| Year |
Citation |
Score |
| 2020 |
Noë M, Niknafs N, Fischer CG, Hackeng WM, Beleva Guthrie V, Hosoda W, Debeljak M, Papp E, Adleff V, White JR, Luchini C, Pea A, Scarpa A, Butturini G, Zamboni G, ... ... Karchin R, et al. Genomic characterization of malignant progression in neoplastic pancreatic cysts. Nature Communications. 11: 4085. PMID 32796935 DOI: 10.1038/S41467-020-17917-8 |
0.334 |
|
| 2020 |
Douville C, Cohen JD, Ptak J, Popoli M, Schaefer J, Silliman N, Dobbyn L, Schoen RE, Tie J, Gibbs P, Goggins M, Wolfgang CL, Wang TL, Shih IM, Karchin R, et al. Assessing aneuploidy with repetitive element sequencing. Proceedings of the National Academy of Sciences of the United States of America. PMID 32075918 DOI: 10.1073/Pnas.1910041117 |
0.357 |
|
| 2019 |
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 class II neoantigens with MHCnuggets. Cancer Immunology Research. PMID 31871119 DOI: 10.1158/2326-6066.Cir-19-0464 |
0.369 |
|
| 2019 |
Niknafs N, Zhong Y, Moral JA, Zhang L, Shao MX, Lo A, Makohon-Moore A, Iacobuzio-Donahue CA, Karchin R. Characterization of genetic subclonal evolution in pancreatic cancer mouse models. Nature Communications. 10: 5435. PMID 31780749 DOI: 10.1038/S41467-019-13100-W |
0.343 |
|
| 2019 |
Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, et al. Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants. Human Mutation. PMID 31301157 DOI: 10.1002/Humu.23868 |
0.421 |
|
| 2019 |
Tokheim C, Karchin R. CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. Cell Systems. PMID 31202631 DOI: 10.1016/J.Cels.2019.05.005 |
0.431 |
|
| 2019 |
Fischer CG, Guthrie VB, Braxton AM, Zheng L, Wang P, Song Q, Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S, Molin MD, Masica D, Scharpf RB, Thompson ED, ... ... Karchin R, et al. Intraductal Papillary Mucinous Neoplasms Arise from Multiple Independent Clones, Each With Distinct Mutations. Gastroenterology. PMID 31175866 DOI: 10.1053/J.Gastro.2019.06.001 |
0.38 |
|
| 2018 |
Kuboki Y, Fischer CG, Beleva Guthrie V, Huang W, Yu J, Chianchiano P, Hosoda W, Zhang H, Zheng L, Shao X, Thompson ED, Waters K, Poling J, He J, Weiss MJ, ... ... Karchin R, et al. Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions. The Journal of Pathology. PMID 30430578 DOI: 10.1002/Path.5194 |
0.404 |
|
| 2018 |
Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, ... ... Karchin R, et al. Correction: Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy. Elife. 7. PMID 30418154 DOI: 10.7554/Elife.43237 |
0.344 |
|
| 2018 |
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, et al. Minimal functional driver gene heterogeneity among untreated metastases. Science (New York, N.Y.). 361: 1033-1037. PMID 30190408 DOI: 10.1126/Science.Aat7171 |
0.402 |
|
| 2018 |
Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA, Jones S, et al. A machine learning approach for somatic mutation discovery. Science Translational Medicine. 10. PMID 30185652 DOI: 10.1126/Scitranslmed.Aar7939 |
0.425 |
|
| 2018 |
Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin R, Jagtap PD, Griffin TJ. Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics. Journal of Proteome Research. PMID 30130115 DOI: 10.1021/Acs.Jproteome.8B00404 |
0.414 |
|
| 2018 |
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, ... ... Karchin R, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 174: 1034-1035. PMID 30096302 DOI: 10.1016/J.Cell.2018.07.034 |
0.362 |
|
| 2018 |
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, ... ... Karchin R, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 173: 371-385.e18. PMID 29625053 DOI: 10.1016/J.Cell.2018.02.060 |
0.423 |
|
| 2018 |
Wang Y, Li L, Douville C, Cohen JD, Yen TT, Kinde I, Sundfelt K, Kjær SK, Hruban RH, Shih IM, Wang TL, Kurman RJ, Springer S, Ptak J, Popoli M, ... ... Karchin R, et al. Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers. Science Translational Medicine. 10. PMID 29563323 DOI: 10.1126/Scitranslmed.Aap8793 |
