PUBLICATIONS

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

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.

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

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

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]

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. Dynamics of tumor and immune responses during immune checkpoint blockade in non-small cell lung cancer. Cancer Research. Dec 12. pii: canres.1127.2018. doi: 10.1158/0008-5472.CAN-18-1127. [Epub ahead of print]

Kuboki Y, Fischer CG, Beleva Guthrie V, Huang W, Yu J, Chianchiano P, Hosoda W, Zhang H, Zheng L, Shao X, Thompson ED, Waters K, Poling J, He J, Weiss MJ, Wolfgang CL, Goggins MG, Hruban RH, Roberts NJ, Karchin R, Wood LD. (2018). Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions. Journal of Pathology. Nov. 14 doi: 10.1002/path.5194 [Epub ahead of print]

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

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.

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.

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.

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

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

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