Preprints
Ng JK, Chen Y, Akinwe TM, Heins HB, Mehinovic E, Chang Y, Payne ZL, Manuel JG, Karchin R, Turner TN. Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer. Feb 4, 2024. medRxiv
2024
Rhinehart DP, Lai J, Sanin DE, Vakkala V, Mendes A, Bailey C, Antonarakis ES, Paller CJ, Wu X, Lotan TL, Karchin R, Sena LA. Intratumoral heterogeneity drives acquired therapy resistance in a patient with metastatic prostate cancer. NPJ Precis Oncol. 2024 Dec 2;8(1):275. doi: 10.1038/s41698-024-00773-w. PMID: 39623053.
Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau EAW, Greenblatt MS, Harrison SM, Tavtigian SV, Radivojac P, Brenner SE, O’Donnell-Luria A; ClinGen Sequence Variant Interpretation Working Group. Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations. Genet Med. 2024 Jul 25;26(11):101213. doi: 10.1016/j.gim.2024.101213. Epub ahead of print. PMID: 39030733.
Fatteh M, Wehr J, Karaindrou K, Xian RR, Gocke C, Lin MT, Petry D, Visvanathan K, Couzi R, Santa Maria C, Stearns V, Tao JJ, Anagnostou V, Canzoniero JV; and the Johns Hopkins Molecular Tumor Board; Johns Hopkins Molecular Tumor Board. Poly (ADP-ribose) Polymerase Inhibitor Resistance Driven by Emergence of Polyclonal Mutations With Convergent Evolution: A Molecular Tumor Board Discussion. JCO Precis Oncol. 2024 Oct;8:e2400254. doi: 10.1200/PO.24.00254. Epub 2024 Oct 11. PMID: 39393037; PMCID: PMC11485209.
Palmer T, Kessler MD, Shao XM, Balan A, Yarchoan M, Zaidi N, Lopez-Vidal TY, Saeed AM, Gore J, Azad NS, Jaffee EM, Favorov AV, Anagnostou V, Karchin R, Gaykalova DA, Fertig EJ, Danilova L. SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors. Cancer Res Commun. 2024 Oct 29. doi: 10.1158/2767-9764.CRC-23-0309. Epub ahead of print. PMID: 39470352.
Karchin R, Radivojac P, O’Donnell-Luria A, Greenblatt MS, Tolstorukov MY, Sonkin D. Improving transparency of computational tools for variant effect prediction. Nat Genet. 2024 Jul 2. doi: 10.1038/s41588-024-01821-8. Epub ahead of print. PMID: 38956207.
Lai J, Yang Y, Liu Y, Scharpf RB, Karchin R. Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. Bioinformatics Advances, 2024 June. doi: 10.1093/bioadv/vbae094. PMID: 38948008; PMCID: PMC11213631.
Braxton AM, Kiemen AL, Grahn MP, Forjaz A, Parksong J, Mahesh Babu J, Lai J, Zheng L, Niknafs N, Jiang L, Cheng H, Song Q, Reichel R, Graham S, Damanakis AI, Fischer CG, Mou S, Metz C, Granger J, Liu XD, Bachmann N, Zhu Y, Liu Y, Almagro-Pérez C, Jiang AC, Yoo J, Kim B, Du S, Foster E, Hsu JY, Rivera PA, Chu LC, Liu F, Fishman EK, Yuille A, Roberts NJ, Thompson ED, Scharpf RB, Cornish TC, Jiao Y, Karchin R, Hruban RH, Wu PH, Wirtz D, Wood LD. 3D genomic mapping reveals multifocality of human pancreatic precancers. Nature. 2024 May 1. doi: 10.1038/s41586-024-07359-3. Epub ahead of print. PMID: 38693266.
The Critical Assessment of Genome Interpretation Consortium. CAGI, the critical assessment of genome interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology 2024 25(1):53. PMID: 38389099 PMCID: PMC10882881
2023
Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB; ClinGen Sequence Variant Interpretation Working Group. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet. 2023 Jul 6;110(7):1046-1067. doi: 10.1016/j.ajhg.2023.06.002. Epub 2023 Jun 22. PMID: 37352859; PMCID: PMC10357475.
