Karchin, Rachel

Professor
Biomedical Engineering

Hackerman Hall 217A
(410) 516-5578
rkarchi1@jhu.edu

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News

Nine from Hopkins Engineering selected for AIMBE College of Fellows

March 20, 2017

The American Institute for Medical and Biological Engineering will induct nine faculty members from three Johns Hopkins University Whiting School of Engineering departments into its College of Fellows during AIMBE’s 2017 Annual Event.

New bioinformatics tool tests methods for finding mutant genes that ‘drive’ cancer

December 19, 2016

A team of Johns Hopkins computational scientists and cancer experts have devised their own bioinformatics software to evaluate how well the current strategies identify cancer-promoting mutations and distinguish them from benign mutations in cancer cells.

Education

Ph.D. 2003, Univ of California Santa Cruz
Master of Science 2000, University of California, Santa Cruz, CA
Bachelor of Science 1998, University of California, Santa Cruz, CA

Experience

2014 - Present: Joint, SOM Oncology Center
2012 - 2012: Pacific Symposium on Biocomputing. Session chair. Identification of Aberrant Pathway and Network Activity from High-Throughput Data., Pacific Symposium on Biocomputing
2011 - 2011: Co-Chair, Pacific Symposium on Biocomputing
2011 - Present: CAGI (Critical Assessment of Genome Interpretation) Scientific Council, Critical Assessment of Genome Interpretation Scientific Council
2011 - Present: ICGC (International Cancer Genome Consortium) Bioinformatics Analyses Working Group, ICGC
2009 - 2009: NIH-NCI planning meeting about integrating GWAS and somatic studies., NIH-NCI
2009 - 2009: Computational Biology and the Cancer Genome Atlas presentation at Baltimore Polytechnic High School for Women Serious About Science series, Baltimore Polytechnic High School
2009 - 2009: What is computational biology? presentation at Baltimore Polytechnic High School, Baltimore Polytechnic High School
2008 - 2008: Lustgarten Pancreatic Cancer Research Foundation think tank, Lustgarten Pancreatic Cancer Research Foundation
2008 - 2008: What is computational biology? presentation at Baltimore Polytechnic High School, Baltimore Polytechnic High School
2007 - 2007: Bioinformatics and breast cancer risk presentation at Baltimore Polytechnic High School for Women Serious About Science series, Baltimore Polytechnic High School
2007 - 2007: Bioinformatics of Disease Mutations Workshop at McKinley Technical High School, Washington D.C. Free Vector NTI software licenses provided by Invitrogen 2007 2007, McKinley Technical High School, Washington D.C

Awards

2013: William R. Brody Faculty Scholar
2011: mentor for Ph.D. student Hannah Carter - Siebel Scholar
2011: mentor for undergraduate student Jean Fan - PURA award
2008: Provost's Framework for the Future Award
2008: Provost's Framework for the Future Award

Presentations

"MOCA: Multivariate Organization of Combinatorial Alterations, Applications to Cancer Genomics", Agensys Bioinformatics Seminar Series. Santa Monica, CA USA. December 30, 1899
"A Bayesian network model to predict phenotype from genotype", CAGI. Berlin, Germany. December 30, 1899
"Tools to interpret genome variation", SBMI Research Seminar Series. Houston, TX USA. December 30, 1899
"Challenges for computational analysis of cancer exomes", Bioinformatics seminar series. College Park, Maryland USA. December 30, 1899

