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Masica D, Sosnay P, Cutting G, Karchin R (2012)
Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis submitted |
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Sosnay P, VanGoor F, Castellani C, Corey M, Dorfman R, Zielenski J, Karchin R, Lewis M, Yu H, Rommens J, Penland C, Cutting G (2012)
Correlation of CFTR genotype with sweat chloride concentration and lung function in cystic fibrosis submitted |
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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 submitted |
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Woods N, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu N, Nguyen H, Marsillac S, Karchin R, Koomen J, Monteiro ANA(2012)
Charting the landscape of tandem BRCT domain-mediated protein interactions submitted |
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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. In press. |
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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. Dec 8 2011 [Epub ahead of print] |
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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 |
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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 |
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Lee D, Karchin R, Beer M. (2011)
Discriminative prediction of mammalian enhancers from DNA sequence Genome Research. Epub 2011 Aug 29 |
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Tyekucheva S, Marchionni L, Karchin R, Parmigianni G. (2011)
Integrating diverse genomic data using gene sets Genome Biology. 23:R105, Oct. 21, 2011 |
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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 Epub. 2011 July 23 |
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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 Epub 2011 June 17 |
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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. Epub 2011 Jun 24 |
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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 Epub 2011 May 26 |
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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. (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 May 25 [Epub ahead of print] |
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The Cancer Genome Atlas Research Network (2011)
Integrated genomic analysis of ovarian carcinoma Nature. 2011;474:609-615 |
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Masica DL and Karchin R (2011)
Correlation among somatic mutation expression identifies genes important in human glioblastoma progression and survival Cancer Research. Epub 2011 May 9 |
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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 |
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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 Epub 2010 Dec 16 |
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Cline MS and Karchin R (2011)
Using bioinformatics to predict the functional impact of SNVs Bioinformatics. Feb 15;27(4):441-8. Epub 2010 Dec 15 |
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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 |
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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. Proc Natl Acad Sci USA. Oct 26;107(43):18545-50. Epub 2010 Sep 27. |
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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. Protein Science. Nov. 19(11):2110-21 |
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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. Sep 31;10(6):582-7. Epub 2010 Oct. 1 |
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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. 37(18):5959-68. Epub 2009 Aug 6. |
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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. Nov 1;24(21):2453-9. Epub 2008 Aug 30 |
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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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