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Proteome-wide assessment of differential missense variant clustering in neurodevelopmental disorders and cancer Ng, Jeffrey K.; Chen, Yilin; Akinwe, Titilope M.; Heins, Hillary B.; Mehinovic, Elvisa; Chang, Yoonhoo; Gutmann, David H.; Gurnett, Christina A.; Payne, Zachary L.; Manuel, Juana G.; Karchin, Rachel; Turner, Tychele N. Share Save
Intratumoral heterogeneity drives acquired therapy resistance in a patient with metastatic prostate cancer Rhinehart, Dena P.; Lai, Jiaying; Sanin, David E.; Vakkala, Varsha; Mendes, Adrianna; Bailey, Christopher; Antonarakis, Emmanuel S.; Paller, Channing J.; Wu, Xiaojun; Lotan, Tamara L.; Karchin, Rachel; Sena, Laura A. Share Save
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CRISPR-cas9 genetic targeting of metastatic pancreatic cancer Bowland, Kirsten; Lai, Jiaying; Teh, Selina Shiqing K.; Bennett, Alexis; Skaist, Alyza; Zhang, Yan; Thompson, Elizabeth; Hruban, Ralph H.; Roberts, Nicholas J.; Karchin, Rachel; Iacobuzio-Donahue, Christine A.; Eshleman, James R. Share Save
Liquid biopsy-informed precision oncology clinical trial to evaluate the utility of ctDNA comprehensive genomic profiling Fatteh, Maria; Conroy, Michael; Wanchoo, Timsy; Teh, Selina Shiqing; Wehr, Jaime; Balan, Archana; Karchin, Rachel; Verner, Ellen; Karaindrou, Katerina; Xian, Rena; Gocke, Christopher; Lin, Ming-Tseh; Fitzpatrick, Peggy; Hann, Christine L.; Murray, Joseph C.; Lam, Vincent K.; Feliciano, Josephine L.; Brahmer, Julie R.; Marrone, Kristen A.; Forde, Patrick M.; Fiallos, Katie; Petry, Dana; Botsis, Taxiarchis; Sausen, Mark; Canzoniero, Jenna; Tao, Jessica; Anagnostou, Valsamo Share Save
Scratch: A highly modular pipeline for single-cell cancer research Fonseca, Andre F.; Han, Guangchun; Ribeiro-Dantas, Marcel; Dai, Enyu; Grewal, Diljot; Zatzman, Matthew; Havasov, Eliyahu; McPherson, Andrew; Noble, Michael N.; Beroukhim, Rameen; Karchin, Rachel; Shah, Sohrab P.; Wang, Linghua Share Save
Combination pembrolizumab and radiotherapy induces anti-tumor immune responses in immunologically-cold non-small cell lung cancer Huang, Justin; Theelen, Willemijn S.; Belcaid, Zineb; Najjar, Mimi; Cherry, Christopher; Balan, Archana; White, James R.; Niknafs, Noushin; Wehr, Jaime; van den Heuvel, M. M.; Karchin, Rachel; Baas, Paul; Velculescu, Victor E.; Anagnostou, Valsamo Share Save
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; Repo, Susanna; Hoskins, Roger A.; Andreoletti, Gaia; Barsky, Daniel; Chellapan, Ajithavalli; Chu, Hoyin; Dabbiru, Navya; Kollipara, Naveen K.; Ly, Melissa; Neumann, Andrew J.; Pal, Lipika R.; Odell, Eric; Pandey, Gaurav; Peters-Petrulewicz, Robin C.; Srinivasan, Rajgopal; Yee, Stephen F.; Yeleswarapu, Sri Jyothsna; Zuhl, Maya; Adebali, Ogun; Patra, Ayoti; Beer, Michael A.; Hosur, Raghavendra; Peng, Jian; Bernard, Brady M.; Berry, Michael; Dong, Shengcheng; Boyle, Alan P.; Adhikari, Aashish; Chen, Jingqi; Hu, Zhiqiang; Wang, Robert; Wang, Yaqiong; Miller, Maximilian; Wang, Yanran; Bromberg, Yana; Turina, Paola; Capriotti, Emidio; Han, James