0.302 |
|
| 2018 |
Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, ... ... Karchin R, et al. Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy. Elife. 7. PMID 29557778 DOI: 10.7554/Elife.32143 |
0.347 |
|
| 2018 |
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, ... ... Karchin R, et al. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell. 33: 450-462.e10. PMID 29533785 DOI: 10.1016/J.Ccell.2018.01.021 |
0.421 |
|
| 2018 |
Beleva Guthrie V, Masica DL, Fraser A, Federico J, Fan Y, Camps M, Karchin R. Network Analysis of Protein Adaptation: modeling the functional impact of multiple mutations. Molecular Biology and Evolution. PMID 29522102 DOI: 10.1093/Molbev/Msy036 |
0.396 |
|
| 2018 |
Douville C, Springer S, Kinde I, Cohen JD, Hruban RH, Lennon AM, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R. Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs). Proceedings of the National Academy of Sciences of the United States of America. PMID 29432176 DOI: 10.1073/Pnas.1717846115 |
0.33 |
|
| 2018 |
Guidugli L, Shimelis H, Masica DL, Pankratz VS, Lipton GB, Singh N, Hu C, Monteiro ANA, Lindor NM, Goldgar DE, Karchin R, Iversen ES, Couch FJ. Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches. American Journal of Human Genetics. PMID 29394989 DOI: 10.1016/J.Ajhg.2017.12.013 |
0.414 |
|
| 2018 |
Anagnostou V, Forde P, Naidoo J, Marrone K, Adleff V, White J, Phallen J, Leal A, Hruban C, Sivakumar A, Verde F, Karchin R, Brahmer J, Velculescu V. Abstract 3668: ctDNA and TCR dynamics predict response toimmune checkpoint blockade in non-small cell lung cancer Cancer Research. 78: 3668-3668. DOI: 10.1158/1538-7445.Am2018-3668 |
0.353 |
|
| 2018 |
Wood D, White J, Georgiadis A, Emburgh BV, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, Loverso P, Riley D, Diaz LA, Jones S, et al. Abstract 3271: A machine learning approach for somatic mutation discovery Cancer Research. 78: 3271-3271. DOI: 10.1158/1538-7445.Am2018-3271 |
0.413 |
|
| 2017 |
Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, ... ... Karchin R, et al. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Medicine. 9: 113. PMID 29254494 DOI: 10.1186/S13073-017-0509-Y |
0.427 |
|
| 2017 |
Labidi-Galy SI, Papp E, Hallberg D, Niknafs N, Adleff V, Noe M, Bhattacharya R, Novak M, Jones S, Phallen J, Hruban CA, Hirsch MS, Lin DI, Schwartz L, Maire CL, ... ... Karchin R, et al. High grade serous ovarian carcinomas originate in the fallopian tube. Nature Communications. 8: 1093. PMID 29061967 DOI: 10.1038/S41467-017-00962-1 |
0.309 |
|
| 2017 |
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, Grace Yeo HT, Fan J, Sengupta S, ... ... Karchin R, et al. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Human Mutation. PMID 28544481 DOI: 10.1002/Humu.23265 |
0.662 |
|
| 2016 |
Rettig EM, Talbot CC, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Ling S, Fakhry C, et al. Correction: Whole-genome sequencing of salivary gland adenoid cystic carcinoma (Cancer Prevention Research (2016) 9 (265-274) DOI: 10.1158/1940-6207.CAPR-15-0316) Cancer Prevention Research. 11. PMID 28642227 DOI: 10.1158/1940-6207.Capr-17-0178 |
0.349 |
|
| 2016 |
Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, ... ... Karchin R, et al. Evolution of Neoantigen Landscape During Immune Checkpoint Blockade in Non-Small Cell Lung Cancer. Cancer Discovery. PMID 28031159 DOI: 10.1158/2159-8290.Cd-16-0828 |
0.305 |
|
| 2016 |
Tokheim CJ, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R. Evaluating the evaluation of cancer driver genes. Proceedings of the National Academy of Sciences of the United States of America. PMID 27911828 DOI: 10.1073/Pnas.1616440113 |
0.411 |
|
| 2016 |
Karchin R, Nussinov R. Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation. Plos Computational Biology. 12: e1005043. PMID 27536867 DOI: 10.1371/Journal.Pcbi.1005043 |
0.443 |
|
| 2016 |
Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan MC, Masica D, Karchin R. Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure. Cancer Research. PMID 27197156 DOI: 10.1158/0008-5472.Can-15-3190 |
0.453 |
|
| 2016 |
Masica DL, Karchin R. Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants. Plos Computational Biology. 12: e1004725. PMID 27171182 DOI: 10.1371/Journal.Pcbi.1004725 |
0.434 |
|
| 2016 |
Rettig EM, Talbot C, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Fakhry C, Papadopoulos N, et al. Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer Prevention Research (Philadelphia, Pa.). PMID 26862087 DOI: 10.1158/1940-6207.Capr-15-0316 |
0.353 |
|
| 2016 |
Oetting WS, Brenner SE, Brookes AJ, Greenblatt MS, Hart RK, Karchin R, Sunyaev SR, Taschner PE. Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society. Human Mutation. PMID 26791113 DOI: 10.1002/Humu.22958 |
0.342 |
|
| 2015 |
Roberts NJ, Norris AL, Petersen GM, Bondy ML, Brand R, Gallinger S, Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stoffel EM, Syngal S, Zogopoulos G, Ali SZ, Axilbund J, ... ... Karchin R, et al. Whole genome sequencing defines the genetic heterogeneity of familial pancreatic cancer. Cancer Discovery. PMID 26658419 DOI: 10.1158/2159-8290.Cd-15-0402 |
0.367 |
|
| 2015 |
Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R. Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel). Human Mutation. PMID 26442818 DOI: 10.1002/Humu.22911 |
0.427 |
|
| 2015 |
Niknafs N, Beleva-Guthrie V, Naiman DQ, Karchin R. SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. Plos Computational Biology. 11: e1004416. PMID 26436540 DOI: 10.1371/Journal.Pcbi.1004416 |
0.416 |
|
| 2015 |
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, ... ... Karchin R, et al. The genomic landscape of response to EGFR blockade in colorectal cancer. Nature. PMID 26416732 DOI: 10.1038/Nature14969 |
0.323 |
|
| 2015 |
Turner TN, Douville C, Kim D, Stenson PD, Cooper DN, Chakravarti A, Karchin R. Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns. Human Molecular Genetics. 24: 5995-6002. PMID 26246501 DOI: 10.1093/Hmg/Ddv309 |
0.334 |
|
| 2015 |
Karchin R, Cline MS. Human genetics special issue on computational molecular medicine. Human Genetics. 134: 455-7. PMID 25805167 DOI: 10.1007/S00439-015-1545-6 |
0.71 |
|
| 2015 |
Chung CH, Guthrie VB, Masica DL, Tokheim C, Kang H, Richmon J, Agrawal N, Fakhry C, Quon H, Subramaniam RM, Zuo Z, Seiwert T, Chalmers ZR, Frampton GM, Ali SM, ... ... Karchin R, et al. Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Annals of Oncology : Official Journal of the European Society For Medical Oncology / Esmo. 26: 1216-23. PMID 25712460 DOI: 10.1093/Annonc/Mdv109 |
0.34 |
|
| 2015 |
Rettig EM, Chung CH, Bishop JA, Howard JD, Sharma R, Li RJ, Douville C, Karchin R, Izumchenko E, Sidransky D, Koch W, Califano J, Agrawal N, Fakhry C. Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features. Cancer Prevention Research (Philadelphia, Pa.). 8: 287-95. PMID 25633867 DOI: 10.1158/1940-6207.Capr-14-0366 |
0.302 |
|
| 2015 |
Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD. Germline & somatic mosaicism: the 2014 annual scientific meeting of the Human Genome Variation Society. Human Mutation. 36: 390-3. PMID 25597405 DOI: 10.1002/Humu.22757 |
0.303 |
|
| 2015 |
Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R. Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Human Molecular Genetics. 24: 1908-17. PMID 25489051 DOI: 10.1093/Hmg/Ddu607 |
0.349 |
|
| 2015 |
Masica DL, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch WM, Chung CH, Karchin R. Predicting survival in head and neck squamous cell carcinoma from TP53 mutation. Human Genetics. 134: 497-507. PMID 25108461 DOI: 10.1007/S00439-014-1470-0 |
0.379 |
|
| 2014 |
Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R. A probabilistic model to predict clinical phenotypic traits from genome sequencing. Plos Computational Biology. 10: e1003825. PMID 25188385 DOI: 10.1371/Journal.Pcbi.1003825 |
