Publications

2020
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. (2020) The genetic evolution of treatment-resistant cutaneous, acral and uveal melanomas Clin Cancer Res. Dec 15:clincanres.2984.2020 Online ahead of print.

Anagnostou V, Bruhm DC, Niknafs N, White JR, Shao XM, Sidhom JW, Stein J, Tsai HL, Wang H, Belcaid Z, Murray J, Balan A, Ferreira L, Ross-Macdonald P, Wind-Rotolo M, Baras AS, Taube J, Karchin R, Scharpf RB, Grasso C, Ribas A, Pardoll DM, Topalian SL, Velculescu VE.. (2020) Integrative tumor and immune cell multi-omic analyses predict response to immune checkpoint blockade in melanoma Cell Rep Med. Nov 17;1(8):100139

Fujikura K, Hosoda W, Felsenstein M, Song Q, Reiter JG, Zheng L, Beleva Guthrie V, Rincon N, Dal Molin M, Dudley J, Cohen JD, Wang P, Fischer CG, Braxton AM, Noë M, Jongepier M, Fernández-Del Castillo C, Mino-Kenudson M, Schmidt CM, Yip-Schneider MT, Lawlor RT, Salvia R, Roberts NJ, Thompson ED, Karchin R, Lennon AM, Jiao Y, Wood LD. (2020) Multiregion whole-exome sequencing of intraductral papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions. Gut. 2020 Oct 7:gutjnl-2020-321217. doi: 10.1136/gutjnl-2020-321217. Online ahead of print.

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, Castelli P, Hong SM, Yachida S, Hiraoka N, Gill AJ, Samra JS, Offerhaus GJA, Hoorens A, Verheij J, Jansen C, Adsay NV, Jiang W, Winter J, Albores-Saavedra J, Terris B, Thompson ED, Roberts NJ, Hruban RH, Karchin R, Scharpf RB, Brosens LAA, Velculescu VE, Wood LD. (2020) Genomic characterization of malignant progression in neoplastic pancreatic cysts. Nat. Comm. Aug 14;11(1):4085. doi: 10.1038/s41467-020-17917-8.

Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R. (2020) Integrated informatics analysis of cancer-related variants. JCO CCI Mar;4:310-317. doi: 10.1200/CCI.19.00132.

Brnich SE, Abou Tayoun AN, Couch FJ, Cutting GR, Greenblatt MS, Heinen CD, Kanavy DM, Luo X, McNulty SM, Starita LM, Tavtigian SV, Wright MW, Harrison SM, Biesecker LG, Berg JS; Clinical Genome Resource Sequence Variant Interpretation Working Group. Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Med. 2019 Dec 31;12(1):3. doi: 10.1186/s13073-019-0690-2.

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, Lennon AM, Hruban RH, Tomasetti C, Bettegowda C, Kinzler KW, Papadopoulos N, Vogelstein B. (2020) Assessing aneuploidy with repetitive element sequencing Proc Natl Acad Sci USA Feb 19. pii: 201910041. doi: 10.1073/pnas.1910041117. [Epub ahead of print]

Anagnostou V, Niknafs N, Marrone K, Bruhm DC, White JR, Naidoo J, Hummelink K, Monkhorst K, Lalezari F, Lanis M, Rosner S, Reuss JE, Smith KN, Adleff V, Rodgers K,Belcaid Z, Rhymee L, Levy B, Feliciano J, Hann CL, Ettinger DS, Georgiades C, Verde F, Illei P, Li QK, Baras AS, Gabrielson E, Brock MB, Karchin R, Pardoll DM, Baylin SB, Brahmer JR, Scharpf RB, Forde PM, Velculescu VE. (2020) Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer Nature Cancer 1 (1), 99-111

2019

Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, 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 Imm. Res. doi: 10.1158/2326-6066.CIR-19-0464

