Walter, Vonn, Mose, Lisle E, Troester, Melissa A, Hammerman, Peter S, Parker, Joel S, Perou, Charles M, Hayes, D Neil

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ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking von Wilkerson, Matthew D., Hayes, D. Neil

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Germline mutation landscape of DNA damage repair genes in African Americans with prostate cancer highlights potentially targetable RAD genes von Kohaar, Indu, Zhang, Xijun, Tan, Shyh-Han, Nousome, Darryl, Babcock, Kevin, Ravindranath, Lakshmi, Sukumar, Gauthaman, Mcgrath-Martinez, Elisa, Rosenberger, John, Alba, Camille, Ali, Amina, Young, Denise, Chen, Yongmei, Cullen, Jennifer, Rosner, Inger L., Sesterhenn, Isabell A., Dobi, Albert, Chesnut, Gregory, Turner, Clesson, Dalgard, Clifton, Wilkerson, Matthew D., Pollard, Harvey B., Srivastava, Shiv, Petrovics, Gyorgy

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Identification of germline population variants misclassified as cancer-associated somatic variants von Pollard, Rebecca D, Wilkerson, Matthew D, Rajagopal, Padma Sheila

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The influence of microbial colonization on inflammatory versus pro-healing trajectories in combat extremity wounds von Schobel, Seth A., Gann, Eric R., Unselt, Desiree, Grey, Scott F., Lisboa, Felipe A., Upadhyay, Meenu M., Rouse, Michael, Tallowin, Simon, Be, Nicholas A., Zhang, Xijun, Dalgard, Clifton L., Wilkerson, Matthew D., Hauskrecht, Milos, Badylak, Stephen F., Zamora, Ruben, Vodovotz, Yoram, Potter, Benjamin K., Davis, Thomas A., Elster, Eric A.

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Transcriptomic Analysis of Mouse Brain After Traumatic Brain Injury Reveals That the Angiotensin Receptor Blocker Candesartan Acts Through Novel Pathways von Attilio, Peter J., Snapper, Dustin M., Rusnak, Milan, Isaac, Akira, Soltis, Anthony R., Wilkerson, Matthew D., Dalgard, Clifton L., Symes, Aviva J.

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Immune response profiles from humans experimentally exposed to Phlebotomus duboscqi bites von de Araujo, Fernanda Fortes, Abdeladhim, Maha, Teixeira, Clarissa, Hummer, Kelly, Wilkerson, Matthew D, Ressner, Roseanne, Lakhal-Naouar, Ines, Ellis, Michael W, Meneses, Claudio, Nurmukhambetova, Saule, Gomes, Regis, Tolbert, W David, Turiansky, George W, Pazgier, Marzena, Oliveira, Fabiano, Valenzuela, Jesus G, Kamhawi, Shaden, Aronson, Naomi

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