0.426 |
|
| 2014 |
Sharma N, Sosnay PR, Ramalho AS, Douville C, Franca A, Gottschalk LB, Park J, Lee M, Vecchio-Pagan B, Raraigh KS, Amaral MD, Karchin R, Cutting GR. Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions. Human Mutation. 35: 1249-59. PMID 25066652 DOI: 10.1002/Humu.22624 |
0.383 |
|
| 2014 |
Carter H, Karchin R. Predicting the functional consequences of somatic missense mutations found in tumors. Methods in Molecular Biology (Clifton, N.J.). 1101: 135-59. PMID 24233781 DOI: 10.1007/978-1-62703-721-1_8 |
0.441 |
|
| 2014 |
Masica D, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch W, Karchin R, Chung CH. Evaluation of computational tools to determine prognostic significance of TP53 mutation in head and neck squamous cell carcinoma (HNSCC). Journal of Clinical Oncology. 32: 6035-6035. DOI: 10.1200/Jco.2014.32.15_Suppl.6035 |
0.377 |
|
| 2014 |
Masica DL, Karchin R. Abstract 5322: Collections of simultaneously altered genes as highly predictive markers of cancer cell drug response Cancer Research. 74: 5322-5322. DOI: 10.1158/1538-7445.Am2014-5322 |
0.37 |
|
| 2013 |
Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, Niknafs N, Guthrie VB, Maitra A, Argani P, Offerhaus GJ, Roa JC, Roberts LR, Gores GJ, Popescu I, ... ... Karchin R, et al. Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nature Genetics. 45: 1470-3. PMID 24185509 DOI: 10.1038/Ng.2813 |
0.376 |
|
| 2013 |
Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, Ramalho AS, Amaral MD, Dorfman R, Zielenski J, Masica DL, Karchin R, Millen L, Thomas PJ, Patrinos GP, et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nature Genetics. 45: 1160-7. PMID 23974870 DOI: 10.1038/Ng.2745 |
0.317 |
|
| 2013 |
Hoang ML, Chen CH, Sidorenko VS, He J, Dickman KG, Yun BH, Moriya M, Niknafs N, Douville C, Karchin R, Turesky RJ, Pu YS, Vogelstein B, Papadopoulos N, Grollman AP, et al. Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing Science Translational Medicine. 5. PMID 23926200 DOI: 10.1126/Scitranslmed.3006200 |
0.386 |
|
| 2013 |
Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, ... ... Karchin R, et al. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proceedings of the National Academy of Sciences of the United States of America. 110: 13481-6. PMID 23901115 DOI: 10.1073/Pnas.1304227110 |
0.43 |
|
| 2013 |
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10: 723-9. PMID 23900255 DOI: 10.1038/Nmeth.2562 |
0.415 |
|
| 2013 |
Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. Identifying Mendelian disease genes with the variant effect scoring tool. Bmc Genomics. 14: S3. PMID 23819870 DOI: 10.1186/1471-2164-14-S3-S3 |
0.375 |
|
| 2013 |
Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Human Genetics. 132: 1235-43. PMID 23793516 DOI: 10.1007/S00439-013-1325-0 |
0.396 |
|
| 2013 |
Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R. A hybrid likelihood model for sequence-based disease association studies. Plos Genetics. 9: e1003224. PMID 23358228 DOI: 10.1371/Journal.Pgen.1003224 |
0.376 |
|
| 2013 |
Masica DL, Karchin R. Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Research. 73: 1699-708. PMID 23338612 DOI: 10.1158/0008-5472.Can-12-3122 |
0.354 |
|
| 2013 |
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics (Oxford, England). 29: 647-8. PMID 23325621 DOI: 10.1093/Bioinformatics/Btt017 |
0.431 |
|
| 2012 |
Liang H, Cheung LW, Li J, Ju Z, Yu S, Stemke-Hale K, Dogruluk T, Lu Y, Liu X, Gu C, Guo W, Scherer SE, Carter H, Westin SN, Dyer MD, ... ... Karchin R, et al. Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Research. 22: 2120-9. PMID 23028188 DOI: 10.1101/Gr.137596.112 |
0.397 |
|
| 2012 |
Masica DL, Sosnay PR, Cutting GR, Karchin R. Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Human Mutation. 33: 1267-74. PMID 22573477 DOI: 10.1002/Humu.22110 |
0.42 |
|
