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C. Tokheim · SciRah

Researcher profile · Semantic Scholar

C. Tokheim

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C. Tokheim — researcher profile on SciRah

h-index: 26
Works: 54
Citations: 5,778

Most-cited papers

Comprehensive Characterization of Cancer Driver Genes and Mutations
M. Bailey, C. Tokheim, E. Porta-Pardo, Sohini Sengupta +496 more
2018Cell2,066 citations Open access
Semantic Scholar
The Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer
A. Bertotti, E. Papp, Siân Jones, V. Adleff +31 more
2015Nature464 citations Open access
Semantic Scholar
Evaluating the evaluation of cancer driver genes
C. Tokheim, N. Papadopoulos, K. Kinzler, B. Vogelstein +1 more
2016Proceedings of the National Academy of Sciences of the United States of America361 citations Open access
Semantic Scholar
Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
L. Ding, M. Bailey, E. Porta-Pardo, V. Thorsson +30 more
2018Cell358 citations Open access
Semantic Scholar
Minimal functional driver gene heterogeneity among untreated metastases
Johannes G. Reiter, Alvin P. Makohon-Moore, Jeffrey M. Gerold, A. Heyde +12 more
2018Science266 citations Open access
Semantic Scholar
Comprehensive Characterization of Cancer Driver Genes and Mutations (vol 173, 371.e1, 2018)
M. Bailey, C. Tokheim, E. Porta-Pardo, Sohini Sengupta +41 more
2018230 citations
Semantic Scholar
Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing.
C. Chung, V. Guthrie, David L. Masica, C. Tokheim +16 more
2015Annals of Oncology194 citations Open access
Semantic Scholar
Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade
S. Gu, Wubing Zhang, Xiao-Qing Wang, Peng Jiang +29 more
2021Cancer Discovery193 citations Open access
Semantic Scholar
In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target
Xiao-Qing Wang, C. Tokheim, S. Gu, Binbin Wang +18 more
2021Cell180 citations Open access
Semantic Scholar
High-throughput prediction of MHC class I and class II neoantigens with MHCnuggets
X. Shao, R. Bhattacharya, Justin C. Huang, I. K. Ashok Sivakumar +11 more
2019Cancer immunology research143 citations Open access
Semantic Scholar
Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure
C. Tokheim, R. Bhattacharya, N. Niknafs, Derek M. Gygax +4 more
2016Cancer Research129 citations Open access
Semantic Scholar
Integrated Informatics Analysis of Cancer-Related Variants
K. Pagel, Rick Kim, Kyle Moad, Ben Busby +4 more
2020JCO Clinical Cancer Informatics123 citations Open access
Semantic Scholar
CHASMplus reveals the scope of somatic missense mutations driving human cancers
C. Tokheim, R. Karchin
2018bioRxiv123 citations Open access
Semantic Scholar
Pan-cancer proteogenomics connects oncogenic drivers to functional states.
Yi-Ze Li, E. Porta-Pardo, C. Tokheim, M. Bailey +46 more
2023Cell112 citations Open access
Semantic Scholar
Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS.
J. Park, C. Tokheim, Shihao Shen, Yi Xing
2013Methods in molecular biology83 citations
Semantic Scholar
WHOLE-GENOME SEQUENCING OF SALIVARY GLAND ADENOID CYSTIC CARCINOMA
E. Rettig, C. Talbot, M. Sausen, Siân Jones +16 more
2016Cancer Prevention Research81 citations Open access
Semantic Scholar
Systematic Characterization of Mutations Altering Protein Degradation in Human Cancers
C. Tokheim, Xiao-Qing Wang, R. Timms, Bo-Ning Zhang +9 more
2021Molecules and Cells74 citations Open access
Semantic Scholar
Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization
Zhi-Xiang Lu, Qin Huang, J. Park, Shihao Shen +4 more
2014Molecular Cancer Research67 citations Open access
Semantic Scholar
Determinants of transcription factor regulatory range
Chenhao Chen, Rongbin Zheng, C. Tokheim, Xin Dong +7 more
2020Nature Communications63 citations Open access
Semantic Scholar
CRAVAT 4: Cancer-Related Analysis of Variants Toolkit
David L. Masica, C. Douville, C. Tokheim, R. Bhattacharya +4 more
2017bioRxiv59 citations Open access
Semantic Scholar
Comprehensive Characterization of Cancer Driver Genes and Mutations
Matthew H. Bailey, C. Tokheim, E. Porta-Pardo, Sohini Sengupta +41 more
2018Cell55 citations Open access
Semantic Scholar
Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation
Wubing Zhang, Shourya S. Roy Burman, Jiaye Chen, K. Donovan +10 more
2021bioRxiv41 citations Open access
Semantic Scholar
The spatial landscape of cancer hallmarks reveals patterns of tumor ecological dynamics and drug sensitivity.
M. Sibai, Sergi Cervilla, D. Grases, E. Musulén +15 more
2025Cell Reports35 citations Open access
Semantic Scholar
Evaluation of machine learning methods to predict peptide binding to MHC Class I proteins
R. Bhattacharya, A. Sivakumar, C. Tokheim, V. Guthrie +3 more
2017bioRxiv35 citations Open access
Semantic Scholar
Genetic fusions favor tumorigenesis through degron loss in oncogenes
Jing Liu, C. Tokheim, Jonathan D. Lee, Wenjian Gan +4 more
2021Nature Communications33 citations Open access
Semantic Scholar
PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data
C. Tokheim, J. Park, Yi Xing
2014Genomics, Proteomics & Bioinformatics27 citations Open access
Semantic Scholar
Discovery of targets for immune-metabolic antitumor drugs identifies Estrogen Related Receptor Alpha
A. Sahu, Xiao-Man Wang, P. Munson, J. Klomp +28 more
2023Cancer Discovery26 citations Open access
Semantic Scholar
Clonal tracing reveals diverse patterns of response to immune checkpoint blockade
