CHASMplus reveals the scope of somatic missense mutations driving human cancers

द्वारा Tokheim, Collin, Karchin, Rachel
में प्रकाशित Cell Syst (2019)

PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data

द्वारा Tokheim, Collin, Park, Juw Won, Xing, Yi
में प्रकाशित Genomics Proteomics Bioinformatics (2014)

Evaluating the evaluation of cancer driver genes

द्वारा Tokheim, Collin J., Papadopoulos, Nickolas, Kinzler, Kenneth W., Vogelstein, Bert, Karchin, Rachel
में प्रकाशित Proc Natl Acad Sci U S A (2016)

Species-Specific Exon Loss in Human Transcriptomes

द्वारा Wang, Jinkai, Lu, Zhi-xiang, Tokheim, Collin J., Miller, Sara E., Xing, Yi
में प्रकाशित Mol Biol Evol (2015)

Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure

द्वारा Tokheim, Collin, Bhattacharya, Rohit, Niknafs, Noushin, Gygax, Derek M., Kim, Rick, Ryan, Michael, Masica, David, Karchin, Rachel
में प्रकाशित Cancer Res (2016)

Integrated Informatics Analysis of Cancer-Related Variants

द्वारा Pagel, Kymberleigh A., Kim, Rick, Moad, Kyle, Busby, Ben, Zheng, Lily, Tokheim, Collin, Ryan, Michael, Karchin, Rachel
में प्रकाशित JCO Clin Cancer Inform (2020)

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit

द्वारा Masica, David L., Douville, Christopher, Tokheim, Collin, Bhattacharya, Rohit, Kim, RyangGuk, Moad, Kyle, Ryan, Michael C., Karchin, Rachel
में प्रकाशित Cancer Res (2017)

Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization

द्वारा Lu, Zhi-xiang, Huang, Qin, Park, Juw Won, Shen, Shihao, Lin, Lan, Tokheim, Collin J., Henry, Michael D., Xing, Yi
में प्रकाशित Mol Cancer Res (2014)

Determinants of transcription factor regulatory range

द्वारा Chen, Chen-Hao, Zheng, Rongbin, Tokheim, Collin, Dong, Xin, Fan, Jingyu, Wan, Changxin, Tang, Qin, Brown, Myles, Liu, Jun S., Meyer, Clifford A., Liu, X. Shirley
में प्रकाशित Nat Commun (2020)

High-throughput prediction of MHC class I and class II neoantigens with MHCnuggets

द्वारा Shao, Xiaoshan M., Bhattacharya, Rohit, Huang, Justin, Sivakumar, I.K. Ashok, Tokheim, Collin, Zheng, Lily, Hirsch, Dylan, Kaminow, Benjamin, Omdahl, Ashton, Bonsack, Maria, Riemer, Angelika B., Velculescu, Victor E., Anagnostou, Valsamo, Pagel, Kymberleigh A., Karchin, Rachel
में प्रकाशित Cancer Immunol Res (2019)

Minimal functional driver gene heterogeneity among untreated metastases

द्वारा Reiter, Johannes G., Makohon-Moore, Alvin P., Gerold, Jeffrey M., Heyde, Alexander, Attiyeh, Marc A., Kohutek, Zachary A., Tokheim, Collin J., Brown, Alexia, DeBlasio, Rayne M., Niyazov, Juliana, Zucker, Amanda, Karchin, Rachel, Kinzler, Kenneth W., Iacobuzio-Donahue, Christine A., Vogelstein, Bert, Nowak, Martin A.
में प्रकाशित Science (2018)

WHOLE-GENOME SEQUENCING OF SALIVARY GLAND ADENOID CYSTIC CARCINOMA

द्वारा Rettig, Eleni M, Talbot, C Conover, Sausen, Mark, Jones, Sian, Bishop, Justin A, Wood, Laura D, Tokheim, Collin, Niknafs, Noushin, Karchin, Rachel, Fertig, Elana J, Wheelan, Sarah J, Marchionni, Luigi, Considine, Michael, Ling, Shizhang, Fakhry, Carole, Papadopoulos, Nickolas, Kinzler, Kenneth W, Vogelstein, Bert, Ha, Patrick K, Agrawal, Nishant
में प्रकाशित Cancer Prev Res (Phila) (2016)