Ghanem P, Fatteh M, Kamson DO, Balan A, Chang M, Tao J, Blakeley J; Johns Hopkins Molecular Tumor Board Investigators; Canzoniero J, Grossman SA, Marrone K, Schreck KC, Anagnostou V. Druggable genomic landscapes of high-grade gliomas. Front Med (Lausanne). 2023 Dec 8;10:1254955. doi: 10.3389/fmed.2023.1254955. PMID: 38143440; PMCID: PMC10749203.
Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, El Noafal M, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH. (2023) Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front. Immunol. 2023 Sep 6:14:1188831
Albert BA, Yang Y, Shao XM, Singh D, Smith KN, Anagnostou V, Karchin R Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity (2023) Nat Mach Intell. https://doi.org/10.1038/s42256-023-00694-6
Niknafs N, Balan A, Cherry C, Hummelink K, Monkhorst K, Shao XM, Belcaid Z, Marrone KA, Murray J, Smith KN, Levy B, Feliciano J, Hann CL, Lam V, Pardoll DM, Karchin R, Seiwert TY, Brahmer JR, Forde PM, Velculescu VE, Anagnostou V. (2023) Persistent mutation burden drives sustained anti-tumor immune responses. Nat Med. Feb;29(2):440-449
Gong X, Karchin R (2023) Clustering by antigen-presenting genes reveals immune landscapes and predicts response to checkpoint immunotherapy Sci Rep. Jan 18;13(1):950
2022
Rodriguez CP, Kang H, Geiger JL, Burtness B, Chung CH, Pickering CR, Fakhry C, Le QT, Yom SS, Galloway TJ, Golemis E, Li A, Shoop J, Wong S, Mehra R, Skinner H, Saba NF, Flores ER, Myers JN, Ford JM, Karchin R, Ferris RL, Kunos C, Lynn JM, Malik S. Clinical Trial Development in TP53-Mutated Locally Advanced and Recurrent and/or Metastatic Head and Neck Squamous Cell Carcinoma. J Natl Cancer Inst. 2022 Dec 8;114(12):1619-1627. doi: 10.1093/jnci/djac163. PMID: 36053203; PMCID: PMC9745425.
Standley M, Blay V, Beleva Guthrie B, Kim J, Lyman A, Moya A, Karchin R, Camps M. (2022) Experimental and in silico analysis of TEM beta lactamase adaptive evolution”. ACS Infectious Diseases 8(12):2451-63
Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O’Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE; ClinGen Sequence Variant Interpretation Working Group. Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. doi: 10.1016/j.ajhg.2022.10.013. Epub 2022 Nov 21. PMID: 36413997; PMCID: PMC9748256.
Gong X, Karchin R. Pan-Cancer HLA Gene-Mediated Tumor Immunogenicity and Immune Evasion. Mol Cancer Res. 2022 Aug 5;20(8):1272-1283. doi: 10.1158/1541-7786.MCR-21-0886. PMID: 35533264; PMCID: PMC9357147.
Scott SC, Shao XM, Niknafs N, Balan A, Pereira G, Marrone KA, Lam VK, Murray JC, Feliciano JL, Levy BP, Ettinger DS, Hann CL, Brahmer JR, Forde PM, Karchin R, Naidoo J, Anagnostou V. (2022) Sex-specific differences in immunogenic features of response to immune checkpoint blockade Front Oncol. 2022 Aug;12:945798.
Zheng L, Niknafs N, Wood LD, Karchin R, Scharpf RB. Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. Bioinformatics. 2022 Aug 2;38(15):3677-3683. doi: 10.1093/bioinformatics/btac367. PMID: 35642899; PMCID: PMC9344857.
Shao XM, Huang J, Niknafs N, Balan A, Cherry C, White J, Velculescu VE, Anagnostou V, Karchin R. HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade. Ann Oncol. 2022 Jul;33(7):728-738. doi: 10.1016/j.annonc.2022.03.013. Epub 2022 Mar 23. Erratum in: Ann Oncol. 2023 Jul;34(7):634. PMID: 35339648; PMCID: PMC10621650.
2021
Forde PM, Anagnostou V, Sun Z, Dahlberg SE, Kindler HL, Niknafs N, Purcell T, Santana-Davila R, Dudek AZ, Borghaei H, Lanis M, Belcaid Z, Smith KN, Balan A, White JR, Cherry C, Ashok Sivakumar IK, Shao XM, Chan HY, Singh D, Thapa S, Illei PB, Pardoll DM, Karchin R, Velculescu VE, Brahmer JR, Ramalingam SS.(2021) Durvalumab with platimum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial Nat Med. Nov;27(11):1910-1920
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. (2021) Multiregion whole-exome sequencing of intraductral papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions. Gut. May;70(5):928-939
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. (2021) The genetic evolution of treatment-resistant cutaneous, acral and uveal melanomas Clin Cancer Res. Mar 1:27(5):1516-1525
2020
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
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.
