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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) Pathways underlying pancreatic tumorigenesis. submitted.
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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 glioblastoma multiforme submitted.
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Mankoo P, Sukumar S, Karchin R. (2008)
PIK3CA somatic mutations in breast cancer: mechanistic insights from Langevin dynamics simulations. submitted |
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Carvalho M, Pino MA, Karchin R, 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, Grist11 SA, Monteiro ANA and Billack B. (2008) Analysis of missense, frameshift, and in-frame deletion variants of BRCA1. submitted. |
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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. In press. |
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Karchin R. (2008)
Next generation tools for the annotation of human SNPs. Briefing in Bioinformatics. In press. |
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Karchin R, Couch F, Agarwal M, Sali A,& Beattie M.S.(2008)
Classification of 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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