Clonal tracing reveals diverse patterns of response to immune checkpoint blockade

द्वारा Gu, Shengqing Stan, Wang, Xiaoqing, Hu, Xihao, Jiang, Peng, Li, Ziyi, Traugh, Nicole, Bu, Xia, Tang, Qin, Wang, Chenfei, Zeng, Zexian, Fu, Jingxin, Meyer, Cliff, Zhang, Yi, Cejas, Paloma, Lim, Klothilda, Wang, Jin, Zhang, Wubing, Tokheim, Collin, Sahu, Avinash Das, Xing, Xiaofang, Kroger, Benjamin, Ouyang, Zhangyi, Long, Henry, Freeman, Gordon J., Brown, Myles, Liu, X. Shirley
में प्रकाशित Genome Biol (2020)

The genetic evolution of treatment-resistant cutaneous, acral and uveal melanomas

द्वारा Makohon-Moore, Alvin P., Lipson, Evan J., Hooper, Jody E., Zucker, Amanda, Hong, Jungeui, Bielski, Craig M., Hayashi, Akimasa, Tokheim, Collin, Baez, Priscilla, Kappagantula, Rajya, Kohutek, Zachary, Makarov, Vladimir, Riaz, Nadeem, Postow, Michael A., Chapman, Paul B., Karchin, Rachel, Socci, Nicholas D., Solit, David B., Chan, Timothy A., Taylor, Barry, Topalian, Suzanne L., Iacobuzio-Donahue, Christine A.
में प्रकाशित Clin Cancer Res (2020)

The Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer

द्वारा Bertotti, Andrea, Papp, Eniko, Jones, Siân, Adleff, Vilmos, Anagnostou, Valsamo, Lupo, Barbara, Sausen, Mark, Phallen, Jillian, Hruban, Carolyn A., Tokheim, Collin, Niknafs, Noushin, Nesselbush, Monica, Lytle, Karli, Sassi, Francesco, Cottino, Francesca, Migliardi, Giorgia, Zanella, Eugenia R., Ribero, Dario, Russolillo, Nadia, Mellano, Alfredo, Muratore, Andrea, Paraluppi, Gianluca, Salizzoni, Mauro, Marsoni, Silvia, Kragh, Michael, Lantto, Johan, Cassingena, Andrea, Li, Qing Kay, Karchin, Rachel, Scharpf, Robert, Sartore-Bianchi, Andrea, Siena, Salvatore, Diaz, Luis A., Trusolino, Livio, Velculescu, Victor E.
में प्रकाशित Nature (2015)

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

द्वारा Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan-lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Josh M., Mills, Gordon B, Wyczalkowski, Matthew A., Vincent, Benjamin, Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David, Getz, Gad
में प्रकाशित Cell (2018)

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges

द्वारा Cai, Binghuang, Li, Biao, Kiga, Nikki, Thusberg, Janita, Bergquist, Timothy, Chen, Yun-Ching, Niknafs, Noushin, Carter, Hannah, Tokheim, Collin, Beleva-Guthrie, Violeta, Douville, Christopher, Bhattacharya, Rohit, Yeo, Hui Ting Grace, Fan, Jean, Sengupta, Sohini, Kim, Dewey, Cline, Melissa, Turner, Tychele, Diekhans, Mark, Zaucha, Jan, Pal, Lipika R., Cao, Chen, Yu, Chen-Hsin, Yin, Yizhou, Carraro, Marco, Giollo, Manuel, Ferrari, Carlo, Leonardi, Emanuela, Tosatto, Silvio C.E., Bobe, Jason, Ball, Madeleine, Hoskins, Roger A., Repo, Susanna, Church, George, Brenner, Steven E., Moult, John, Gough, Julian, Stanke, Mario, Karchin, Rachel, Mooney, Sean D.
में प्रकाशित Hum Mutat (2017)