Niknafs N, Zhong Y, Moral JAG, Zhang L, Shao X, Lo A, Makohon-Moore A, Iacobuzio-Donahue C, Karchin R. Characterization of Genetic Subclonal Evolution in Pancreatic Cancer Mouse Models. Nat Comm. 2019 Nov;10(1):5435

Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X. Voices in methods development. Nat Methods 2019 Oct; 16(10):945-951

Springer S, Masica DL, Dal Molin M, Douville C, Thoburn CJ, Afsari B, Li L, Cohen JD, Thompson E, Allen PJ, Klimstra DS, Schattner MA, Schmidt CM, Yip-Schneider M, Simpson RE, Fernandez-Del Castillo C, Mino-Kenudson M, Brugge W, Brand RE, Singhi AD, Scarpa A, Lawlor R, Salvia R, Zamboni G, Hong SM, Hwang DW, Jang JY, Kwon W, Swan N, Geoghegan J, Falconi M, Crippa S, Doglioni C, Paulino J, Schulick RD, Edil BH, Park W, Yachida S, Hijioka S, van Hooft J, He J, Weiss MJ, Burkhart R, Makary M, Canto MI, Goggins MG, Ptak J, Dobbyn L, Schaefer J, Sillman N, Popoli M, Klein AP, Tomasetti C, Karchin R, Papadopoulos N, Kinzler KW, Vogelstein B, Wolfgang CL, Hruban RH, Lennon AM.I. A multimodality test to guide the management of patients with a pancreatic cyst. Sci Transl Med. 2019 Jul 17;11(501). pii: eaav4772. doi:

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, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Pal LR, Radivojac P, Rousseau F, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I. Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants Hum Mutat. 2019 Jul 13. doi: 10.1002/humu.23868. [Epub ahead of print]

Tokheim C, Karchin R. CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. Cell Syst. May 31. pii: S2405-4712(19)30154-1. doi: 10.1016/j.cels.2019.05.005. [Epub ahead of print]

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, He J, Wolfgang CL, Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood LD. Intraductal Papillary Mucinous Neoplasms Arise from Multiple Independent Clones, Each With Distinct Mutations. Gastroenterology. Jun 5. pii: S0016-5085(19)40987-6. doi: 10.1053/j.gastro.2019.06.001.

2018

Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone KA, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE. Dynamics of tumor and immune responses during immune checkpoint blockade in non-small cell lung cancer. Cancer Research. Dec 12. pii: canres.1127.2018. doi: 10.1158/0008-5472.CAN-18-1127. [Epub ahead of print]

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, Wolfgang CL, Goggins MG, Hruban RH, Roberts NJ, Karchin R, Wood LD. (2018). Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions. Journal of Pathology. Nov. 14 doi: 10.1002/path.5194 [Epub ahead of print]

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. (2018). Minimal functional driver gene heterogeneity among untreated metastases. Science. Sep 7;361(6406):1033-1037.

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 Jr, Jones S, Sausen M, Velculescu VE, Angiuoli SV. (2018). A machine learning approach for somatic mutation discovery. Sci Transl Med. Sep 5;10(457). pii: eaar7939. doi: 10.1126/scitranslmed.aar7939.

Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin R, Jagtap PD, Griffin TJ. (2018). Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics. J. Proteome Res. Sep 5. doi: 10.1021/acs.jproteome.8b00404. [Epub ahead of print]

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng KS, 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 W, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen E, Liang H, The MC3 Working Group, The Cancer Genome Atlas Research Network, Lawrence M, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L (2018). Comprehensive Discovery and Characterization of Driver Genes and Mutations in Cancer. Cell. 173(2):371-385.e18.

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, Schaefer J, Silliman N, Dobbyn L, Tanner EJ, Angarita A, Lycke M, Jochumsen K, Afsari B, Danilova L, Levine DA, Jardon K, Zeng X, Arseneau J, Fu L, Diaz LA Jr, Karchin R, Tomasetti C, Kinzler KW, Vogelstein B, Fader AN, Gilbert L, Papadopoulos N. (2018). Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers. Sci Transl Med. Mar 21;10(433)

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, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang CY, Shun CT, Turesky RJ, Yun BH, Rosenquist TA, Pu YS, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ. (2018). Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy. Elife. Mar 20;7. pii: e32143.