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]
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.
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
Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunol Res. 2020 Mar;8(3):396-408. doi: 10.1158/2326-6066.CIR-19-0464. Epub 2019 Dec 23. PMID: 31871119; PMCID: PMC7056596.
2019
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.
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
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.
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
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. 2019 Jul 24;9(1):9-23.e8. doi: 10.1016/j.cels.2019.05.005. Epub 2019 Jun 12. PMID: 31202631; PMCID: PMC6857794.
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:
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. (2019). 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]
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, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network; Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Erratum in: Cell. 2018 Aug 9;174(4):1034-1035. doi: 10.1016/j.cell.2018.07.034. PMID: 29625053; PMCID: PMC6029450.
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]
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]
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.
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. IPMNs with co-occurring invasive cancers: neighbours but not always relatives. Gut. 2018 Sep;67(9):1652-1662. doi: 10.1136/gutjnl-2017-315062. Epub 2018 Mar 2. PMID: 29500184; PMCID: PMC10489026.
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]
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
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.
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
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. High grade serous ovarian carcinomas originate in the fallopian tube. Nat Commun. 2017 Oct 23;8(1):1093. doi: 10.1038/s41467-017-00962-1. PMID: 29061967; PMCID: PMC5653668.
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]
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.
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.
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. Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer. Cancer Discov. 2017 Mar;7(3):264-276. doi: 10.1158/2159-8290.CD-16-0828. Epub 2016 Dec 28. PMID: 28031159; PMCID: PMC5733805.
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.
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
Tokheim CJ, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R. Evaluating the evaluation of cancer driver genes. Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):14330-14335. doi: 10.1073/pnas.1616440113. Epub 2016 Nov 22. PMID: 27911828; PMCID: PMC5167163.
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
Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure. Cancer Res. 2016 Jul 1;76(13):3719-31. doi: 10.1158/0008-5472.CAN-15-3190. Epub 2016 Apr 28. PMID: 27197156; PMCID: PMC4930736.
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
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.
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, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Ling S, Fakhry C, Papadopolous N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N (2016) Whole-genome sequencing of salivary gland adenoid cystic carcinoma. Cancer Prevention Research. 2016 Apr;9(4):265-74. doi: 10.1158/1940-6207.CAPR-15-0316.
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
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
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
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 Comput Biol. 2015 Oct 5;11(10):e1004416. doi: 10.1371/journal.pcbi.1004416. PMID: 26436540; PMCID: PMC4593588.
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. Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Ann Oncol. 2015 Jun;26(6):1216-1223. doi: 10.1093/annonc/mdv109. Epub 2015 Feb 23. PMID: 25712460; PMCID: PMC4516044.
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):455-7
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
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
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
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
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
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
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. Hum Genet. 2013 Nov;132(11):1235-43. doi: 10.1007/s00439-013-1325-0. Epub 2013 Jun 23. PMID: 23793516; PMCID: PMC3797853.
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
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
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
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.
Masica DL and Karchin R (2013) Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Research. 73(6):1699-708
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
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
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
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
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
2011
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
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
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
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
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
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
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
Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. Erratum in: Nature. 2012 Oct 11;490(7419):298. PMID: 21720365; PMCID: PMC3163504.
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
Cline MS and Karchin R (2011) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. Feb 15;27(4):441-8. Dec 15
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
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
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
2010
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
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.
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
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
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
Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 2009 Jun 1;25(11):1431-2. doi: 10.1093/bioinformatics/btp242. Epub 2009 Apr 15. PMID: 19369493; PMCID: PMC6276889.
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.
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.
Karchin R. (2009) Next generation tools for the annotation of human SNPs. Briefing in Bioinformatics. 10(1):35-52
2008
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.
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
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
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
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 AN, Tavtigian SV, Carvalho MA, Sali A. Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol. 2007 Feb 16;3(2):e26. doi: 10.1371/journal.pcbi.0030026. Epub 2006 Dec 28. PMID: 17305420; PMCID: PMC1797820.
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
Kelly L, Karchin R, & Sali A. (2007) Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium on Biocomputing 12:51-63
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
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