Publications
2023
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
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
Zheng L, Niknafs N, Wood LD, Karchin R, Scharpf RB (2022) Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. Bioinformatics. 38(15):3677-83
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 (2022) Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria. Am J Hum Genet Dec 1,109(12):2163-2177.
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.
Shao XM, Huang J, Niknafs N, Balan A, Cherry C, White J, Velculescu VE, Anagnostou V, Karchin R. (2022) HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade Ann Oncol. 2022 Jul;33(7):728-738.
Gong X, Karchin R. (2022) Pan-cancer HLA Gene-mediated Tumor Immunogenicity and Immune Evasion Mol Cancer Res. 2022 May 9:molcanres.MCR-21-0886-A.2021.doi: 10.1158/1541-7786.MCR-21-0886.
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.
Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R. (2020) Integrated informatics analysis of cancer-related variants. JCO CCI Mar;4:310-317. doi: 10.1200/CCI.19.00132.
Brnich SE, Abou Tayoun AN, Couch FJ, Cutting GR, Greenblatt MS, Heinen CD, Kanavy DM, Luo X, McNulty SM, Starita LM, Tavtigian SV, Wright MW, Harrison SM, Biesecker LG, Berg JS; Clinical Genome Resource Sequence Variant Interpretation Working Group. Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Med. 2019 Dec 31;12(1):3. doi: 10.1186/s13073-019-0690-2.
Douville C, Cohen JD, Ptak J, Popoli M, Schaefer J, Silliman N, Dobbyn L, Schoen RE, Tie J, Gibbs P, Goggins M, Wolfgang CL, Wang TL, Shih IM, Karchin R, Lennon AM, Hruban RH, Tomasetti C, Bettegowda C, Kinzler KW, Papadopoulos N, Vogelstein B. (2020)
Assessing aneuploidy with repetitive element sequencing Proc Natl Acad Sci USA Feb 19. pii: 201910041. doi: 10.1073/pnas.1910041117. [Epub ahead of print]
Anagnostou V, Niknafs N, Marrone K, Bruhm DC, White JR, Naidoo J, Hummelink K, Monkhorst K, Lalezari F, Lanis M, Rosner S, Reuss JE, Smith KN, Adleff V, Rodgers K,Belcaid Z, Rhymee L, Levy B, Feliciano J, Hann CL, Ettinger DS, Georgiades C, Verde F, Illei P, Li QK, Baras AS, Gabrielson E, Brock MB, Karchin R, Pardoll DM, Baylin SB, Brahmer JR, Scharpf RB, Forde PM, Velculescu VE. (2020)
Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer Nature Cancer 1 (1), 99-111
2019
Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L,
Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou
V, Pagel KA, Karchin R.