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. (2018). Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell. 33(3):450-462.e10

Guthrie VB, Masica DL, Fraser A, Federico J, Fan Y, Camps M, Karchin R (2018). Network Analysis of Protein Adaptation: modeling the functional impact of multiple mutations. Mol. Biol. Evo. msy036, https://doi.org/10.1093/molbev/msy036 [Epub ahead of print]

Felsenstein M, Noë M, Masica DL, Hosoda W, Chianchiano P, Fischer CG, Lionheart G, Brosens LAA, Pea A, Yu J, Gemenetzis G, Groot VP, Makary MA, He J, Weiss MJ, Cameron JL, Wolfgang CL, Hruban RH, Roberts NJ, Karchin R, Goggins MG, Wood LD. (2018) IPMNs with co-occurring invasive cancers: neighbours but not always relatives. Gut Mar 2. pii: gutjnl-2017-315062. doi: 10.1136/gutjnl-2017-315062. [Epub ahead of print]

Douville C, Springer S, Kinde I, Cohen JD, Hruban RH, Lennon AM, Papadopolous N, Kinzler KW, Vogelstein B, Karchin R (2018) Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs) Proc Natl Acad Sci USA 115(8):1871-1876

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 (2018) Assessment of the clinical relevance of BRCA2 missense variants by functional and computational approaches. Am. Journal of Human Genetics. S0002-9297(17)30502-5

2017

Oetting WS, Béroud C, Brenner SE, Greenblatt MS, Karchin R, Mooney SD. (2017) Methods and tools for assessing the impact of genetic variations: The 2017 annual scientific meeting of the Human Genome Variation Society Human Mutation. 39(3):460-463.

Masica DL, Douville C, Tokheim C, Bhattacharya R, Kim R, Moad K, Ryan MC, Karchin R (2017) CRAVAT 4: Cancer-Related Analysis of Variants Toolkit. Cancer Research. Nov 1;77(21):e35-38.

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, Tille JC, Bowden M, Ayhan A, Wood LD, Scharpf RB, Kurman R, Wang TL, Shih IM, Karchin R, Drapkin R, Velculescu VE. (2017) High grade serous ovarian carcinomas originate in the fallopian tube. Nat. Commun. Oct 23;8(1):1093.

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, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW. (2017) Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med. 8;9(1):113

Monson ET, Pirooznia M, Parla J, Kramer M, Goes FS, Gaine ME, Gaynor SC, de Klerk K, Jancic D, Karchin R, McCombie WR, Zandi PP, Potash JB, Willour VL (2017) Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort. Mol Neuropsychiatry. Jul;3(1):1-11.

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, 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 R, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD (2017) Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Hum Mutat. May 23. doi: 10.1002/humu.23265. [Epub ahead of print]

Fu J, Sen R, Masica DL, Karchin R, Pardoll D, Walter V, Hayes DN, Chung CH, Kim YJ (2017) Autologous reconstitution of human cancer and immune system in vivo. Oncotarget. Jan 10;8(2):2053-2068.

Oetting WS, Béroud C, Brenner SE, Greenblatt M, Karchin R, Mooney SD, Sunyaev S. (2017) Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society. Hum Mutat. 38(4):460-463.

Masica DL, Dal Molin M, Wolfgang CL, Tomita T, Ostovaneh MR, Blackford A, Moran RA, Law JK, Barkley T, Goggins M, Irene Canto M, Pittman M, Eshleman JR, Ali SZ, Fishman EK, Kamel IR, Raman SP, Zaheer A, Ahuja N, Makary MA, Weiss MJ, Hirose K, Cameron JL, Rezaee N, He J, Joon Ahn Y, Wu W, Wang Y, Springer S, Diaz LL Jr, Papadopoulos N, Hruban RH, Kinzler KW, Vogelstein B, Karchin R, Marie Lennon A (2017) A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts. J Am Med Inform Assoc Jan;24(1):145-152.

