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Collin Tokheim, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Gu SS, Zhang W, Wang X, Jiang P, Traugh N, Li Z, Meyer C, Stewig B, Xie Y, Bu X, Manos MP, Font-Tello A, Gjini E, Lako A, Lim K, Conway J, Tewari AK, Zeng Z, Sahu AD, Tokheim C, Weirather JL, Fu J, Zhang Y, Kroger B, Liang JH, Cejas P, Freeman GJ, Rodig S, Long HW, Gewurz BE, Hodi FS, Brown M, Liu XS. Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade. Cancer Discov. 2021 Jun; 11(6):1524-1541. PMID: 33589424.
    Citations:    Fields:    
  2. Tokheim C, Wang X, Timms RT, Zhang B, Mena EL, Wang B, Chen C, Ge J, Chu J, Zhang W, Elledge SJ, Brown M, Liu XS. Systematic characterization of mutations altering protein degradation in human cancers. Mol Cell. 2021 03 18; 81(6):1292-1308.e11. PMID: 33567269.
    Citations:    Fields:    Translation:HumansCells
  3. Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Das Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen QR, Enos RA, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla SA, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal PA, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu C. Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network. Clin Cancer Res. 2020 Dec 15. PMID: 33323402.
    Citations:    Fields:    
  4. Makohon-Moore AP, Lipson EJ, Hooper JE, Zucker A, Hong J, Bielski CM, Hayashi A, Tokheim C, Baez P, Kappagantula R, Kohutek Z, Makarov V, Riaz N, Postow MA, Chapman PB, Karchin R, Socci ND, Solit DB, Chan TA, Taylor BS, Topalian SL, Iacobuzio-Donahue CA. The Genetic Evolution of Treatment-Resistant Cutaneous, Acral, and Uveal Melanomas. Clin Cancer Res. 2021 Mar 01; 27(5):1516-1525. PMID: 33323400.
    Citations:    Fields:    
  5. Gu SS, Wang X, Hu X, Jiang P, Li Z, Traugh N, Bu X, Tang Q, Wang C, Zeng Z, Fu J, Meyer C, Zhang Y, Cejas P, Lim K, Wang J, Zhang W, Tokheim C, Sahu AD, Xing X, Kroger B, Ouyang Z, Long H, Freeman GJ, Brown M, Liu XS. Clonal tracing reveals diverse patterns of response to immune checkpoint blockade. Genome Biol. 2020 10 15; 21(1):263. PMID: 33059736.
    Citations:    Fields:    
  6. Chen CH, Zheng R, Tokheim C, Dong X, Fan J, Wan C, Tang Q, Brown M, Liu JS, Meyer CA, Liu XS. Determinants of transcription factor regulatory range. Nat Commun. 2020 05 18; 11(1):2472. PMID: 32424124.
    Citations: 4     Fields:    Translation:AnimalsCells
  7. Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R. Integrated Informatics Analysis of Cancer-Related Variants. JCO Clin Cancer Inform. 2020 03; 4:310-317. PMID: 32228266.
    Citations: 4     Fields:    Translation:Humans
  8. Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunol Res. 2020 03; 8(3):396-408. PMID: 31871119.
    Citations: 11     Fields:    Translation:HumansCells
  9. Tokheim C, Karchin R. CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. Cell Syst. 2019 07 24; 9(1):9-23.e8. PMID: 31202631.
    Citations: 13     Fields:    Translation:Humans
  10. Reiter JG, Makohon-Moore AP, Gerold JM, Heyde A, Attiyeh MA, Kohutek ZA, Tokheim CJ, Brown A, DeBlasio RM, Niyazov J, Zucker A, Karchin R, Kinzler KW, Iacobuzio-Donahue CA, Vogelstein B, Nowak MA. Minimal functional driver gene heterogeneity among untreated metastases. Science. 2018 09 07; 361(6406):1033-1037. PMID: 30190408.
    Citations: 53     Fields:    Translation:Humans
  11. Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 08 09; 174(4):1034-1035. PMID: 30096302.
    Citations: 91     Fields:    
  12. Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 04 05; 173(2):371-385.e18. PMID: 29625053.
    Citations: 351     Fields:    Translation:Humans
  13. Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell. 2018 03 12; 33(3):450-462.e10. PMID: 29533785.
    Citations: 48     Fields:    Translation:Humans
  14. Masica DL, Douville C, Tokheim C, Bhattacharya R, Kim R, Moad K, Ryan MC, Karchin R. CRAVAT 4: Cancer-Related Analysis of Variants Toolkit. Cancer Res. 2017 11 01; 77(21):e35-e38. PMID: 29092935.
    Citations: 13     Fields:    Translation:Humans
  15. Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Hum Mutat. 2017 09; 38(9):1266-1276. PMID: 28544481.
    Citations: 4     Fields:    Translation:Humans
  16. Tokheim CJ, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R. Evaluating the evaluation of cancer driver genes. Proc Natl Acad Sci U S A. 2016 12 13; 113(50):14330-14335. PMID: 27911828.
    Citations: 106     Fields:    Translation:Humans
  17. Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure. Cancer Res. 2016 07 01; 76(13):3719-31. PMID: 27197156.
    Citations: 36     Fields:    Translation:HumansCells
  18. Rettig EM, Talbot CC, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Ling S, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N. Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer Prev Res (Phila). 2016 04; 9(4):265-74. PMID: 26862087.
    Citations: 13     Fields:    Translation:HumansCells
  19. Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Lupo B, Sausen M, Phallen J, Hruban CA, Tokheim C, Niknafs N, Nesselbush M, Lytle K, Sassi F, Cottino F, Migliardi G, Zanella ER, Ribero D, Russolillo N, Mellano A, Muratore A, Paraluppi G, Salizzoni M, Marsoni S, Kragh M, Lantto J, Cassingena A, Li QK, Karchin R, Scharpf R, Sartore-Bianchi A, Siena S, Diaz LA, Trusolino L, Velculescu VE. The genomic landscape of response to EGFR blockade in colorectal cancer. Nature. 2015 Oct 08; 526(7572):263-7. PMID: 26416732.
    Citations: 151     Fields:    Translation:HumansAnimals
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.