High-throughput prediction of MHC Class I and Class II neoantigens
with MHCnuggets Cancer Imm. Res. doi: 10.1158/2326-6066.CIR-19-0464
Niknafs N, Zhong Y, Moral JAG, Zhang L, Shao X, Lo A, Makohon-Moore A,
Iacobuzio-Donahue C, Karchin R. Characterization of Genetic
Subclonal Evolution in Pancreatic Cancer Mouse Models. Nat
Comm. 2019 Nov;10(1):5435
Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P,
Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ,
Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P,
Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A,
Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK,
Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang
HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang
X. Voices in methods development.
Nat Methods 2019 Oct; 16(10):945-951
Springer S, Masica DL, Dal Molin M, Douville C, Thoburn CJ, Afsari B,
Li L, Cohen JD, Thompson E, Allen PJ, Klimstra DS, Schattner MA,
Schmidt CM, Yip-Schneider M, Simpson RE, Fernandez-Del Castillo C,
Mino-Kenudson M, Brugge W, Brand RE, Singhi AD, Scarpa A, Lawlor R,
Salvia R, Zamboni G, Hong SM, Hwang DW, Jang JY, Kwon W, Swan N,
Geoghegan J, Falconi M, Crippa S, Doglioni C, Paulino J, Schulick RD,
Edil BH, Park W, Yachida S, Hijioka S, van Hooft J, He J, Weiss MJ,
Burkhart R, Makary M, Canto MI, Goggins MG, Ptak J, Dobbyn L, Schaefer
J, Sillman N, Popoli M, Klein AP, Tomasetti C, Karchin R, Papadopoulos
N, Kinzler KW, Vogelstein B, Wolfgang CL, Hruban RH, Lennon
AM.I. A multimodality test to guide the management of patients with a pancreatic cyst. Sci Transl Med. 2019 Jul 17;11(501). pii: eaav4772. doi:
Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G,
De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J,
Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL,
Masica D, Mooney SD, Olatubosun A, Pal LR, Radivojac P, Rousseau F,
Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M,
Väliaho J, Repo S, Moult J, Brenner SE, Friedberg
I. Assessing Computational Predictions of the
Phenotypic Effect of Cystathionine-beta-Synthase Variants Hum Mutat. 2019 Jul 13. doi: 10.1002/humu.23868. [Epub ahead of
print]
Tokheim C, Karchin R. CHASMplus Reveals the Scope of Somatic Missense
Mutations Driving Human Cancers. Cell Syst. May 31. pii:
S2405-4712(19)30154-1. doi: 10.1016/j.cels.2019.05.005.
Fischer CG, Guthrie VB, Braxton AM, Zheng L, Wang P, Song Q,
Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S,
Molin MD, Masica D, Scharpf RB, Thompson ED, He J, Wolfgang CL,
Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood
LD. Intraductal Papillary Mucinous Neoplasms Arise from Multiple
Independent Clones, Each With Distinct Mutations. Gastroenterology. Jun 5. pii:
S0016-5085(19)40987-6. doi: 10.1053/j.gastro.2019.06.001.
2018
Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J,
Marrone KA, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A,
Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy
B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E,
Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R,
Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE.
Dynamics of tumor and immune responses during
immune checkpoint blockade in non-small cell lung cancer.
Cancer Research. Dec 12. pii: canres.1127.2018. doi:
10.1158/0008-5472.CAN-18-1127. [Epub ahead of print]
Kuboki Y, Fischer CG, Beleva Guthrie V, Huang W, Yu J,
Chianchiano P, Hosoda W, Zhang H, Zheng L, Shao X, Thompson ED,
Waters K, Poling J, He J, Weiss MJ, Wolfgang CL, Goggins MG,
Hruban RH, Roberts NJ, Karchin R, Wood LD. (2018).
Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions.
Journal of Pathology. Nov. 14 doi: 10.1002/path.5194 [Epub ahead of print]
Reiter JG, Makohon-Moore AP, Gerold JM, Heyde A, Attiyeh MA, Kohutek
ZA, Tokheim CJ, Brown A, DeBlasio RM, Niyazov J, Zucker A, Karchin R,
Kinzler KW, Iacobuzio-Donahue CA, Vogelstein B, Nowak MA. (2018).
Minimal functional driver gene heterogeneity among untreated metastases.
Science. Sep 7;361(6406):1033-1037.
Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA Jr, Jones S, Sausen M, Velculescu VE, Angiuoli SV. (2018).
A machine learning approach for somatic mutation discovery.
Sci Transl Med. Sep 5;10(457). pii: eaar7939. doi: 10.1126/scitranslmed.aar7939.
Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin
R, Jagtap PD, Griffin TJ. (2018).
Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.
J. Proteome Res. Sep 5. doi: 10.1021/acs.jproteome.8b00404. [Epub ahead of print]
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D,
Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng KS,
Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni
L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang
W, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A,
Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen E, Liang H,
The MC3 Working Group, The Cancer Genome Atlas Research Network,
Lawrence M, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz
G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L (2018).
Comprehensive Discovery and Characterization of Driver Genes and Mutations in Cancer.
Cell. 173(2):371-385.e18.
Wang Y, Li L, Douville C, Cohen JD, Yen TT, Kinde I, Sundfelt K,
Kjær SK, Hruban RH, Shih IM, Wang TL, Kurman RJ, Springer S,
Ptak J, Popoli M, Schaefer J, Silliman N, Dobbyn L, Tanner EJ,
Angarita A, Lycke M, Jochumsen K, Afsari B, Danilova L, Levine
DA, Jardon K, Zeng X, Arseneau J, Fu L, Diaz LA Jr, Karchin R,
Tomasetti C, Kinzler KW, Vogelstein B, Fader AN, Gilbert L,
Papadopoulos N. (2018).
Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers.
Sci Transl Med. Mar 21;10(433)
Springer SU, Chen CH, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang CY, Shun CT, Turesky RJ, Yun BH, Rosenquist TA, Pu YS, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ. (2018).
Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy.
Elife. Mar 20;7. pii: e32143.
Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z,
Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk
T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z,
Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y,
Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni
N, Liang H, Mills GB. (2018).
Systematic Functional Annotation of Somatic Mutations in Cancer.
Cancer Cell. 33(3):450-462.e10
Guthrie VB, Masica DL, Fraser A, Federico J, Fan Y, Camps M, Karchin R
(2018). Network Analysis of Protein Adaptation: modeling the functional impact of multiple
mutations. Mol. Biol. Evo. msy036, https://doi.org/10.1093/molbev/msy036 [Epub ahead of print]
Felsenstein M, Noë M, Masica DL, Hosoda W, Chianchiano P, Fischer
CG, Lionheart G, Brosens LAA, Pea A, Yu J, Gemenetzis G, Groot VP,
Makary MA, He J, Weiss MJ, Cameron JL, Wolfgang CL, Hruban RH,
Roberts NJ, Karchin R, Goggins MG, Wood LD. (2018)
IPMNs with co-occurring invasive cancers: neighbours but not always
relatives. Gut Mar 2. pii: gutjnl-2017-315062. doi: 10.1136/gutjnl-2017-315062. [Epub ahead of print]
Douville C, Springer S, Kinde I, Cohen JD, Hruban RH, Lennon AM,
Papadopolous N, Kinzler KW, Vogelstein B, Karchin R (2018)
Detection of aneuploidy in patients with
cancer through amplification of long interspersed nucleotide
elements (LINEs)
Proc Natl Acad Sci USA 115(8):1871-1876
Guidugli L, Shimelis H, Masica DL, Pankratz VS, Lipton GB, Singh N, Hu
C, Monteiro ANA, Lindor NM, Goldgar DE, Karchin R, Iversen ES, Couch
FJ (2018)
Assessment of the clinical relevance of BRCA2
missense variants by functional and computational approaches.
Am. Journal of Human Genetics. S0002-9297(17)30502-5
2017
Oetting WS, Béroud C, Brenner SE, Greenblatt MS, Karchin R,
Mooney SD. (2017)
Methods and tools for assessing the impact of genetic variations: The 2017 annual scientific meeting of the Human Genome Variation Society
Human Mutation. 39(3):460-463.
Masica DL, Douville C, Tokheim C, Bhattacharya R, Kim R, Moad K, Ryan
MC, Karchin R (2017) CRAVAT 4: Cancer-Related Analysis of Variants Toolkit.
Cancer Research. Nov 1;77(21):e35-38.
Labidi-Galy SI, Papp E, Hallberg D, Niknafs N, Adleff V, Noe M,
Bhattacharya R, Novak M, Jones S, Phallen J, Hruban CA, Hirsch MS, Lin
DI, Schwartz L, Maire CL, Tille JC, Bowden M, Ayhan A, Wood LD,
Scharpf RB, Kurman R, Wang TL, Shih IM, Karchin R, Drapkin R,
Velculescu VE. (2017) High grade serous
ovarian carcinomas originate in the fallopian tube.
Nat. Commun. Oct 23;8(1):1093.
Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.
(2017) Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.
Genome Med. 8;9(1):113
Monson ET, Pirooznia M, Parla J, Kramer M, Goes FS, Gaine ME, Gaynor
SC, de Klerk K, Jancic D, Karchin R, McCombie WR, Zandi PP, Potash JB,
Willour VL (2017)
Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort.
Mol Neuropsychiatry. Jul;3(1):1-11.
Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N,
Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R,
Grace Yeo HT, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M,
Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C,
Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins R, Repo S, Church G,
Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD (2017)
Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.
Hum Mutat. May 23. doi: 10.1002/humu.23265. [Epub ahead of print]
Fu J, Sen R, Masica DL, Karchin R, Pardoll D, Walter V, Hayes DN,
Chung CH, Kim YJ (2017)
Autologous reconstitution of human cancer and immune system in vivo.