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, Sharfman WH, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf R, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE. (2016) Evolution of Neoantigen Landscape During Immune Checkpoint Blockade in Non-Small Cell Lung Cancer. Cancer Discov. 7(3):264-276

Tokheim C, Papdopoulis N, Kinzler KW, Vogelstein B, Karchin R (2016) Evaluating the evaluation of cancer driver genes. Proc Natl Acad Sci U S A. Dec 13;113(50):14330-14335.

Karchin R, Nussinov R (2016) Genome landscapes of disease: strategies to predict the phenotypic consequences of human germline and somatic variation. PLoS Comput Biol. Aug 18;12(8):e1005043

Mascia DL, Karchin R (2016) Towards increasing the clinical relevance of in silico methods to predict pathogenic missense variants. PLoS Computational Biology. May 12;12(5):e1004725.

Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R (2016) Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure Cancer Research. 1;76(13):3719-31

Goes FS, Pirooznia M, Parla JS, Kramer M, Ghiban E, Mavruk S, Chen YC, Monson ET, Willour VL, Karchin R, Flickinger M, Locke AE, Levy SE, Scott LJ, Boehnke M, Stahl E, Moran JL, Hultman CM, Landén M, Purcell SM, Sklar P, Zandi PP, McCombie WR, Potash JB. (2016) Exome sequencing of bipolar disorder JAMA Psychiatry. Jun 1:73(6):590-7

Oetting WS, Brenner SE, Brookes AJ, Greenblatt MS, Hart RK, Karchin R, Sunyaev SR, Taschner PE (2016) Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society. Human Mutation. Jan 21. doi: 10.1002/humu.22958. [Epub ahead of print]

Rettig EM, Talbot Jr CC, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N (2016) Whole-genome sequencing of salivary gland adenoid cystic carcinoma. Cancer Prevention Research. Feb 9. pii:canprevres.0316.2015. [Epub ahead of print].

Roberts NJ, Norris A, Petersen GM, Bondy ML, Brand R, Gallinger S, Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stofel E, Syngal S, Zogopoulos G, Ali SZ, Axilbund J, Chaffe KG, Chen YC, Cote ML, Childs EJ, Douville C, Goes FS, Herman JM, Iacobuzio-Donahue C, Kramer M, Makohon-Moore A, McCombie WR, McMahon K, Niknafs N, Parla J, Pirooznia M, Potash JB, Rhim AD, Smith AL, Wang Y, Wolofgang CL, Wood LD, Zandi PP, Goggins M, Karchin R, Eshleman J, Papadopoulos N, Kinzler KW, Vogelstein B, Hruban RH, Klein AP (2016) Whole genome sequencing of patients with familial pancreatic cancer Cancer Discovery. Dec 9. pii: CD-15-0402. [Epub ahead of print].

Douville C, Masica DL, Stenson PD, Cooper DN, Gygax D, Kim R, Ryan M, Karchin R (2016) Assessing the pathogenicity of insertion and deletion variants with the Variant Effect Scoring Tool (VEST-indel) Human Mutation. 37(1):28-35

2015

Niknafs N, Guthrie VB, Naiman DQ, Karchin R (2015) SubClonal Hierarchy Inference from Somatic Mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing. PLoS Computational Biology. 11(10):e1004416

Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Sausen M, Phallen J, Tokheim C, Niknafs N, Nesselbush M, Lytle K, 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 (2015) The Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer. Nature. 526(7572):263-7

