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Jiao X, Wood L, Lindman M, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, Jones S, Vogelstein B, Velculescu, V, Kinzler K, and Sjöblom T (2010)
Somatic mutations the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers submitted |
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Lee D, Karchin R, Beer M. (2010)
Successful enhancer prediction from DNA sequence. submitted |
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Tyekucheva S, Marchionni L, Karchin R, Parmigianni G. (2010)
Integrating diverse genomic data using gene sets. submitted |
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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. submitted |
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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. (2010)
Identification of a mutational footprint of E. coli DNA polymerase indicative of extensive role in lagging strand replication and suggestive of functional redundancy with Pol III. submitted |
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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. submitted |
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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. in press |
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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  |
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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. Aug 6. [Epub ahead of print] |
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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 |
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Karchin R. (2009)
Next generation tools for the annotation of human SNPs. Briefing in Bioinformatics. 10(1):35-52 |
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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. Epub 2008 Oct 23
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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. Epub 2008 Oct 17
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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
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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
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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
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Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K (2008)
Predict-2nd: a tool for generalized protein local structure prediction Bioinformatics. Aug 30 [Epub ahead of print] |
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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
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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 |
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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] |
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Kelly L, Karchin R, & Sali A. (2007) Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium on Biocomputing 12:51-63
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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 |
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| 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 |
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| 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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| Karchin R, Diekhans M, Kelly L, Thomas D, Pieper U, Eswar N, Haussler D & Sali A (2005) LS-SNP: large-scale annotation of coding non-synonynous SNPs based on multiple information sources. Bioinformatics 21(12):2814-20 |
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| Karchin R, Kelly L & Sali A (2005)
Improving functional annotation of non-synonymous SNPs with information theory. Pacific Symposium on Biocomputing 10:397-408 |
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| Karchin R, Cline M & Karplus K (2004) Evaluation of local structure alphabets based on residue burial. Proteins 55(3):508-18 |
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| Karchin R, Cline M, Mandel-Gutfreund Y. & Karplus K. (2003)
Hidden Markov models that use predicted local structure for fold recognition: alphabets of protein backbone geometry. Proteins 51(4):504-514 |
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| Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diehkans, M & Hughey R (2003) Combining local structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins 53(S6):491-496 |
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| Karchin R, Karplus K & Haussler, D (2002)
Classifying G-Protein Coupled Receptors with Support Vector Machines. Bioinformatics 18(1):147-159 |
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| Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M Grate, L Casper, J & Hughey R. (2001) What is the value added by human intervention in protein structure prediction? Proteins 45(S5):86-91 |
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| Karchin R & Hughey R (1998)
Weighting Hidden Markov Models for Maximum Discrimination. Bioinformatics 14(9):772-82
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