Oncotarget. Jan 10;8(2):2053-2068.
Oetting WS, Béroud C, Brenner SE, Greenblatt M, Karchin R, Mooney SD,
Sunyaev S. (2017) Non-Coding Variation: The
2016 Annual Scientific Meeting of the Human Genome Variation
Society.
Hum Mutat. 38(4):460-463.
Masica DL, Dal Molin M, Wolfgang CL, Tomita T, Ostovaneh MR, Blackford A, Moran RA, Law JK, Barkley T, Goggins M, Irene Canto M, Pittman M, Eshleman JR, Ali SZ, Fishman EK, Kamel IR, Raman SP, Zaheer A, Ahuja N, Makary MA, Weiss MJ, Hirose K, Cameron JL, Rezaee N, He J, Joon Ahn Y, Wu W, Wang Y, Springer S, Diaz LL Jr, Papadopoulos N, Hruban RH, Kinzler KW, Vogelstein B, Karchin R, Marie Lennon A (2017)
A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts. J Am Med Inform Assoc Jan;24(1):145-152.
2016
Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman WH, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf R, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE. (2016)
Evolution of Neoantigen Landscape During
Immune Checkpoint Blockade in Non-Small Cell Lung
Cancer. Cancer Discov. 7(3):264-276
Tokheim C, Papdopoulis N, Kinzler KW, Vogelstein B, Karchin R (2016)
Evaluating the evaluation of cancer driver
genes.
Proc Natl Acad Sci U S A. Dec 13;113(50):14330-14335.
Karchin R, Nussinov R (2016)
Genome landscapes of disease: strategies to
predict the phenotypic consequences of human germline and somatic
variation. PLoS Comput Biol. Aug 18;12(8):e1005043
Mascia DL, Karchin R (2016)
Towards increasing the clinical relevance of in silico methods to
predict pathogenic missense variants. PLoS Computational
Biology. May 12;12(5):e1004725.
Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M,
Masica DL, Karchin R (2016)
Exome-scale discovery of hotspot mutation
regions in human cancer using 3D protein
structure Cancer Research. 1;76(13):3719-31
Goes FS, Pirooznia M, Parla JS, Kramer M, Ghiban E, Mavruk S, Chen YC, Monson ET, Willour VL, Karchin R, Flickinger M, Locke AE, Levy SE, Scott LJ, Boehnke M, Stahl E, Moran JL, Hultman CM, Landén M, Purcell SM, Sklar P, Zandi PP, McCombie WR, Potash JB. (2016)
Exome sequencing of bipolar disorder
JAMA Psychiatry. Jun 1:73(6):590-7
Oetting WS, Brenner SE, Brookes AJ, Greenblatt MS, Hart RK, Karchin
R, Sunyaev SR, Taschner PE
(2016) Pathogenicity Interpretation in the
Age of Precision Medicine: The 2015 Annual Scientific Meeting of the
Human Genome Variation Society. Human Mutation. Jan 21. doi:
10.1002/humu.22958. [Epub ahead of print]
Rettig EM, Talbot Jr CC, Sausen M, Jones S, Bishop JA, Wood LD,
Tokheim C, Niknafs N, Karchin R, Papadopoulos N, Kinzler KW,
Vogelstein B, Ha PK, Agrawal N (2016)
Whole-genome sequencing of salivary gland
adenoid cystic carcinoma. Cancer Prevention Research.
Feb 9. pii:canprevres.0316.2015. [Epub ahead of print].
Roberts NJ, Norris A, Petersen GM, Bondy ML, Brand R, Gallinger S,
Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stofel E, Syngal S,
Zogopoulos G, Ali SZ, Axilbund J, Chaffe KG, Chen YC, Cote ML, Childs
EJ, Douville C, Goes FS, Herman JM, Iacobuzio-Donahue C, Kramer M,
Makohon-Moore A, McCombie WR, McMahon K, Niknafs N, Parla J,
Pirooznia M, Potash JB, Rhim AD, Smith AL, Wang Y, Wolofgang CL, Wood
LD, Zandi PP, Goggins M, Karchin R, Eshleman J, Papadopoulos N,
Kinzler KW, Vogelstein B, Hruban RH, Klein AP (2016) Whole genome sequencing of patients
with familial pancreatic cancer Cancer Discovery. Dec 9. pii:
CD-15-0402. [Epub ahead of print].