J.; Ozturk, Kivilcim; Carter, Hannah; Babbi, Giulia; Bovo, Samuele; Di Lena, Pietro; Martelli, Pier Luigi; Savojardo, Castrense; Casadio, Rita; Cline, Melissa S.; De Baets, Greet; Bonache, Sandra; Diez, Orland; Gutierrez-Enriquez, Sara; Fernandez, Alejandro; Montalban, Gemma; Ootes, Lars; Ozkan, Selen; Padilla, Natalia; Riera, Casandra; De la Cruz, Xavier; Diekhans, Mark; Huwe, Peter J.; Wei, Qiong; Xu, Qifang; Dunbrack, Roland L.; Gotea, Valer; Elnitski, Laura; Margolin, Gennady; Fariselli, Piero; Kulakovskiy, Ivan V.; Makeev, Vsevolod J.; Penzar, Dmitry D.; Vorontsov, Ilya E.; Favorov, Alexander V.; Forman, Julia R.; Hasenahuer, Marcia; Fornasari, Maria S.; Parisi, Gustavo; Avsec, Ziga; Celik, Muhammed H.; Thi Yen Duong Nguyen; Gagneur, Julien; Shi, Fang-Yuan; Edwards, Matthew D.; Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; Gifford, David K.; Goke, Jonathan; Zaucha, Jan; Gough, Julian; Ritchie, Graham R. S.; Frankish, Adam; Mudge, Jonathan M.; Harrow, Jennifer; Young, Erin L.; Yu, Yao; Huff, Chad D.; Murakami, Katsuhiko; Nagai, Yoko; Imanishi, Tadashi; Mungall, Christopher J.; Jacobsen, Julius O. B.; Kim, Dongsup; Jeong, Chan-Seok; Jones, David T.; Li, Mulin Jun; Guthrie, Violeta Beleva; Bhattacharya, Rohit; Chen, Yun-Ching; Douville, Christopher; Fan, Jean; Kim, Dewey; Masica, David; Niknafs, Noushin; Sengupta, Sohini; Tokheim, Collin; Turner, Tychele N.; Yeo, Hui Ting Grace; Karchin, Rachel; Shin, Sunyoung; Welch, Rene; Keles, Sunduz; Li, Yue; Kellis, Manolis; Corbi-Verge, Carles; Strokach, Alexey V.; Kim, Philip M.; Klein, Teri E.; Mohan, Rahul; Sinnott-Armstrong, Nicholas A.; Wainberg, Michael; Kundaje, Anshul; Gonzaludo, Nina; Mak, Angel C. Y.; Chhibber, Aparna; Lam, Hugo Y. K.; Dahary, Dvir; Fishilevich, Simon; Lancet, Doron; Lee, Insuk; Bachman, Benjamin; Katsonis, Panagiotis; Lua, Rhonald C.; Wilson, Stephen J.; Lichtarge, Olivier; Bhat, Rajendra R.; Sundaram, Laksshman; Viswanath, Vivek; Bellazzi, Riccardo; Nicora, Giovanna; Rizzo, Ettore; Limongelli, Ivan; Mezlini, Aziz M.; Chang, Ray; Kim, Serra; Lai, Carmen; O'Connor, Robert; Topper, Scott; van den Akker, Jeroen; Zhou, Alicia Y.; Zimmer, Anjali D.; Mishne, Gilad; Bergquist, Timothy R.; Breese, Marcus R.; Guerrero, Rafael F.; Jiang, Yuxiang; Kiga, Nikki; Li, Biao; Mort, Matthew; Pagel, Kymberleigh A.; Pejaver, Vikas; Stamboulian, Moses H.; Thusberg, Janita; Mooney, Sean D.; Teerakulkittipong, Nuttinee; Cao, Chen; Kundu, Kunal; Yin, Yizhou; Yu, Chen-Hsin; Kleyman, Michael; Lin, Chiao-Feng; Stackpole, Mary; Mount, Stephen M.; Eraslan, Gokcen; Mueller, Nikola S.; Naito, Tatsuhiko; Rao, Aliz R.; Azaria, Johnathan R.; Brodie, Aharon; Ofran, Yanay; Garg, Aditi; Pal, Debnath; Hawkins-Hooker, Alex; Kenlay, Henry; Reid, John; Mucaki, Eliseos J.; Rogan, Peter K.; Schwarz, Jana M.; Searls, David B.; Lee, Gyu Rie; Seok, Chaok; Kramer, Andreas; Shah, Sohela; Huang, ChengLai V.; Kirsch, Jack F.; Shatsky, Maxim; Cao, Yue; Chen, Haoran; Karimi, Mostafa; Moronfoye, Oluwaseyi; Sun, Yuanfei; Shen, Yang; Shigeta, Ron; Ford, Colby