Springer S, Wang Y, Dal Molin M, Masica DL, Jiao Y, Kinde I, Blackford A, Raman SP, Wolfgang CL, Tomita T, Niknafs N, Douville C, Ptak J, Dobbyn L, Allen PJ, Klimstra D, Schattner MA, Schmidt CM, Yip-Schneider M, Cummings OW, Brand RE, Zeh JH, Singhi AD, Scarpa A, Salvia R, Malleo G, Zamboni G, Falconi M, Jang JY, Kim SW, Kwon W, Hong SM, Song KB, Kim SC, Swan N, Murphy J, Geoghegan J, Brugge W, Fernandez-Del Castillo C, Mino-Kenudson M, Schulick R, Edil BH, Adsay V, Paulino J, van Hoof J, Yachida S, Nara S, Hiraoka N, Yamao K, Hijoka S, van der Merwe S, Goggins M, Canto MI, AHuga N, Hirose K, Makary M, Weiss MJ, Cameron J, Pittman M, Eshleman JR, Diaz Jr LA, Papadopoulos N, Kinzler KW, Karchin R, Hruban R, Vogelstein B, Lennon AM (2015) A Combination of Molecular Markers and Clinical Features Improve the Classification of Pancreatic Cysts. Gasteroenterology. 149(6):1501-10

Turner TN, Douville C, Kim D, Stenson PD, Cooper DN, Chakravarti A, Karchin R (2015) Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns Hum Mol Genet. 24(21):5995-6002

Chung CH,Guthrie VB, Masica D, Tokheim C, Kang H, Richmon J, Agrawa N, Gourin C, Quon H, Zuo Z, Seiwert T, Ali SM, Miller VA, Frampton GM, Chalmers ZR, Karchin R, Bishop J (2015) Genetic alterations in head and neck squamous cell carcinoma determined by a cancer gene-targeted sequencing. Ann Oncol. 26(6):1216-23

Karchin R, Cline MS. (2015) Human genetics special issue on computational molecular medicine Human Genetics. 134(5):455-7

Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD (2015) Germline and somatic mosaicism: the 2014 annual scientific meeting of the Human Genome Variation Society. Human Mutat. 36(3):390-3

Rettig EM, Chung CH, Bishop JA, Howard JD, Sharma R, Li RJ, Douville C, Karchin R, Izumchenko E, Sidransky D, Koch WM, Califano J, Agrawal N, Fakhry C (2015) Cleaved NOTCH1 expression pattern in head and neck squamous cell carcinoma is associated with NOTCH1 mutation, HPV status and high-risk clinical features. Cancer Prev Res. 8(4):287-95

Masica DL, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch WM, Chung CH, Karchin R (2015) Predicting survival in head and neck squamous-cell carcinoma from TP53 mutation. Human Genetics. 134(5):497-507

2014

Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R (2014) Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Human Mol. Genetics. 24(7):1908-17

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 (2014) A probabilistic model to predict clinical phenotypic traits from genome sequencing. PLoS Computational Biology. Sep 4. 10(9):e1003825

Sharma N, Sosnay PR, Ramalho AS, Douville C, Franca A, Gottschalk LB, Park J, Lee M, Vecchio-Pagan B, Siklosi K, Amaral MD, Karchin R, Cutting G (2014) Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions Human Mutation. 35(10):1249-59

Li L, Masica DL, Ishida M, Tomuleasa C, Umegak S, Kalloo AN, Georgiades C, Singh VK, Khashab M, Amateau S, Li Z, Okolo P, Lennon AM, Saxena P, Geschwind JF, Schlachter T, Hong K, Pawlik TM, Canto M, Law J, Sharaiha R, Weiss CR, Peng H, Thuluvath P, Goggins M, Shin EJ, Kumbhari V, Hutfless S, Zhou L, Mezey E, Meltzer SJ, Karchin R, Selaru FM. (2014) Human bile contains microRNA-laden exosomes that can be used for cholangiocarcinoma diagnosis. Hepatology. 60(3):896-907

Carter H, Karchin R (2014) Predicting the functional consequences of somatic missense mutations found in tumors. Methods in Molecular Biology, Gene Function Analysis, 2nd Edition), Ed. Ochs MF. Humana Press.  