Douville C, Masica DL, Stenson PD, Cooper DN, Gygax D, Kim R,
Ryan M, Karchin R (2016)
Assessing the pathogenicity of insertion and
deletion variants with the Variant Effect Scoring Tool
(VEST-indel) Human Mutation. 37(1):28-35
2015
Niknafs N, Guthrie VB, Naiman DQ, Karchin R
(2015) SubClonal Hierarchy Inference from
Somatic Mutations: automatic reconstruction of cancer evolutionary
trees from multi-region next generation sequencing. PLoS
Computational Biology. 11(10):e1004416
Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Sausen M,
Phallen J, Tokheim C, Niknafs N, Nesselbush M, Lytle K, Cottino F,
Migliardi G, Zanella ER, Ribero D, Russolillo N, Mellano A, Muratore
A, Paraluppi G, Salizzoni M, Marsoni S, Kragh M, Lantto J,
Cassingena A, Li QK, Karchin R, Scharpf R, Sartore-Bianchi A, Siena
S, Diaz LA, Trusolino L, Velculescu VE (2015)
The Genomic Landscape of Response to EGFR
Blockade in Colorectal Cancer. Nature. 526(7572):263-7
Springer S, Wang Y, Dal Molin M, Masica DL, Jiao Y, Kinde I, Blackford A, Raman SP,
Wolfgang CL, Tomita T, Niknafs N, Douville C, Ptak J, Dobbyn L, Allen
PJ, Klimstra D, Schattner MA, Schmidt CM, Yip-Schneider M, Cummings
OW, Brand RE, Zeh JH, Singhi AD, Scarpa A, Salvia R, Malleo G,
Zamboni G, Falconi M, Jang JY, Kim SW, Kwon W, Hong SM, Song KB,
Kim SC, Swan N, Murphy J, Geoghegan J, Brugge W, Fernandez-Del
Castillo C, Mino-Kenudson M, Schulick R, Edil BH, Adsay V, Paulino
J, van Hoof J, Yachida S, Nara S, Hiraoka N, Yamao K, Hijoka S, van
der Merwe S, Goggins M, Canto MI, AHuga N, Hirose K, Makary M,
Weiss MJ, Cameron J, Pittman M, Eshleman JR, Diaz Jr LA, Papadopoulos N,
Kinzler KW, Karchin R, Hruban R, Vogelstein B, Lennon AM (2015)
A Combination of Molecular Markers and
Clinical Features Improve the Classification of Pancreatic
Cysts. Gasteroenterology. 149(6):1501-10
Turner TN, Douville C, Kim D, Stenson PD, Cooper DN, Chakravarti
A, Karchin R (2015) Proteins linked to
autosomal dominant and autosomal recessive disorders harbor
characteristic rare missense mutation distribution
patterns Hum Mol Genet. 24(21):5995-6002
Chung CH,Guthrie VB, Masica D, Tokheim C, Kang H, Richmon J,
Agrawa N, Gourin C, Quon H, Zuo Z, Seiwert T, Ali SM, Miller VA,
Frampton GM, Chalmers ZR, Karchin R, Bishop J (2015) Genetic alterations in head and neck squamous
cell carcinoma determined by a cancer gene-targeted
sequencing. Ann Oncol. 26(6):1216-23
Karchin R, Cline MS.