Publications

Journal Articles

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. Proceedings of the National Academy of Sciences of the United States of America. 117(9). 4858-4863.
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 (2020). High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer immunology research. 8(3). 396-408.
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, Berg JS, Brenner SE, Ellard S, Harrison SM, Karbassi I, Karchin R, Mester JL, O'Donnell-Luria A, Pesaran T, Plon SE, Rehm H, Topper S (2019). Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Medicine. 12(1).
Niknafs N, Zhong Y, Moral JA, Zhang L, Shao MX, Lo A, Makohon-Moore A, Iacobuzio-Donahue CA, Karchin R (2019). Characterization of genetic subclonal evolution in pancreatic cancer mouse models. Nature Communications. 10(1).
Fischer CG, Beleva Guthrie V, Braxton AM, Zheng L, Wang P, Song Q, Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S, Dal Molin M, Masica D, Scharpf RB, Thompson ED, He J, Wolfgang CL, Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood LD (2019). Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations. Gastroenterology. 157(4). 1123-1137.e22.
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, Radivojac P, Rousseau F, Pal LR, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I (2019). Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Human Mutation. 40(9). 1530-1545.
Tokheim C, Karchin R (2019). CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. Cell Systems. 9(1). 9-23.e8.
Springer S, Masica DL, Molin MD, Douville C, Thoburn CJ, Afsari B, Li L, Cohen JD, Thompson E, Allen PJ, Klimstra DS, Schattner MA, Max Schmidt C, Yip-Schneider M, Simpson RE, Castillo CFD, 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 (2019). A multimodality test to guide the management of patients with a pancreatic cyst. Science Translational Medicine. 11(501).
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 (2019). Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions. Journal of Pathology. 247(3). 347-356.
Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone K, Ashok Sivakumar IK, 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 (2019). Dynamics of tumor and immune responses during immune checkpoint blockade in non–small cell lung cancer. Cancer Research. 79(6). 1214-1225.
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. Journal of Proteome Research. 17(12). 4329-4336.
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. 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, Jones S, Sausen M, Velculescu VE, Angiuoli SV (2018). A machine learning approach for somatic mutation discovery. Science Translational Medicine. 10(457).
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. 67(9). 1652-1662.
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. Molecular Biology and Evolution. 35(6). 1507-1519.
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK-S, 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-W, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Caesar-Johnson SJ, Demchok JA, Felau I, Kasapi M, Ferguson ML, Hutter CM, Sofia HJ, Tarnuzzer R, Yang L, Zenklusen JC, Zhang JJ, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Cho J, DeFreitas T, Frazer S, Gehlenborg N, Getz G, Heiman DI, Lawrence MS, Lin P, Meier S, Noble MS, Saksena G, Voet D, Zhang H, Bernard B, Chambwe N, Dhankani V, Knijnenburg T, Kramer R, Leinonen K, Liu Y, Miller M, Reynolds S, Shmulevich I, Thorsson V, Zhang W, Akbani R, Broom BM, Hegde AM, Ju Z, Kanchi RS, Korkut A, Li J, Ling S, Liu W, Lu Y, Mills GB, Ng K-S, Rao A, Ryan M, Wang J, Weinstein JN, Zhang J,...Karchin R (2018). Comprehensive Characterization of Cancer Driver Genes and Mutations. 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, 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. Science Translational Medicine. 10(433).
Springer SU, Chen CH, Del Carmen Rodriguez Pena M, 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. 7.
Ng PKS, 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.
Oetting WS, Béroud C, Brenner SE, Greenblatt MS, Karchin R, Mooney SD (2018). 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). 454-458.
Douville C, Springer S, Kinde I, Cohen JD, Hruban RH, Lennon AM, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R (2018). 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. 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. American Journal of Human Genetics. 102(2). 233-248.
Glusman G, Rose PW, Prlic 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 JJ, 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 Medicine. 9(1).
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. Nature Communications. 8(1).
Masica DL, Douville C, Tokheim C, Bhattacharya R, Kim RG, Moad K, Ryan MC, Karchin R (2017). CRAVAT 4: Cancer-related analysis of variants toolkit. Cancer Research. 77(21). e35-e38.
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 (2017). Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Human Mutation. 38(9). 1266-1276.
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. Human Mutation. 38(4). 460-463.
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 W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE (2017). Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer. Cancer Discovery. 7(3). 264-276.
Masica DL, Molin MD, Wolfgang CL, Tomita T, Ostovaneh MR, Blackford A, Moran RA, Law JK, Barkley T, Goggins M, Canto MI, 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, Ahn YJ, Wu W, Wang Y, Springer S, Diaz LL, Papadopoulos N, Hruban RH, Kinzler KW, Vogelstein B, Karchin R, Lennon AM (2017). A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts. Journal of the American Medical Informatics Association. 24(1). 145-152.