Systematic Functional Annotation of Somatic Mutations in Cancer

द्वारा Ng, Patrick Kwok-Shing, Li, Jun, Jeong, Kang Jin, Shao, Shan, Chen, Hu, Tsang, Yiu Huen, Sengupta, Sohini, Wang, Zixing, Bhavana, Venkata Hemanjani, Tran, Richard, Soewito, Stephanie, Minussi, Darlan Conterno, Moreno, Daniela, Kong, Kathleen, Dogruluk, Turgut, Lu, Hengyu, Gao, Jianjiong, Tokheim, Collin, Zhou, Daniel Cui, Johnson, Amber M., Zeng, Jia, Ip, Carman Ka Man, Ju, Zhenlin, Wester, Matthew, Yu, Shuangxing, Li, Yongsheng, Vellano, Christopher P., Schultz, Nikolaus, Karchin, Rachel, Ding, Li, Lu, Yiling, Cheung, Lydia Wai Ting, Chen, Ken, Shaw, Kenna R., Meric-Bernstam, Funda, Scott, Kenneth L., Yi, Song, Sahni, Nidhi, Liang, Han, Mills, Gordon B.
में प्रकाशित Cancer Cell (2018)

Comprehensive Characterization of Cancer Driver Genes and Mutations

द्वारा Bailey, Matthew H., Tokheim, Collin, Porta-Pardo, Eduard, Sengupta, Sohini, Bertrand, Denis, Weerasinghe, Amila, Colaprico, Antonio, Wendl, Michael C., Kim, Jaegil, Reardon, Brendan, Ng, Kwok-Shing, Jeong, Kang Jin, Cao, Song, Wang, Zixing, Gao, JianJiong, Gao, Qingsong, Wang, Fang, Liu, Eric Minwei, Mularoni, Loris, Rubio-Perez, Carlota, Nagarajan, Niranjan, Cortés-Ciriano, Isidro, Zhou, Daniel Cui, Liang, Wen-Wei, Hess, Julian M., Yellapantula, Venkata D., Tamborero, David, Gonzalez-Perez, Abel, Suphavilai, Chayaporn, Ko, Jia Yu, Khurana, Ekta, Park, Peter J., Van Allen, Eliezer, Liang, Han, Lawrence, Michael, Godzik, Adam, Lopez-Bigas, Nuria, Stuart, Josh, Wheeler, David, Getz, Gad, Chen, Ken, Lazar, Alexander J., Mills, Gordon B, Karchin, Rachel, Ding, Li
में प्रकाशित Cell (2018)

Comprehensive Characterization of Cancer Driver Genes and Mutations

द्वारा Bailey, Matthew H., Tokheim, Collin, Porta-Pardo, Eduard, Sengupta, Sohini, Bertrand, Denis, Weerasinghe, Amila, Colaprico, Antonio, Wendl, Michael C., Kim, Jaegil, Reardon, Brendan, Ng, Patrick Kwok-Shing, Jeong, Kang Jin, Cao, Song, Wang, Zixing, Gao, Jianjiong, Gao, Qingsong, Wang, Fang, Liu, Eric Minwei, Mularoni, Loris, Rubio-Perez, Carlota, Nagarajan, Niranjan, Cortés-Ciriano, Isidro, Zhou, Daniel Cui, Liang, Wen-Wei, Hess, Julian M., Yellapantula, Venkata D., Tamborero, David, Gonzalez-Perez, Abel, Suphavilai, Chayaporn, Ko, Jia Yu, Khurana, Ekta, Park, Peter J., Van Allen, Eliezer M., Liang, Han, Lawrence, Michael S., Godzik, Adam, Lopez-Bigas, Nuria, Stuart, Josh, Wheeler, David, Getz, Gad, Chen, Ken, Lazar, Alexander J., Mills, Gordon B., Karchin, Rachel, Ding, Li
में प्रकाशित Cell (2018)