(2015) Human genetics special issue on
computational molecular medicine Human Genetics. 134(5):455-7
Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD
(2015) Germline and somatic mosaicism: the
2014 annual scientific meeting of the Human Genome Variation
Society. Human Mutat. 36(3):390-3
Rettig EM, Chung CH, Bishop JA, Howard JD, Sharma R, Li RJ, Douville
C, Karchin R, Izumchenko E, Sidransky D, Koch WM, Califano J, Agrawal
N, Fakhry C (2015) Cleaved NOTCH1 expression
pattern in head and neck squamous cell carcinoma is associated
with NOTCH1 mutation, HPV status and high-risk clinical
features. Cancer Prev Res. 8(4):287-95
Masica DL, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch WM, Chung CH, Karchin R (2015)
Predicting survival in head and neck
squamous-cell carcinoma from TP53 mutation. Human
Genetics. 134(5):497-507
2014
Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R
(2014) Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Human Mol. Genetics. 24(7):1908-17
Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R (2014)
A probabilistic model to predict clinical
phenotypic traits from genome sequencing. PLoS Computational
Biology. Sep 4. 10(9):e1003825
Sharma N, Sosnay PR, Ramalho AS, Douville C, Franca A, Gottschalk LB, Park J, Lee M, Vecchio-Pagan B, Siklosi K, Amaral MD, Karchin R, Cutting G (2014)
Experimental assessment of splicing variants
using expression minigenes and comparison with in silico
predictions Human Mutation. 35(10):1249-59
Li L, Masica DL, Ishida M, Tomuleasa C, Umegak S, Kalloo AN, Georgiades C, Singh VK, Khashab M, Amateau S, Li Z, Okolo P, Lennon AM, Saxena P, Geschwind JF, Schlachter T, Hong K, Pawlik TM, Canto M, Law J, Sharaiha R, Weiss CR, Peng H, Thuluvath P, Goggins M, Shin EJ, Kumbhari V, Hutfless S, Zhou L, Mezey E, Meltzer SJ, Karchin R, Selaru FM. (2014)
Human bile contains microRNA-laden exosomes that can be used for cholangiocarcinoma diagnosis. Hepatology. 60(3):896-907
Carter H, Karchin R (2014)
Predicting the functional consequences of somatic missense mutations found in tumors. Methods in Molecular Biology, Gene Function Analysis, 2nd Edition), Ed. Ochs MF. Humana Press.
2013
Jiao Y, Pawlik TM, Anders RA, Selaru FM, Streppel MM, Lucas DJ, Niknafs N, Guthrie VB, Maitra A, Argani P, Offerhaus GJ, Roa JC, Roberts LR, Gores GJ, Popescu I, Alexandrescu ST, Dima S, Fassan M, Simbolo M, Mafficini A, Capelli P, Lawlor RT, Ruzzenente A, Guglielmi A, Tortora G, de Braud F, Scarpa A, Jarnagin W, Klimstra D, Karchin R, Velculescu VE, Hruban RH, Vogelstein B, Kinzler KW, Papadopoulos N, Wood LD (2013)
Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nat. Genetics. Dec;45(12):1470-3
Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, Ramalho AS, Amaral MD, Dorfman R, Zielenski J, Masica DL, Karchin R, Millen L, Thomas PJ, Patrinos GP, Corey M, Lewis MH, Rommens JM, Castellani C, Penland CM, Cutting GR (2013)
Defining the disease-liability of mutations in the cystic fibrosis transmembrane conductance regulator gene. Nat. Genetics. 45(10):1160-7
Hoang ML, Chen CH, Sidorenko VS, He J, Dickman KG, Yun BH, Moriya M, Niknafs N, Douville C, Karchin R, Turesky RJ, Pu YS, Vogelstein B, Papadopoulos N, Grollman AP, Kinzler KW, Rosenquist T (2013)
A. Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole Exome Sequencing. Science Translational Medicine. 5(197):197ra102
Gartner JJ, Parker SCJ, Prickett TD, Dutton-Reester K, Lin JC, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Bhanot UK, NISC Comparative Sequencing Program, Willard MD, Chen G, Elnitski L, Davies MA, Gershenwald JE, Carter H, Karchin R, Barber TD, Robinson W, Robinson S, Rosenberg SA, Komar AA, Kimchi-Sarfaty C, Hayward NK, Marguiles EH, Samuels Y (2013)
Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci USA. 110(33):13481-6
International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group, Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N. (2013)
Computational approaches to identify functional genetc variants in cancer genomes. Nat Methods.10(8):723-9
Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R (2013)
Identifying Mendelian disease genes with the Variant Effect Scoring Tool. BMC Genomics. 14(3) 1-16.
Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Karchin R (2013)
MuPIT Interactive: Webserver for mapping variant positions to annotated, interactive 3D structures. Human Genetics. 132(11):1235-43
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013)
CRAVAT: Cancer-Related Analysis of VAriants Toolkit. Bioinformatics. 29(5):647-8
Masica DL and Karchin R (2013)
Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Research. 73(6):1699-708
Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R (2013)
A hybrid likelihood model for sequence-based disease association studies. PLoS Genetics. 9(1): e1003224
2012
Woods N, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H, Marsillac S, Karchin R, Koomen J, Monteiro ANA(2012)
Charting the landscape of tandem BRCT domain-mediated protein interactions. Science Signaling. 5(242):rs6
Liang H, Cheung LWT, Li J, Ju Z, Yu S, Stemke-Hale K, Dogruluk T, Lu Y, Liu X, Gu C, Scherer SE, Carter H, Westin SN, Verhaak R, Zhang F, Karchin R, Liu CG, Lu KH, Broaddus RR, Scott KL, Hennessy BT, Mills GB (2012)
Whole-exome Sequencing Combined with Functional Genomics Reveals Novel Candidate Driver Cancer Genes in Endometrial Cancer. Genome Research. Nov;22(11):2120-9
Masica DL, Sosnay P, Cutting G, Karchin R (2012)
Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Human Mutation. 33(8):1267-74
Jiao X, Wood L, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R and Sjobolom T (2012)
Somatic mutations in the notch, NF-KB, PIK3CA and hedgehog pathways in human breast cancers. Genes, Chromosomes and Cancer. 51(5):480-9
Wu J, Jiao Y, Dal Molin M, Maitra A, deWilde RF, Wood LD, Eshleman JR, Goggins MG, Wolfgang CL, Canto ML, Schulick RD, Edil BH, CHoti, MA, Adsay V, Kimstra DS, Offerhaus GJA, Klein AP, Kopelovic L, Carter H, Karchin R, Allen PJ, Schmidt CM, Matio Y, Diaz L, Kinzler KW, Papadopolus N, Hruban RH, Vogelstein B (2011)
Whole exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proc Natl Acad Sci USA. 108(52):21188-93
Karchin R, Ochs MF, Stuart JM, Bader JS (2012)
Identification of aberrant pathway and network activity from high-throughput data.
Pac Symp Biocomput 2012 17:1-6
2011
Beleva-Guthrie V, Allen J, Camps M, and Karchin R (2011)
Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories.
PLoS Computational Biology. 7(9):e1002184
Lee D, Karchin R, Beer M. (2011)
Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research. 21(12):2167-80
Tyekucheva S, Marchionni L, Karchin R, Parmigianni G. (2011)
Integrating diverse genomic data using gene sets. Genome Biology. 23:R105, Oct. 21, 2011
Liu Y, Woods N, Kim D, Monteiro ANA, Karchin R (2011)
Yeast two-hybrid junk sequences contain selected linear motifs. Nucleic Acids Research. 39(19):e128
Wong WC, Kim D, Carter H, Diekhans M, Ryan M and Karchin R (2011)
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 27(15):2147-8
Zhang X, Reis M, Khoriaty R, Li Y, Ouillette P, Samayoa J, Carter H, Karchin R, Li M, Diaz L, Velculescu VE, Kinzler KW, Vogelstein B and Malek SN (2011)
Sequence analysis of 515 kinase genes in Chronic Lymphocytic Leukemia. Leukemia. 25(12):1908-10
Goes FS, Rongione M, Chen YC, Karchin R, Elhalk E, and Potash JB (2011)
Exonic DNA Sequencing of ERBB4 in Bipolar Disorder. PLoS One. 6(5):e20242
Allen J, Simcha D, Ericson N, Alexander D, Troll C, Marquette J, Van Biber B, Hernandez J, Karchin R, Bielas J, Loeb L, Camps M. (2011)
Roles of DNA Polymerase I in leading and lagging-strand replication defined by a high-resolution mutational footprint of ColE1 plasmid replication. Nucleic Acids Res. 39(16):7020-7033
The Cancer Genome Atlas Research Network (2011)
Integrated genomic analysis of ovarian carcinoma. Nature. 2011;474:609-615
Masica DL and Karchin R (2011)
Correlation among somatic mutation expression identifies genes important in human glioblastoma progression and survival. Cancer Research. Jul 1;71(13):4550-61
Sosnay PR, Castellani C, Corey M, Dorfman R, Zielenski J, Karchin R, Penland CM, Cutting GR. (2011)
Evaluation of the Disease Liability of CFTR Variants. Methods Mol Biol. 2011;742:355-72
Parsons DW, Li M, Zhang X, Jones S, Leary R, Lin J, Boca S, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SKN, Shinjo SMO, Clara C, Phillips PC, Minturn JE, Biegel J, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Tasheed BA, Friedman H, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papdopoulos N, Vogelstein B, Kinzler KW and Velculescu V. (2011)
The genetic landscape of the childhood cancer medulloblastoma.