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. 8(2). 2053-2068.
Tokheim CJ, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R (2016). Evaluating the evaluation of cancer driver genes. Proceedings of the National Academy of Sciences of the United States of America. 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 Computational Biology. 12(8).
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. 76(13). 3719-3731.
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 familial bipolar disorder. JAMA Psychiatry. 73(6). 590-597.
Masica DL, Karchin R (2016). Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants. PLoS Computational Biology. 12(5).
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. 37(4). 406-411.
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, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N (2016). Whole-genome sequencing of salivary gland adenoid cystic carcinoma. Cancer Prevention Research. 9(4). 265-274.
Roberts NJ, Norris AL, Petersen GM, Bondy ML, Brand R, Gallinger S, Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stoffel E, Syngal S, Zogopoulos G, Ali SZ, Axilbund J, Chaffee KG, Chen YC, Cote ML, Childs EJ, Douville C, Goes FS, Herman JM, Iacobuzio-Donahue C, Kramer M, Makohon-Moore A, McCombie RW, Wyatt Mcmahon K, Niknafs N, Parla J, Pirooznia M, Potash JB, Rhim AD, Smith AL, Wang Y, Wolfgang CL, Wood LD, Zandi PP, Goggins M, Karchin R, Eshleman JR, Papadopoulos N, Kinzler KW, Vogelstein B, Hruban RH, Klein AP (2016). Whole genome sequencing defines the genetic heterogeneity of familial pancreatic cancer. Cancer Discovery. 6(2). 166-175.
Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, 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.
Douville C, Masica D, Stenson PD, Cooper DN, Gygax DM, 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.
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.
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 DS, Schattner MA, Schmidt CM, Yip-Schneider M, Cummings OW, Brand RE, Zeh HJ, Singhi AD, Scarpa A, Salvia R, Malleo G, Zamboni G, Falconi M, Jang J-Y, Kim S-W, Kwon W, Hong S-M, Song K-B, 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 Hooft J, Yachida S, Nara S, Hiraoka N, Yamao K, Hijioka S, Van Der Merwe S, Goggins M, Canto MI, Ahuja N, Hirose K, Makary M, Weiss MJ, Cameron J, Pittman M, Eshleman JR, Diaz LA, Papadopoulos N, Kinzler KW, Karchin R, Hruban RH, Vogelstein B, Lennon AM (2015). A Combination of Molecular Markers and Clinical Features Improve the Classification of Pancreatic Cysts. Gastroenterology. 149(6). 1501-1510.
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 (2015). The genomic landscape of response to EGFR blockade in colorectal cancer. Nature. 526(7572). 263-267.
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.
Karchin R, Cline MS (2015). Human genetics special issue on computational molecular medicine. Human Genetics. 134(5). 455-457.
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 (2015). 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. 8(4). 287-295.
Karchin R, Cline MS (2015). Human genetics special issue on computational molecular medicine. Human genetics. 134(5). 455-457.
Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD (2015). Germline & somatic mosaicism: The 2014 annual scientific meeting of the human genome variation society. Human mutation. 36(3). 390-393.
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, Yelensky R, Stephens PJ, Miller VA, Karchin R, Bishop JA (2015). Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Annals of Oncology. 26(6). 1216-1223.
Niknafs N, Violeta B, Daniel Q N, Karchin R (2015). SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.. PLoS Comput Biol. 11(10). e1004416.
Rettig EM, Chung CH, Bishop JA, Howard JD, Sharma R, Li RJ, Douville C, Karchin R, Izumchenko E, Sidransky D, others (2015). 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. 8(4). 287-295.
Masica D, Sosnay PR, Raraigh KS, Cutting GR, Karchin R (2015). Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Human molecular genetics. 24(7). 1908-1917.
Masica D, 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.
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. Human Molecular Genetics. ddv309.
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. Human Molecular Genetics. 24(21). 5995-6002.
Niknafs N, Beleva-Guthrie V, 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).
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 Molecular Genetics. 24(7). 1908-1917.
Li L, Masica D, Ishida M, Tomuleasa C, Umegaki 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, Thuluvath P, Goggins M, Shin EJ, Peng H, Kumbhari V, Hutfless S, Zhou L, Mezey E, Meltzer SJ, Karchin R, Selaru FM (2014). Human bile contains MicroRNA-laden extracellular vesicles that can be used for cholangiocarcinoma diagnosis. Hepatology. 60(3). 896-907.
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. 10(9).
Carter H, Karchin R (2014). Predicting the functional consequences of somatic missense mutations found in tumors. Gene Function Analysis. 135-159.
Carter H, Karchin R (2014). Predicting the functional consequences of somatic missense mutations found in tumors. Methods in Molecular Biology. 1101. 135-159.
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 (2014). Experimental Assessment of Splicing Variants Using Expression Minigenes and Comparison with In Silico Predictions. Human Mutation. 35(10). 1249-1259.
Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, Niknafs N, Guthrie VB, Maitra A, Argani P, Offerhaus GJA, 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. Nature Genetics. 45(12). 1470-1473.
Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R (2013). MuPIT interactive: Webserver for mapping variant positions to annotated, interactive 3D structures. Human Genetics. 132(11). 1235-1243.
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 variants in the cystic fibrosis transmembrane conductance regulator gene. Nature Genetics. 45(10). 1160-1167.
Gartner JJ, Parker SCJ, 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, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y (2013). 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(33). 13481-13486.
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 TA (2013). Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing. Science Translational Medicine. 5(197).
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GRS, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BFF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Li D, Sander C, Stuart JM, Stein LD, Lopez-Bigas N (2013). Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10(8). 723-729.
Masica DL, Karchin R (2013). Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Research. 73(6). 1699-1708.
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). 647-648.
Chen Y, 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 Genet. 9(1). e1003224.
Hoang ML, Chen C, Sidorenko VS, He J, Dickman KG, Yun BH, Moriya M, Niknafs N, Douville C, Karchin R, others (2013). Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing. Science translational medicine. 5(197). 197ra102-197ra102.
Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R (2013). MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Human genetics. 132(11). 1235-1243.
Masica D, Karchin R (2013). Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer research. 73(6). 1699-1708.
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). 647-648.
Carter H, Douville C, Stenson PD, Cooper DN, Karchin R (2013). Identifying Mendelian disease genes with the variant effect scoring tool. BMC genomics. 14(3). 1.
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).
Carter H, Douville C, Stenson PD, Cooper DN, Karchin R (2013). Identifying Mendelian disease genes with the variant effect scoring tool.. BMC genomics. 14 Suppl 3.
Karchin R, Ochs MF, Stuart JM, Ideker T, Bader JS (2013). Identification of aberrant pathway and network activity from high-throughput data. Pacific Symposium on Biocomputing.
Liang H, Cheung LWT, 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, Verhaak RGW, 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. 22(11). 2120-2129.
Woods NT, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H, Thomas CE, Iversen ES, Marsillac S, Karchin R, Koomen J, Monteiro ANA (2012). Charting the landscape of tandem BRCT domain-mediated protein interactions. Science Signaling. 5(242).
Masica DL, Sosnay PR, Cutting GR, Karchin R (2012). Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Human Mutation. 33(8). 1267-1274.
Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, Sjöblom T (2012). Somatic mutations in the notch, NF-KB, PIK3CA, and hedgehog pathways in human breast cancers. Genes Chromosomes and Cancer. 51(5). 480-489.
Karchin R, Ochs MF, Stuart JM, Bader JS (2012). Identification of aberrant pathway and network activity from high-throughput data. Pacific Symposium on Biocomputing. 1-6.
Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, others (2012). Somatic mutations in the notch, NF-KB, PIK3CA, and hedgehog pathways in human breast cancers. Genes, Chromosomes and Cancer. 51(5). 480-489.
Karchin R, Ochs MF, Stuart JM, Bader J (2012). Identification of Aberrant Pathway and Network Activity from High-Throughput Data. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 17. 1.
Masica D, Sosnay PR, Cutting GR, Karchin R (2012). Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Human mutation. 33(8). 1267-1274.
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, Offerhaus GJA, Klein AP, Kopelovich L, Carter H, Karchin R, Allen PJ, Schmidt CM, Naito Y, Diaz LA, Kinzler KW, Papadopoulos N, Hruban RH, Vogelstein B (2011). 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(52). 21188-21193.
Lee D, Karchin R, Beer MA (2011). Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research. 21(12). 2167-2180.
Ochs MF, Karchin R, Ressom H, Gentleman R (2011). Identification of aberrant pathway and network activity from high-throughput data-workshop introduction. Pacific Symposium on Biocomputing 2011, PSB 2011. 364-368.
Tyekucheva S, Marchionni L, Karchin R, Parmigiani G (2011). Integrating diverse genomic data using gene sets. Genome Biology. 12(10).
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 in molecular biology (Clifton, N.J.). 742. 355-372.
Guthrie VB, Allen J, Camps M, 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).
Allen JM, Simcha DM, Ericson NG, Alexander DL, Marquette JT, Van Biber BP, Troll CJ, Karchin R, Bielas JH, Loeb LA, Camps M (2011). Roles of DNA polymerase i in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic Acids Research. 39(16). 7020-7033.
Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R (2011). CHASM and SNVBox: Toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 27(15). 2147-2148.
Masica DL, Karchin R (2011). Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Research. 71(13). 4550-4561.