| 2012 |
Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, Sjöblom T. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers. Genes, Chromosomes & Cancer. 51: 480-9. PMID 22302350 DOI: 10.1002/Gcc.21935 |
0.364 |
|
| 2011 |
Wu J, Jiao Y, Dal Molin M, Maitra A, de Wilde RF, Wood LD, Eshleman JR, Goggins MG, Wolfgang CL, Canto MI, Schulick RD, Edil BH, Choti MA, Adsay V, Klimstra DS, ... ... Karchin R, et al. Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proceedings of the National Academy of Sciences of the United States of America. 108: 21188-93. PMID 22158988 DOI: 10.1073/Pnas.1118046108 |
0.404 |
|
| 2011 |
Tyekucheva S, Marchionni L, Karchin R, Parmigiani G. Integrating diverse genomic data using gene sets. Genome Biology. 12: R105. PMID 22018358 DOI: 10.1186/Gb-2011-12-10-R105 |
0.342 |
|
| 2011 |
Guthrie VB, Allen J, Camps M, Karchin R. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. Plos Computational Biology. 7: e1002184. PMID 21966264 DOI: 10.1371/Journal.Pcbi.1002184 |
0.405 |
|
| 2011 |
Lee D, Karchin R, Beer MA. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research. 21: 2167-80. PMID 21875935 DOI: 10.1101/Gr.121905.111 |
0.427 |
|
| 2011 |
Liu Y, Woods NT, Kim D, Sweet M, Monteiro AN, Karchin R. Yeast two-hybrid junk sequences contain selected linear motifs. Nucleic Acids Research. 39: e128. PMID 21785140 DOI: 10.1093/Nar/Gkr600 |
0.376 |
|
| 2011 |
Zhang X, Reis M, Khoriaty R, Li Y, Ouillette P, Samayoa J, Carter H, Karchin R, Li M, Diaz LA, Velculescu VE, Papadopoulos N, Kinzler KW, Vogelstein B, Malek SN. Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia. Leukemia. 25: 1908-10. PMID 21701494 DOI: 10.1038/Leu.2011.163 |
0.337 |
|
| 2011 |
Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics (Oxford, England). 27: 2147-8. PMID 21685053 DOI: 10.1093/Bioinformatics/Btr357 |
0.461 |
|
| 2011 |
Goes FS, Rongione M, Chen YC, Karchin R, Elhaik E, Potash JB. Exonic DNA sequencing of ERBB4 in bipolar disorder. Plos One. 6: e20242. PMID 21637803 DOI: 10.1371/Journal.Pone.0020242 |
0.317 |
|
| 2011 |
Masica DL, Karchin R. Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Research. 71: 4550-61. PMID 21555372 DOI: 10.1158/0008-5472.Can-11-0180 |
0.4 |
|
| 2011 |
Sosnay PR, Castellani C, Corey M, Dorfman R, Zielenski J, Karchin R, Penland CM, Cutting GR. Evaluation of the disease liability of CFTR variants. Methods in Molecular Biology (Clifton, N.J.). 742: 355-72. PMID 21547743 DOI: 10.1007/978-1-61779-120-8_21 |
0.362 |
|
| 2011 |
Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, ... ... Karchin R, et al. The genetic landscape of the childhood cancer medulloblastoma. Science (New York, N.Y.). 331: 435-9. PMID 21163964 DOI: 10.1126/Science.1198056 |
0.749 |
|
| 2011 |
Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics (Oxford, England). 27: 441-8. PMID 21159622 DOI: 10.1093/Bioinformatics/Btq695 |
0.67 |
|
| 2011 |
Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Letter to the editor Protein Science. 20: 4-5. DOI: 10.1002/Pro.555 |
0.341 |
|
| 2010 |
Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA. Accumulation of driver and passenger mutations during tumor progression Proceedings of the National Academy of Sciences of the United States of America. 107: 18545-18550. PMID 20876136 DOI: 10.1073/Pnas.1010978107 |
0.389 |
|
| 2010 |
Carter H, Samayoa J, Hruban RH, Karchin R. Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer Biology & Therapy. 10: 582-7. PMID 20581473 DOI: 10.4161/Cbt.10.6.12537 |
0.748 |
|
| 2009 |
Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T. Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Research. 37: 5959-68. PMID 19661281 DOI: 10.1093/Nar/Gkp634 |
0.356 |
|
| 2009 |
Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R. Cancer-specific high-throughput annotation of somatic mutations: Computational prediction of driver missense mutations Cancer Research. 69: 6660-6667. PMID 19654296 DOI: 10.1158/0008-5472.Can-09-1133 |