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, Alexandrescu ST, Dima S, Fassan M, Simbolo M, Mafficini A, Capelli P, Lawlor RT, Ruzzenente A, Guglielmi A, Tortora G, de Braud F, Scarpa A, Jarnagin W, Klimstra D, Karchin R, Velculescu VE, Hruban RH, Vogelstein B, Kinzler KW, Papadopoulos N, Wood LD (2013) Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nat. Genetics. Dec;45(12):1470-3 

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, Corey M, Lewis MH, Rommens JM, Castellani C, Penland CM, Cutting GR (2013) Defining the disease-liability of mutations in the cystic fibrosis transmembrane conductance regulator gene. Nat. Genetics. 45(10):1160-7 

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, Kinzler KW, Rosenquist T (2013) A. Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole Exome Sequencing. Science Translational Medicine. 5(197):197ra102 

Gartner JJ, Parker SCJ, Prickett TD, Dutton-Reester K, Lin JC, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Bhanot UK, NISC Comparative Sequencing Program, Willard MD, Chen G, Elnitski L, Davies MA, Gershenwald JE, Carter H, Karchin R, Barber TD, Robinson W, Robinson S, Rosenberg SA, Komar AA, Kimchi-Sarfaty C, Hayward NK, Marguiles EH, Samuels Y (2013) Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci USA. 110(33):13481-6

International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group, 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, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N. (2013) Computational approaches to identify functional genetc variants in cancer genomes. Nat Methods.10(8):723-9

Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R (2013) Identifying Mendelian disease genes with the Variant Effect Scoring Tool. BMC Genomics. 14(3) 1-16.

Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Karchin R (2013) MuPIT Interactive: Webserver for mapping variant positions to annotated, interactive 3D structures. Human Genetics. 132(11):1235-43

Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013) CRAVAT: Cancer-Related Analysis of VAriants Toolkit. Bioinformatics. 29(5):647-8

Masica DL and Karchin R (2013) Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Research. 73(6):1699-708

Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R (2013) A hybrid likelihood model for sequence-based disease association studies. PLoS Genetics. 9(1): e1003224

2012

Woods N, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H, Marsillac S, Karchin R, Koomen J, Monteiro ANA(2012) Charting the landscape of tandem BRCT domain-mediated protein interactions. Science Signaling. 5(242):rs6

Liang H, Cheung LWT, Li J, Ju Z, Yu S, Stemke-Hale K, Dogruluk T, Lu Y, Liu X, Gu C, Scherer SE, Carter H, Westin SN, Verhaak R, Zhang F, Karchin R, Liu CG, Lu KH, Broaddus RR, Scott KL, Hennessy BT, Mills GB (2012) Whole-exome Sequencing Combined with Functional Genomics Reveals Novel Candidate Driver Cancer Genes in Endometrial Cancer. Genome Research. Nov;22(11):2120-9

Masica DL, Sosnay P, Cutting G, Karchin R (2012) Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Human Mutation. 33(8):1267-74

Jiao X, Wood L, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R and Sjobolom T (2012) Somatic mutations in the notch, NF-KB, PIK3CA and hedgehog pathways in human breast cancers. Genes, Chromosomes and Cancer. 51(5):480-9

Wu J, Jiao Y, Dal Molin M, Maitra A, deWilde RF, Wood LD, Eshleman JR, Goggins MG, Wolfgang CL, Canto ML, Schulick RD, Edil BH, CHoti, MA, Adsay V, Kimstra DS, Offerhaus GJA, Klein AP, Kopelovic L, Carter H, Karchin R, Allen PJ, Schmidt CM, Matio Y, Diaz L, Kinzler KW, Papadopolus N, Hruban RH, Vogelstein B (2011) Whole exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proc Natl Acad Sci USA. 108(52):21188-93

Karchin R, Ochs MF, Stuart JM, Bader JS (2012) Identification of aberrant pathway and network activity from high-throughput data. Pac Symp Biocomput 2012 17:1-6