Bell D, Berchuck A, Birrer M, Chien J, Cramer DW, Dao F, Dhir R, Disaia P, Gabra H, Glenn P, Godwin AK, Gross J, Hartmann L, Huang M, Huntsman DG, Iacocca M, Imielinski M, Kalloger S, Karlan BY, Levine DA, Mills GB, Morrison C, Mutch D, Olvera N, Orsulic S, Park K, Petrelli N, Rabeno B, Rader JS, Sikic BI, Smith-Mccune K, Sood AK, Bowtell D, Penny R, Testa JR, Chang K, Dinh HH, Drummond JA, Fowler G, Gunaratne P, Hawes AC, Kovar CL, Lewis LR, Morgan MB, Newsham IF, Santibanez J, Reid JG, Trevino LR, Wu Y-Q, Wang M, Muzny DM, Wheeler DA, Gibbs RA, Getz G, Lawrence MS, Cibulskis K, Sivachenko AY, Sougnez C, Voet D, Wilkinson J, Bloom T, Ardlie K, Fennell T, Baldwin J, Gabriel S, Lander ES, Ding L, Fulton RS, Koboldt DC, McLellan MD, Wylie T, Walker J, O'Laughlin M, Dooling DJ, Fulton L, Abbott R, Dees ND, Zhang Q, Kandoth C, Wendl M, Schierding W, Shen D, Harris CC, Schmidt H, Kalicki J, Delehaunty KD, Fronick CC, Demeter R, Cook L, Wallis JW, Lin L, Magrini VJ, Hodges JS, El...Thomson E (2011). Integrated genomic analyses of ovarian carcinoma. Nature. 474(7353). 609-615.
Goes FS, Rongione M, Chen YC, Karchin R, Elhaik E, The Bipolar Genome Study, Potash JB (2011). Exonic DNA sequencing of erbb4 in bipolar disorder. PLoS ONE. 6(5).
Cline MS, Karchin R (2011). Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. 27(4). 441-448.
Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JCH, Boca SM, 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 JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE (2011). The genetic landscape of the childhood cancer medulloblastoma. Science. 331(6016). 435-439.
Zhang X, Reis M, Khoriaty R, Li Y, Ouillette P, Samayoa J, Carter H, Karchin R, Li M, Diaz, Jr L, others (2011). Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia. Leukemia: official journal of the Leukemia Society of America, Leukemia Research Fund, UK. 25(12). 1908.
Cline MS, Karchin R (2011). Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. 27(4). 441-448.
Ochs M, Karchin R, Ressom H, Gentleman R (2011). Identification of aberrant pathway and network activity from high-throughput data-Workshop Introduction. Pac Symp Biocomput. 2011. 364-368.
Tyekucheva S, Marchionni L, Karchin R, Parmigiani G (2011). Integrating diverse genomic data using gene sets. Genome biology. 12(10). 1-14.
Masica D, Karchin R (2011). Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer research. 71(13). 4550-4561.
Goes FS, Rongione M, Chen Y, Karchin R, Elhaik E, Potash JB, others (2011). Exonic DNA sequencing of ERBB4 in bipolar disorder. PloS one. 6(5). e20242.
Lee D, Karchin R, Beer MA (2011). Discriminative prediction of mammalian enhancers from DNA sequence. Genome research. 21(12). 2167-2180.
Guthrie VB, Allen J, Camps M, Karchin R (2011). Network models of TEM $β$-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLoS Comput Biol. 7(9). e1002184.
Allen JM, Simcha DM, Ericson NG, Alexander DL, Marquette JT, Van Biber BP, Troll CJ, Karchin R, Bielas JH, Loeb LA, others (2011). Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic acids research. 39(16). 7020-7033.
Liu Y, Woods NT, Kim D, Sweet M, Monteiro AN, Karchin R (2011). Yeast two-hybrid junk sequences contain selected linear motifs. Nucleic acids research. 39(19). e128-e128.
Liu Y, Woods NT, Kim D, Sweet M, Monteiro ANA, Karchin R (2011). Yeast two-hybrid junk sequences contain selected linear motifs. Nucleic Acids Research. 39(19).
Wong WC, Kim D, Carter H, Diekhans M, Ryan M, Karchin R (2011). CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 27(15). 2147-2148.
Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A (2010). Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Science. 19(11). 2110-2121.
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. Proceedings of the National Academy of Sciences of the United States of America. 107(43). 18545-18550.
Carter H, Samayoa J, Hruban RH, Karchin R (2010). Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer Biology and Therapy. 10(6). 582-587.
Carter H, Samayoa J, Hruban RH, Karchin R (2010). Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer biology & therapy. 10(6). 582-587.
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. Proceedings of the National Academy of Sciences. 107(43). 18545-18550.
Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A (2010). Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Science. 19(11). 2110-2121.
Ochs M, Karchin R, Ressom H, Gentleman R (2010). IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 364-368.
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 Research. 37(18). 5959-5968.
Cutting G, Sosnay P, Karchin R, Zielenski J, Penland C, Castellani C (2009). CFTR2: Defining the clinical and functional consequences of CFTR mutations. Pediatric Pulmonology. 44(SUPPL. 32). 161-162.
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). 6660-6667.
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). 1431-1432.
Mankoo PK, Sukumar S, Karchin R (2009). PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations. Proteins: Structure, Function and Bioinformatics. 75(2). 499-508.
Karchin R (2009). Next generation tools for the annotation of human SNPs. Briefings in Bioinformatics. 10(1). 35-52.
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, Radice P, Grist SA, Monteiro ANA, Billack B (2009). Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 660(1-2). 1-11.
Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A (2009). MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 37(SUPPL. 1).
Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD, Rodarte RS, Vaz DC, Monteiro VA, Manoukian S, others (2009). Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 660(1). 1-11.
Mankoo PK, Sukumar S, Karchin R (2009). PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations. Proteins: Structure, Function, and Bioinformatics. 75(2). 499-508.
Carvalho M, Pino M, Karchin R, Beddor J, Godinho-Netto M, Mesquita R, Rodarte R, Vaz D, Monteiro V, Manoukian S, others (2009). FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS. MUTATION RESEARCH.