Science. Jan 28;331(6016):435-9
Cline MS and Karchin R (2011)
Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. Feb 15;27(4):441-8. Dec 15
Ochs MF, Karchin R, Ressom H, and Gentleman R. (2011)
Identification of aberrant pathway and network activity from high-throughput data - workshop introduction. Pac Symp Biocomput. 2011:364-8
2010
Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA (2010)
Accumulation of driver and passenger mutations during tumor progression. Proc Natl Acad Sci USA. Oct 26;107(43):18545-50.
Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A (2010)
Functional hot spots in human ABC transporter nucleotide binding domains. Protein Science. Nov. 19(11):2110-21
Carter H, Samayoa J, Hruban RH, Karchin R (2010)
Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annnotation of somatic mutations (CHASM). Cancer Biology & Therapy. Sep 31;10(6):582-7.
2009
Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R.(2009)
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.Cancer Research. 69(16):6660-7
Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T. (2009)
Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Res. 37(18):5959-68
Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. (2009)
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 25(11):1431-2
Karchin R. (2009)
Next generation tools for the annotation of human SNPs. Briefing in Bioinformatics. 10(1):35-52
Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan D, Carter H, Mankoo P, Karchin R, Marti-Renom M, Davis F and Sali A. (2009)
MODBASE, a database of annotated comparative structure models, and associated resources. Nucleic Acids Res, 37 (Database issue):D347-54.
Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD, Rodarte RS, Vaz DC, Monteiro VA, Manoukian S, Colombo M, Ripamonti C, Rosenquist-Brandell R, Suthers G, Borg A, Radice P, Grist SA, Monteiro ANA and Billack B. (2009) Analysis of missense, frameshift, and in-frame deletion variants of BRCA1. Mutation Research. Jan 15;660(1-2):1-11.
2008
Jones S, Zhang X, Parsons DW, Lin J, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu, B, Lin, MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman, JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. (2008) Core signaling pathways in human pancreatic cancer revealed by global genomic analyses. Science, 26:1801-1806
Parsons DW, Jones S, Zhang X, Lin J, Leary RJ, Angenendt P, Mankoo P, Carter H, Su IM, Gallia G, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA, Hartigan J, Smith DR, Strausberg RL, Marie SKN, Shinjo SMO, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. (2008) An integrated genomic analysis of human glioblastoma multiforme Science. 26:1807-1812
Mankoo P, Sukumar S, Karchin R. (2008)
PIK3CA somatic mutations in breast cancer: mechanistic insights from Langevin dynamics simulations. Proteins Sep 10;75(2):499-508
Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K (2008)
Predict-2nd: a tool for generalized protein local structure prediction Bioinformatics. Nov 1;24(21):2453-9.
Karchin R, Couch F, Agarwal M, Sali A,& Beattie M.S.(2008)
Classifying BRCA2 unclassified variants using protein likelihood ratios. Cancer Informatics 4:1-14
2007
Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. (2007) The Genomic Landscapes of Human Breast and Colorectal Cancers. Science Nov 16;318(5853):1108-13
Karchin R, Monteiro A.N, Carvalho M.A, Tavtigian S.V. & Sali A. (2007) Functional impact of missense mutants in BRCA1 predicted by supervised learning. PLoS Computational Biology 3(2):e26
Kelly L, Karchin R, & Sali A. (2007) Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium on Biocomputing 12:51-63
Carvalho M.A, Marsillac S.M, Karchin R, Manoukian S, Grist S, Swaby R.F, Urmenyi T.P, Rondinelli E, Silva R, Gayol L. et al. (2007) Determination of cancer risk associated with germline BRCA1 missense variants by functional analysis. Cancer Research 67(4):1494-501
2006 and earlier