T.; Nodzak, Conor; Uppal, Aneeta; Shi, Xinghua; Joseph, Thomas; Kotte, Sujatha; Rana, Sadhna; Rao, Aditya; Saipradeep, V. G.; Sivadasan, Naveen; Sunderam, Uma; Stanke, Mario; Su, Andrew; Adzhubey, Ivan; Jordan, Daniel M.; Sunyaev, Shamil; Rousseau, Frederic; Schymkowitz, Joost; Van Durme, Joost; Tavtigian, Sean V.; Carraro, Marco; Giollo, Manuel; Tosatto, Silvio C. E.; Adato, Orit; Carmel, Liran; Cohen, Noa E.; Fenesh, Izila; Holtzer, Iamar; Juven-Gershon, Tamar; Unger, Ron; Niroula, Abhishek; Olatubosun, Ayodeji; Valiaho, Jouni; Yang, Yang; Vihinen, Mauno; Wahl, Mary E.; Chang, Billy; Chong, Ka Chun; Hu, Inchi; Sun, Rui; Wu, William Ka Kei; Xia, Xiaoxuan; Zee, Benny C.; Wang, Maggie H.; Wang, Meng; Wu, Chunlei; Lu, Yutong; Chen, Ken; Yang, Yuedong; Yates, Christopher M.; Kreimer, Anat; Yan, Zhongxia; Yosef, Nir; Zhao, Huying; Wei, Zhipeng; Yao, Zhaomin; Zhou, Fengfeng; Folkman, Lukas; Zhou, Yaoqi; Daneshjou, Roxana; Altman, Russ B.; Inoue, Fumitaka; Ahituv, Nadav; Arkin, Adam P.; Lovisa, Federica; Bonvini, Paolo; Bowdin, Sarah; Gianni, Stefano; Mantuano, Elide; Minicozzi, Velia; Novak, Leonore; Pasquo, Alessandra; Pastore, Annalisa; Petrosino, Maria; Puglisi, Rita; Toto, Angelo; Veneziano, Liana; Chiaraluce, Roberta; Ball, Mad P.; Bobe, Jason R.; Church, George M.; Consalvi, Valerio; Mort, Matthew; Cooper, David N.; Buckley, Bethany A.; Sheridan, Molly B.; Cutting, Garry R.; Scaini, Maria Chiara; Cygan, Kamil J.; Fredericks, Alger M.; Glidden, David T.; Neil, Christopher; Rhine, Christy L.; Fairbrother, William G.; Alontaga, Aileen Y.; Fenton, Aron W.; Matreyek, Kenneth A.; Starita, Lea M.; Fowler, Douglas M.; Loescher, Britt-Sabina; Franke, Andre; Adamson, Scott I.; Graveley, Brenton R.; Gray, Joe W.; Malloy, Mary J.; Kane, John P.; Kousi, Maria; Katsanis, Nicholas; Schubach, Max; Kircher, Martin; Tang, Paul L. F.; Kwok, Pui-Yan; Lathrop, Richard H.; Clark, Wyatt T.; Yu, Guoying K.; LeBowitz, Jonathan H.; Benedicenti, Francesco; Bettella, Elisa; Bigoni, Stefania; Cesca, Federica; Mammi, Isabella; Marino-Bus-Ije, Cristina; Milani, Donatella; Peron, Angela; Polli, Roberta; Sartori, Stefano; Stanzial, Franco; Ioldo, Irene; Turolla, Licia; Aspromonte, Maria C.; Bellini, Mariagrazia; Leonardi, Emanuela; Liu, Xiaoming; Marshall, Christian; McCombie, W. Richard; Elefanti, Lisa; Menin, Chiara; Meyn, M. Stephen; Murgia, Alessandra; Nadeau, Kari C. Y.; Neuhausen, Susan L.; Nussbaum, Robert L.; Pirooznia, Mehdi; Potash, James B.; Dimster-Denk, Dago F.; Rine, Jasper D.; Sanford, Jeremy R.; Snyder, Michael; Tavtigian, Sean V.; Cole, Alina G.; Sun, Song; Verby, Marta W.; Weile, Jochen; Roth, Frederick P.; Tewhey, Ryan; Sabeti, Pardis C.; Campagna, Joan; Refaat, Marwan M.; Wojciak, Julianne; Grubb, Soren; Schmitt, Nicole; Shendure, Jay; Spurdle, Amanda B.; Stavropoulos, Dimitri J.; Walton, Nephi A.; Zandi, Peter P.; Ziv, Elad; Burke, Wylie; Chen, Flavia; Carr, Lawrence R.; Martinez, Selena; Paik, Jodi; Harris-Wai, Julie; Yarborough, Mark; Fullerton, Stephanie M.; Koenig, Barbara A.; McInnes, Gregory; Shigaki, Dustin; Chandonia, John-Marc; Furutsuki, Mabel; Kasak, Laura; Yu, Changhua; Chen, Rui; Cline, Melissa