Karchin R (2009). Next generation tools for the annotation of human SNPs. Briefings in bioinformatics. 10(1). 35-52.
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). 6660-6667.
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 research. 37(18). 5959-5968.
Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, others (2009). MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 37(suppl 1). D347-D354.
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). 1431-1432.
Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K (2008). Predict-2nd: A tool for generalized protein local structure prediction. Bioinformatics. 24(21). 2453-2459.
Jones S, Zhang X, Parsons DW, Lin JCH, 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 cancers revealed by global genomic analyses. Science. 321(5897). 1801-1806.
Parsons DW, Jones S, Zhang X, Lin JCH, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, 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. 321(5897). 1807-1812.
Karchin R, Agarwal M, Sali A, Couch F, Beattie MS (2008). Classifying variants of undetermined significance in BRCA2 with protein likelihood ratios. Cancer Informatics. 6. 203-216.
Karchin R, Agarwal M, Sali A, Couch F, Beattie MS (2008). Classifying variants of undetermined significance in BRCA2 with protein likelihood ratios. Cancer informatics. 6. 203.
Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K (2008). PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics. 24(21). 2453-2459.
Kelly L, Karchin R, Sali A (2007). Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium on Biocomputing 2007, PSB 2007. 51-63.
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, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JKV, Sukumar S, Polyak K, Ben HP, Pethiyagoda CL, Pant PVK, 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. 318(5853). 1108-1113.
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, Goldgar D, Couch FJ, Radice P, Monteiro ANA (2007). Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Research. 67(4). 1494-1501.
Karchin R, Monteiro ANA, Tavtigian SV, Carvalho MA, Sali A (2007). Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Computational Biology. 3(2). 0268-0281.
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 MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF, Urmenyi TP, Rondinelli E, Silva R, Gayol L, others (2007). Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer research. 67(4). 1494-1501.
Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A (2007). Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol. 3(2). e26.
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 (2006). MODBASE: a database of annotated comparative protein structure models and associated resources.. Nucleic acids research. 34(Database issue).
Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, others (2006). MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic acids research. 34(suppl 1). D291-D295.
Karchin R, Kelly L, Sali A (2005). Improving functional annotation of no n-s yno no mo us s nps with information theory. Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005. 397-408.
Karplus K, Karchin R, Shackelford G, Hughey R (2005). Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics. 21(22). 4107-4115.
Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A (2005). LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 21(12). 2814-2820.
Madhusudhan M, Marti-Renom MA, Eswar N, John B, Pieper U, Karchin R, Shen M, Sali A (2005). Comparative protein structure modeling. The Proteomics Protocols Handbook. 831-860.
Karplus K, Karchin R, Shackelford G, Hughey R (2005). Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics. 21(22). 4107-4115.
Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A (2005). LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 21(12). 2814-2820.
Karchin R, Cline M, Karplus K (2004). Evaluation of Local Structure Alphabets Based on Residue Burial. Proteins: Structure, Function and Genetics. 55(3). 508-518.
Karchin R, Cline M, Karplus K (2004). Evaluation of local structure alphabets based on residue burial. Proteins: Structure, Function, and Bioinformatics. 55(3). 508-518.
Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R (2003). Combining Local-Structure, Fold-Recognition, and New Fold Methods for Protein Structure Prediction. Proteins: Structure, Function and Genetics. 53(SUPPL. 6). 491-496.
Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K (2003). Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry. Proteins: Structure, Function and Genetics. 51(4). 504-514.
Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K (2003). Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins: Structure, Function, and Bioinformatics. 51(4). 504-514.
Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R (2003). Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins: Structure, Function, and Bioinformatics. 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.
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: Structure, Function and Genetics. 45(SUPPL. 5). 86-91.
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: Structure, Function, and Bioinformatics. 45(S5). 86-91.
Hughey R, Karchin R (1998). Weighting hidden Markov models for maximum discrimination.. Bioinformatics. 14(9). 772-782.
Karchin R, Hughey R (1998). Weighting hidden Markov models for maximum discrimination. Bioinformatics. 14(9). 772-782.
KELLY L, FUKUSHIMA H, Karchin R, GOW JM, CHINN LW, PIEPER U, SEGAL MR, KROETZ DL, SALI A Response to ''Predictable difficulty or difficulty to predict''.