2011

Beleva-Guthrie V, Allen J, Camps M, and Karchin R (2011) Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLoS Computational Biology. 7(9):e1002184

Lee D, Karchin R, Beer M. (2011) Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research. 21(12):2167-80

Tyekucheva S, Marchionni L, Karchin R, Parmigianni G. (2011) Integrating diverse genomic data using gene sets. Genome Biology. 23:R105, Oct. 21, 2011

Liu Y, Woods N, Kim D, Monteiro ANA, Karchin R (2011) Yeast two-hybrid junk sequences contain selected linear motifs. Nucleic Acids Research. 39(19):e128

Wong WC, Kim D, Carter H, Diekhans M, Ryan M and Karchin R (2011) CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 27(15):2147-8

Zhang X, Reis M, Khoriaty R, Li Y, Ouillette P, Samayoa J, Carter H, Karchin R, Li M, Diaz L, Velculescu VE, Kinzler KW, Vogelstein B and Malek SN (2011) Sequence analysis of 515 kinase genes in Chronic Lymphocytic Leukemia. Leukemia. 25(12):1908-10

Goes FS, Rongione M, Chen YC, Karchin R, Elhalk E, and Potash JB (2011) Exonic DNA Sequencing of ERBB4 in Bipolar Disorder. PLoS One. 6(5):e20242

Allen J, Simcha D, Ericson N, Alexander D, Troll C, Marquette J, Van Biber B, Hernandez J, Karchin R, Bielas J, Loeb L, Camps M. (2011) Roles of DNA Polymerase I in leading and lagging-strand replication defined by a high-resolution mutational footprint of ColE1 plasmid replication. Nucleic Acids Res. 39(16):7020-7033

The Cancer Genome Atlas Research Network (2011) Integrated genomic analysis of ovarian carcinoma. Nature. 2011;474:609-615

Masica DL and Karchin R (2011) Correlation among somatic mutation expression identifies genes important in human glioblastoma progression and survival. Cancer Research. Jul 1;71(13):4550-61

Sosnay PR, Castellani C, Corey M, Dorfman R, Zielenski J, Karchin R, Penland CM, Cutting GR. (2011) Evaluation of the Disease Liability of CFTR Variants. Methods Mol Biol. 2011;742:355-72

Parsons DW, Li M, Zhang X, Jones S, Leary R, Lin J, Boca S, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SKN, Shinjo SMO, Clara C, Phillips PC, Minturn JE, Biegel J, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Tasheed BA, Friedman H, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papdopoulos N, Vogelstein B, Kinzler KW and Velculescu V. (2011) The genetic landscape of the childhood cancer medulloblastoma. Science. Jan 28;331(6016):435-9

Cline MS and Karchin R (2011) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. Feb 15;27(4):441-8. Dec 15

Ochs MF, Karchin R, Ressom H, and Gentleman R. (2011) Identification of aberrant pathway and network activity from high-throughput data - workshop introduction. Pac Symp Biocomput. 2011:364-8

2010

Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA (2010) Accumulation of driver and passenger mutations during tumor progression. Proc Natl Acad Sci USA. Oct 26;107(43):18545-50.

Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A (2010) Functional hot spots in human ABC transporter nucleotide binding domains. Protein Science. Nov. 19(11):2110-21

Carter H, Samayoa J, Hruban RH, Karchin R (2010) Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annnotation of somatic mutations (CHASM). Cancer Biology & Therapy. Sep 31;10(6):582-7.

2009

Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R.(2009) Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.Cancer Research. 69(16):6660-7

Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T. (2009) Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Res. 37(18):5959-68

Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. (2009) LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 25(11):1431-2

Karchin R. (2009) Next generation tools for the annotation of human SNPs. Briefing in Bioinformatics. 10(1):35-52

Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan D, Carter H, Mankoo P, Karchin R, Marti-Renom M, Davis F and Sali A. (2009) MODBASE, a database of annotated comparative structure models, and associated resources. Nucleic Acids Res, 37 (Database issue):D347-54.

Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD, Rodarte RS, Vaz DC, Monteiro VA, Manoukian S, Colombo M, Ripamonti C, Rosenquist-Brandell R, Suthers G, Borg A, Radice P, Grist SA, Monteiro ANA and Billack B. (2009) Analysis of missense, frameshift, and in-frame deletion variants of BRCA1. Mutation Research. Jan 15;660(1-2):1-11.

2008

Jones S, Zhang X, Parsons DW, Lin J, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu, B, Lin, MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman, JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. (2008) Core signaling pathways in human pancreatic cancer revealed by global genomic analyses. Science, 26:1801-1806

Parsons DW, Jones S, Zhang X, Lin J, Leary RJ, Angenendt P, Mankoo P, Carter H, Su IM, Gallia G, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA, Hartigan J, Smith DR, Strausberg RL, Marie SKN, Shinjo SMO, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. (2008) An integrated genomic analysis of human glioblastoma multiforme Science. 26:1807-1812

Mankoo P, Sukumar S, Karchin R. (2008) PIK3CA somatic mutations in breast cancer: mechanistic insights from Langevin dynamics simulations. Proteins Sep 10;75(2):499-508

Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K (2008) Predict-2nd: a tool for generalized protein local structure prediction Bioinformatics. Nov 1;24(21):2453-9.

Karchin R, Couch F, Agarwal M, Sali A,& Beattie M.S.(2008) Classifying BRCA2 unclassified variants using protein likelihood ratios. Cancer Informatics 4:1-14

2007

Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. (2007) The Genomic Landscapes of Human Breast and Colorectal Cancers. Science Nov 16;318(5853):1108-13

Karchin R, Monteiro A.N, Carvalho M.A, Tavtigian S.V. & Sali A. (2007) Functional impact of missense mutants in BRCA1 predicted by supervised learning. PLoS Computational Biology 3(2):e26

Kelly L, Karchin R, & Sali A. (2007) Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium on Biocomputing 12:51-63

Carvalho M.A, Marsillac S.M, Karchin R, Manoukian S, Grist S, Swaby R.F, Urmenyi T.P, Rondinelli E, Silva R, Gayol L. et al. (2007) Determination of cancer risk associated with germline BRCA1 missense variants by functional analysis. Cancer Research 67(4):1494-501

2006 and earlier
Pieper U, Eswar N, Davis F, Braberg H, Madhusudhan M, Rossi A, Marti-Renom M, Karchin R, Webb B, Eramian D, Shen M, Kelly L, Melo F. & Sali A. (2006) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research 34:D291-5

Karplus K, Karchin R, Shackelford G. & Hughey, R. (2005) Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics 21(22):4107-15

Karchin R, Diekhans M, Kelly L, Thomas D, Pieper U, Eswar N, Haussler D & Sali A (2005) LS-SNP: large-scale annotation of coding non-synonynous SNPs based on multiple information sources. Bioinformatics 21(12):2814-20

Karchin R, Kelly L & Sali A (2005) Improving functional annotation of non-synonymous SNPs with information theory. Pacific Symposium on Biocomputing 10:397-408

Karchin R, Cline M & Karplus K (2004) Evaluation of local structure alphabets based on residue burial. Proteins 55(3):508-18

Karchin R, Cline M, Mandel-Gutfreund Y. & Karplus K. (2003) Hidden Markov models that use predicted local structure for fold recognition: alphabets of protein backbone geometry. Proteins 51(4):504-514

Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diehkans, M & Hughey R (2003) Combining local structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins 53(S6):491-496

Karchin R, Karplus K & Haussler, D (2002) Classifying G-Protein Coupled Receptors with Support Vector Machines. Bioinformatics 18(1):147-159

Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M Grate, L Casper, J & Hughey R. (2001) What is the value added by human intervention in protein structure prediction? Proteins 45(S5):86-91

Karchin R & Hughey R (1998) Weighting Hidden Markov Models for Maximum Discrimination. Bioinformatics 14(9):772-82