S.; Pandey, Gaurav; Friedberg, Iddo; Getz, Gad A.; Cong, Qian; Kinch, Lisa N.; Zhang, Jing; Grishin, Nick V.; Voskanian, Alin; Kann, Maricel G.; Clark, Wyatt T.; Tran, Elizabeth; Ioannidis, Nilah M.; Hunter, Jesse M.; Udani, Rupa; Cai, Binghuang; Morgan, Alexander A.; Sokolov, Artem; Stuart, Joshua M.; Tavtigian, Sean V.; Minervini, Giovanni; Monzon, Alexander M.; Batzoglou, Serafim; Butte, Atul J.; Church, George M.; Greenblatt, Marc S.; Hart, Reece K.; Hernandez, Ryan; Hubbard, Tim J. P.; Kahn, Scott; O'Donnell-Luria, Anne; Ng, Pauline C.; Shon, John; Tavtigian, Sean V.; Veltman, Joris; Zook, Justin M. Share Save
Spatial proteomics and transcriptomics reveal early immune cell organization in human pancreatic intraepithelial neoplasia Lyman, Melissa R.; Mitchell, Jacob T.; Kagohara, Luciane T.; Huff, Amanda L.; Haldar, Daniel; Shin, Sarah; Guinn, Samantha; Barrett, Benjamin; Longway, Gabriella; Hernandez, Alexei; Coyne, Erin; Yuan, Xuan; Andaloori, Lalitya; Lai, Jiaying; Liu, YunZhou; Karchin, Rachel; Gupta, Anuj; Kiemen, Ashley; Forjaz, Andre; Wirtz, Denis; Wu, Pei-Hsun; Deshpande, Atul; Armstrong, Todd; Azad, Nilofer S.; Thompson, Elizabeth; Anders, Robert; Ho, Won Jin; Jaffee, Elizabeth; Fertig, Elana; Zaidi, Neeha Share Save
Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer Mistretta, Brandon; Rankothgedera, Sakuni; Castillo, Micah; Rao, Mitchell; Holloway, Kimberly; Bhardwaj, Anjana; El Noafal, Maha; Albarracin, Constance; El-Zein, Randa; Rezaei, Hengameh; Su, Xiaoping; Akbani, Rehan; Shao, Xiaoshan M.; Czerniecki, Brian J.; Karchin, Rachel; Bedrosian, Isabelle; Gunaratne, Preethi H. Share Save
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Persistent mutation burden drives sustained anti-tumor immune responses in human cancers Niknafs, Noushin; Balan, Archana; Cherry, Christopher; Hummelink, Karlijn; Monkhorst, Kim; Shao, Xiaoshan M.; Belcaid, Zineb; Marrone, Kristen A.; Murray, Joseph; Smith, Kellie N.; Levy, Benjamin; Feliciano, Josephine; Hann, Christine L.; Lam, Vincent; Pardoll, Drew M.; Karchin, Rachel; Seiwert, Tanguy Y.; Brahmer, Julie R.; Forde, Patrick M.; Velculescu, Victor E.; Anagnostou, Valsamo K. Share Save
Persistent mutation burden drives sustained anti-tumor immune responses Niknafs, Noushin; Balan, Archana; Cherry, Christopher; Hummelink, Karlijn; Monkhorst, Kim; Shao, Xiaoshan M.; Belcaid, Zineb; Marrone, Kristen A.; Murray, Joseph; Smith, Kellie N.; Levy, Benjamin; Feliciano, Josephine; Hann, Christine L.; Lam, Vincent; Pardoll, Drew M.; Karchin, Rachel; Seiwert, Tanguy Y.; Brahmer, Julie R.; Forde, Patrick M.; Velculescu, Victor E.; Anagnostou, Valsamo Share Save
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Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria Pejaver, Vikas; Byrne, Alicia B.; Feng, Bing-Jian; Pagel, Kymberleigh A.; Mooney, Sean D.; Karchin, Rachel; O'Donnell-Luria, Anne; Harrison, Steven M.; Tavtigian, Sean, V; Greenblatt, Marc S.; Biesecker, Leslie G.; Radivojac, Predrag; Brenner, Steven E. Share Save
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