S. Gu, Xiao-Qing Wang, Xi-Hao Hu, Peng Jiang +22 more
2020Genome Biology23 citations Open access
Semantic Scholar
Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA
Lin Yang, Jin Wang, J. Altreuter, Aashna Jhaveri +16 more
2023Nature Protocols19 citations
Semantic Scholar
High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets
XM Shao, R. Bhattacharya, J. Huang, Ika Sivakumar +11 more
2019bioRxiv18 citations Open access
Semantic Scholar
In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target
Xiao-Qing Wang, C. Tokheim, Binbin Wang, S. Gu +17 more
2020bioRxiv16 citations Open access
Semantic Scholar
Prediction of peptide binding to MHC Class I proteins in the age of deep learning
R. Bhattacharya, C. Tokheim, A. Sivakumar, V. Guthrie +3 more
201716 citations
Semantic Scholar
Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges
Bing-Huang Cai, Biao Li, Nikki Kiga, J. Thusberg +36 more
2017Human Mutation14 citations Open access
Semantic Scholar
The genetic evolution of treatment-resistant cutaneous, acral and uveal melanomas
Alvin P. Makohon-Moore, E. Lipson, J. E. Hooper, A. Zucker +18 more
2020Clinical Cancer Research13 citations Open access
Semantic Scholar
Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network
Ze-Xian Zeng, Jing-Xin Fu, C. Cibulskis, Aashna Jhaveri +44 more
2020Clinical Cancer Research11 citations Open access
Semantic Scholar
The spatial landscape of Cancer Hallmarks reveals patterns of tumor ecology
Mustafa Sibai, Sergi Cervilla, D. Grases, E. Musulén +15 more
2023bioRxiv8 citations Open access
Semantic Scholar
OpenCRAVAT, an open source collaborative platform for the annotation of human genetic variation
K. Pagel, Rick Kim, Kyle Moad, Ben Busby +5 more
2019bioRxiv8 citations Open access
Semantic Scholar
Species-specific exon loss in human transcriptomes.
Jin-Kai Wang, Zhi-Xiang Lu, C. Tokheim, Sara E. Miller +1 more
2015Molecular biology and evolution8 citations Open access
Semantic Scholar
Systematic Functional Annotation of Somatic Mutations in Cancer
P. Ng, Jun Li, K. Jeong, Shan H. Shao +36 more
2018Cancer Cell6 citations Open access
Semantic Scholar
Supplementary Data for "CHASMplus reveals the scope of somatic missense mutations driving human cancers"
C. Tokheim, R. Karchin
20184 citations
Semantic Scholar
Author Correction: Genetic fusions favor tumorigenesis through degron loss in oncogenes
Jing Liu, C. Tokheim, Jonathan D. Lee, Wenjian Gan +4 more
2025Nature Communications1 citations Open access
Semantic Scholar
Abstract P108: In vivo CRISPR screens identify E3 ligase COP1 as a modulator of macrophage infiltration and cancer immunotherapy target
Xiao-Qing Wang, C. Tokheim, S. Gu, Binbin Wang +16 more
2021Poster Presentations - Proffered Abstracts1 citations
Semantic Scholar
Clonal tracing reveals diverse patterns of response to immune checkpoint blockade
S. Gu, Xiao-Qing Wang, Xi-Hao Hu, Peng Jiang +22 more
2020Genome Biology1 citations Open access
Semantic Scholar
THE CANCER GENOME ATLAS PANCANCER ATLAS
Liang Wen Ding, M. Bailey, E. Porta-Pardo, V. Thorsson +18 more
1 citations
Semantic Scholar
Author Correction: The genomic landscape of response to EGFR blockade in colorectal cancer
A. Bertotti, E. Papp, S. Jones, V. Adleff +31 more
2026Nature0 citations
Semantic Scholar
Data-driven discovery of targets for bipotent anticancer drugs identifies Estrogen Related Receptor Alpha
A. Sahu, Xiao-Man Wang, P. Munson, J. Klomp +28 more
2021bioRxiv0 citations Open access
Semantic Scholar
Abstract 65: Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade
S. Gu, Wubing Zhang, Xiao-Qing Wang, Peng Jiang +29 more
2021Immunology0 citations
Semantic Scholar
In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target
C. Tokheim, Binbin Wang
20210 citations
Semantic Scholar
Peer Review #2 of "Machine learning analysis of TCGA cancer data (v0.1)"
Jose Liares-Blanco, Alejandro Pazos, C. Fernandez-Lozano, Jose Li ares-Blanco +467 more
20210 citations Open access
Semantic Scholar
Abstract 4879: Identification of degron motifs and mutations by analyzing a deep neural network
Cynthia Chen, C. Tokheim, Shirley X. Liu
2020Immunology0 citations
Semantic Scholar

Frequent co-authors

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R. Karchin×20
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R. Karchin — researcher profile on SciRah
Ze-Xian Zeng×11
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Ze-Xian Zeng — researcher profile on SciRah
S. Gu×10
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S. Gu — researcher profile on SciRah
Xiao-Qing Wang×10
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Jing-Xin Fu — researcher profile on SciRah

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X. Liu — researcher profile on SciRah

E. Porta-Pardo×9

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E. Porta-Pardo — researcher profile on SciRah

Wubing Zhang×9

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Wubing Zhang — researcher profile on SciRah

Clifford A. Meyer×9

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Clifford A. Meyer — researcher profile on SciRah

Myles A. Brown×9

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Myles A. Brown — researcher profile on SciRah

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M. Bailey — researcher profile on SciRah

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Peng Jiang — researcher profile on SciRah