0.397 |
|
| 2009 |
Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics (Oxford, England). 25: 1431-2. PMID 19369493 DOI: 10.1093/Bioinformatics/Btp242 |
0.338 |
|
| 2009 |
Karchin R. Next generation tools for the annotation of human SNPs. Briefings in Bioinformatics. 10: 35-52. PMID 19181721 DOI: 10.1093/Bib/Bbn047 |
0.305 |
|
| 2009 |
Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD, Rodarte RS, Vaz DC, Monteiro VA, Manoukian S, Colombo M, Ripamonti CB, Rosenquist R, Suthers G, Borg A, et al. Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutation Research. 660: 1-11. PMID 18992264 DOI: 10.1016/J.Mrfmmm.2008.09.017 |
0.389 |
|
| 2009 |
Mankoo PK, Sukumar S, Karchin R. PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations. Proteins. 75: 499-508. PMID 18951408 DOI: 10.1002/Prot.22265 |
0.324 |
|
| 2008 |
Karchin R, Agarwal M, Sali A, Couch F, Beattie MS. Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. Cancer Informatics. 6: 203-16. PMID 19043619 DOI: 10.4137/Cin.S618 |
0.442 |
|
| 2008 |
Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, ... ... Karchin R, et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science (New York, N.Y.). 321: 1801-6. PMID 18772397 DOI: 10.1126/Science.1164368 |
0.408 |
|
| 2008 |
Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, ... ... Karchin R, et al. An integrated genomic analysis of human glioblastoma multiforme. Science (New York, N.Y.). 321: 1807-12. PMID 18772396 DOI: 10.1126/Science.1164382 |
0.433 |
|
| 2008 |
Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K. PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics (Oxford, England). 24: 2453-9. PMID 18757875 DOI: 10.1093/Bioinformatics/Btn438 |
0.715 |
|
| 2007 |
Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, ... ... Karchin R, et al. The genomic landscapes of human breast and colorectal cancers. Science (New York, N.Y.). 318: 1108-13. PMID 17932254 DOI: 10.1126/science.1145720 |
0.305 |
|
| 2007 |
Carvalho MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF, Urmenyi TP, Rondinelli E, Silva R, Gayol L, Baumbach L, Sutphen R, Pickard-Brzosowicz JL, Nathanson KL, Sali A, et al. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Research. 67: 1494-501. PMID 17308087 DOI: 10.1158/0008-5472.Can-06-3297 |
0.404 |
|
| 2007 |
Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A. Functional impact of missense variants in BRCA1 predicted by supervised learning. Plos Computational Biology. 3: e26. PMID 17305420 DOI: 10.1371/Journal.Pcbi.0030026 |
0.39 |
|
| 2006 |
Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 34: D291-5. PMID 16381869 DOI: 10.1093/nar/gkj059 |
0.305 |
|
| 2005 |
Karplus K, Karchin R, Shackelford G, Hughey R. Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics (Oxford, England). 21: 4107-15. PMID 16123115 DOI: 10.1093/Bioinformatics/Bti629 |
0.733 |
|
| 2004 |
Karchin R, Cline M, Karplus K. Evaluation of local structure alphabets based on residue burial. Proteins. 55: 508-18. PMID 15103615 DOI: 10.1002/Prot.20008 |
0.754 |
|
| 2003 |
Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins. 53: 491-6. PMID 14579338 DOI: 10.1002/Prot.10540 |
0.662 |
|
| 2003 |
Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins. 51: 504-14. PMID 12784210 DOI: 10.1002/Prot.10369 |
0.771 |
|
| 2002 |
Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics (Oxford, England). 18: 147-59. PMID 11836223 DOI: 10.1093/Bioinformatics/18.1.147 |
0.69 |
|
| 2001 |
Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R. What is the value added by human intervention in protein structure prediction? Proteins. 86-91. PMID 11835485 DOI: 10.1002/Prot.10021 |
0.768 |
|
| 1998 |
Karchin R, Hughey R. Weighting hidden Markov models for maximum discrimination Bioinformatics. 14: 772-782. PMID 9918947 DOI: 10.1093/Bioinformatics/14.9.772 |
0.369 |
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