Search Results - "Tokheim, Collin"

Evaluating the evaluation of cancer driver genes by Tokheim, Collin J., Papadopoulos, Nickolas, Kinzler, Kenneth W., Vogelstein, Bert, Karchin, Rachel

“…Sequencing has identified millions of somatic mutations in human cancers, but distinguishing cancer driver genes remains a major challenge. Numerous methods…”
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Minimal functional driver gene heterogeneity among untreated metastases by 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

“…Metastases are responsible for the majority of cancer-related deaths. Although genomic heterogeneity within primary tumors is associated with relapse,…”
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In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target by Wang, Xiaoqing, Tokheim, Collin, Gu, Shengqing Stan, Wang, Binbin, Tang, Qin, Li, Yihao, Traugh, Nicole, Zeng, Zexian, Zhang, Yi, Li, Ziyi, Zhang, Boning, Fu, Jingxin, Xiao, Tengfei, Li, Wei, Meyer, Clifford A., Chu, Jun, Jiang, Peng, Cejas, Paloma, Lim, Klothilda, Long, Henry, Brown, Myles, Liu, X. Shirley

“…Despite remarkable clinical efficacy of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits for triple-negative breast cancer (TNBC) remain…”
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Determinants of transcription factor regulatory range by 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

“…Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from…”
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Genetic fusions favor tumorigenesis through degron loss in oncogenes by Liu, Jing, Tokheim, Collin, Lee, Jonathan D., Gan, Wenjian, North, Brian J., Liu, X. Shirley, Pandolfi, Pier Paolo, Wei, Wenyi

“…Chromosomal rearrangements can generate genetic fusions composed of two distinct gene sequences, many of which have been implicated in tumorigenesis and…”
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The genomic landscape of response to EGFR blockade in colorectal cancer by 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.

“…The effect of somatic genetic changes in colorectal cancer on sensitivity to anti-EGFR antibody therapy is analysed. Genomics of a cancer during targeted…”
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Systematic Functional Annotation of Somatic Mutations in Cancer by 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.

“…The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision…”
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Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade by Gu, Shengqing Stan, Zhang, Wubing, Wang, Xiaoqing, Jiang, Peng, Traugh, Nicole, Li, Ziyi, Meyer, Clifford, Stewig, Blair, Xie, Yingtian, Bu, Xia, Manos, Michael P, Font-Tello, Alba, Gjini, Evisa, Lako, Ana, Lim, Klothilda, Conway, Jake, Tewari, Alok K, Zeng, Zexian, Sahu, Avinash Das, Tokheim, Collin, Weirather, Jason L, Fu, Jingxin, Zhang, Yi, Kroger, Benjamin, Liang, Jin Hua, Cejas, Paloma, Freeman, Gordon J, Rodig, Scott, Long, Henry W, Gewurz, Benjamin E, Hodi, F Stephen, Brown, Myles, Liu, X Shirley

“…Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined…”
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CRAVAT 4: Cancer-Related Analysis of Variants Toolkit by Masica, David L, Douville, Christopher, Tokheim, Collin, Bhattacharya, Rohit, Kim, RyangGuk, Moad, Kyle, Ryan, Michael C, Karchin, Rachel

“…Cancer sequencing studies are increasingly comprehensive and well powered, returning long lists of somatic mutations that can be difficult to sort and…”
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Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure by Tokheim, Collin, Bhattacharya, Rohit, Niknafs, Noushin, Gygax, Derek M, Kim, Rick, Ryan, Michael, Masica, David L, Karchin, Rachel

“…The impact of somatic missense mutation on cancer etiology and progression is often difficult to interpret. One common approach for assessing the contribution…”
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Transcriptome-wide landscape of pre-mRNA alternative splicing associated with metastatic colonization by Lu, Zhi-xiang, Huang, Qin, Park, Juw Won, Shen, Shihao, Lin, Lan, Tokheim, Collin J, Henry, Michael D, Xing, Yi

“…Metastatic colonization is an ominous feature of cancer progression. Recent studies have established the importance of pre-mRNA alternative splicing (AS) in…”
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Clonal tracing reveals diverse patterns of response to immune checkpoint blockade by 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

“…Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple…”
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Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma by Rettig, Eleni M, Talbot, Jr, 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

“…Adenoid cystic carcinomas (ACC) of the salivary glands are challenging to understand, treat, and cure. To better understand the genetic alterations underlying…”
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Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation by Zhang, Wubing, Roy Burman, Shourya S., Chen, Jiaye, Donovan, Katherine A., Cao, Yang, Shu, Chelsea, Zhang, Boning, Zeng, Zexian, Gu, Shengqing, Zhang, Yi, Li, Dian, Fischer, Eric S., Tokheim, Collin, Shirley Liu, X.

“…Targeted protein degradation (TPD) has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell’s…”
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Species-specific exon loss in human transcriptomes by Wang, Jinkai, Lu, Zhi-xiang, Tokheim, Collin J, Miller, Sara E, Xing, Yi

“…Changes in exon-intron structures and splicing patterns represent an important mechanism for the evolution of gene functions and species-specific regulatory…”
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PrimerSeq： Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data by Tokheim, Collin, Park, Juw Won, Xing, Yi

“…The vast majority of multi-exon genes in higher eukaryotes are alternatively spliced and changes in alternative splicing（AS） can impact gene function or cause…”
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700 Increasing MHC-I expression to potentiate immune checkpoint blockade therapy by Gu, Shengqing, Zhang, Wubing, Wang, Xiaoqing, Jiang, Peng, Traugh, Nicole, Li, Ziyi, Meyer, Clifford, Stewig, Blair, Xie, Yingtian, Bu, Xia, Manos, Michael, Font-Tello, Alba, Gjini, Evisa, Lako, Ana, Lim, Klothilda, Conway, Jake, Tewari, Alok, Zeng, Zexian, Sahu, Avinash Das, Tokheim, Collin, Weirather, Jason, Fu, Jingxin, Zhang, Yi, Kroger, Benjamin, Liang, Jin Hua, Cejas, Paloma, Freeman, Gordon, Rodig, Scott, Long, Henry, Gewurz, Benjamin, Stephen Hodi, F., Brown, Myles, Shirley Liu, X

“…BackgroundCancer immunotherapy, especially immune checkpoint blockade (ICB) therapy, is leading to a paradigm shift in cancer treatment, as a small percentage…”
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Abstract 4879: Identification of degron motifs and mutations by analyzing a deep neural network by Chen, Cynthia, Tokheim, Collin, Liu, Shirley

“…Abstract Degrons, short amino acid sequences on protein substrates, play a critical role in the ubiquitin-proteasome system (UPS), which regulates over 80…”
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Abstract 2298A: Enhanced consideration of context dependence reveals the scope of somatic missense drivers in human cancers by Tokheim, Collin J., Nanda, Neha, Roberts, Nicholas J., Karchin, Rachel

“…Abstract Large-scale sequencing studies of patient cohorts have enabled identification of many driver genes whose somatic alterations confer a selective…”
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Integrated Informatics Analysis of Cancer-Related Variants by Pagel, Kymberleigh A, Kim, Rick, Moad, Kyle, Busby, Ben, Zheng, Lily, Tokheim, Collin, Ryan, Michael, Karchin, Rachel

“…The modern researcher is confronted with hundreds of published methods to interpret genetic variants. There are databases of genes and variants,…”
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