Book Chapters

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. Cystic Fibrosis. Humana Press. 355-372.

Conference Proceedings

Masica D, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch W, Karchin R, Chung CH (2014). Evaluation of computational tools to determine prognostic significance of TP53 mutation in head and neck squamous cell carcinoma (HNSCC). JOURNAL OF CLINICAL ONCOLOGY. (15).
Sosnay P, Siklosi KR, Michelle LH, Kaniecki K, Corey M, Dorfman R, Karchin R, Rommens JM, Penland C, Castellani C, others (2012). DEFINING CF BASED ON GENOTYPE: A WORLDWIDE PERSPECTIVE. PEDIATRIC PULMONOLOGY. 211-211.
Masica D, Sosnay P, Cutting G, Karchin R (2011). CYSTIC FIBROSIS-CAUSING MISSENSE MUTATIONS IN THE CFTR GENE PREDICTED USING PHENOTYPE-OPTIMIZED SEQUENCE ENSEMBLES. PEDIATRIC PULMONOLOGY. 224-224.
Cutting G, Sosnay P, Karchin R, Zielenski J, Penland C, Castellani C (2009). CFTR2: DEFINING THE CLINICAL AND FUNCTIONAL CONSEQUENCES OF CFTR MUTATIONS. PEDIATRIC PULMONOLOGY. 161-162.
Karchin R, Beattie M, McLennen J, Toland A, Sali A (2005). Variants of undetermined significance in BRCA2: protein modeling, loss of heterozygosity, ethnicity, and clinical correlations. BREAST CANCER RESEARCH AND TREATMENT. S22-S23.
Karchin R, Kelly L, Sali A (2005). Improving functional annotation of non-synonomous SNPs with information theory.. Pacific Symposium on Biocomputing.

Patents

"Genetic alterations in isocitrate dehydrogenase and other genes in malignant glioma", 2016.
"Genetic alterations in isocitrate dehydrogenase and other genes in malignant glioma", 2014.

The G.W.C. Whiting School of Engineering