Rachel Karchin, Ph.D. - Publications

Affiliations: 
2003 University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
Computer Science, Molecular Biology

81 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 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, ... ... Karchin R, et al. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Human Mutation. PMID 28544481 DOI: 10.1002/humu.23265  0.48
2016 Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan MC, Masica D, Karchin R. Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure. Cancer Research. PMID 27197156 DOI: 10.1158/0008-5472.CAN-15-3190  0.84
2016 Masica DL, Karchin R. Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants. Plos Computational Biology. 12: e1004725. PMID 27171182 DOI: 10.1371/journal.pcbi.1004725  0.84
2016 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, et al. Exome Sequencing of Familial Bipolar Disorder. Jama Psychiatry. PMID 27120077 DOI: 10.1001/jamapsychiatry.2016.0251  0.84
2016 Rettig EM, Talbot C, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Fakhry C, Papadopoulos N, et al. Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer Prevention Research (Philadelphia, Pa.). PMID 26862087 DOI: 10.1158/1940-6207.CAPR-15-0316  0.84
2016 Oetting WS, Brenner SE, Brookes AJ, Greenblatt MS, Hart RK, Karchin R, Sunyaev SR, Taschner PE. Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society. Human Mutation. PMID 26791113 DOI: 10.1002/humu.22958  0.84
2015 Roberts NJ, Norris AL, Petersen GM, Bondy ML, Brand R, Gallinger S, Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stoffel EM, Syngal S, Zogopoulos G, Ali SZ, Axilbund J, ... ... Karchin R, et al. Whole genome sequencing defines the genetic heterogeneity of familial pancreatic cancer. Cancer Discovery. PMID 26658419 DOI: 10.1158/2159-8290.CD-15-0402  0.84
2015 Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R. Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel). Human Mutation. PMID 26442818 DOI: 10.1002/humu.22911  0.84
2015 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 Computational Biology. 11: e1004416. PMID 26436540 DOI: 10.1371/journal.pcbi.1004416  0.84
2015 Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Lupo B, Sausen M, Phallen J, Hruban CA, Tokheim C, Niknafs N, Nesselbush M, Lytle K, Sassi F, Cottino F, ... ... Karchin R, et al. The genomic landscape of response to EGFR blockade in colorectal cancer. Nature. PMID 26416732 DOI: 10.1038/nature14969  0.84
2015 Springer S, Wang Y, Molin MD, Masica DL, Jiao Y, Kinde I, Blackford A, Raman SP, Wolfgang CL, Tomita T, Niknafs N, Douville C, Ptak J, Dobbyn L, Allen PJ, ... ... Karchin R, et al. A Combination of Molecular Markers and Clinical Features Improve the Classification of Pancreatic Cysts. Gastroenterology. PMID 26253305 DOI: 10.1053/j.gastro.2015.07.041  0.84
2015 Turner TN, Douville C, Kim D, Stenson PD, Cooper DN, Chakravarti A, Karchin R. Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns. Human Molecular Genetics. 24: 5995-6002. PMID 26246501 DOI: 10.1093/hmg/ddv309  0.84
2015 Karchin R, Cline MS. Human genetics special issue on computational molecular medicine. Human Genetics. 134: 455-7. PMID 25805167 DOI: 10.1007/s00439-015-1545-6  0.84
2015 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, ... ... Karchin R, et al. Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Annals of Oncology : Official Journal of the European Society For Medical Oncology / Esmo. 26: 1216-23. PMID 25712460 DOI: 10.1093/annonc/mdv109  0.84
2015 Rettig EM, Chung CH, Bishop JA, Howard JD, Sharma R, Li RJ, Douville C, Karchin R, Izumchenko E, Sidransky D, Koch W, Califano J, Agrawal N, Fakhry C. Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features. Cancer Prevention Research (Philadelphia, Pa.). 8: 287-95. PMID 25633867 DOI: 10.1158/1940-6207.CAPR-14-0366  0.84
2015 Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD. Germline & somatic mosaicism: the 2014 annual scientific meeting of the Human Genome Variation Society. Human Mutation. 36: 390-3. PMID 25597405 DOI: 10.1002/humu.22757  0.84
2015 Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R. Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity. Human Molecular Genetics. 24: 1908-17. PMID 25489051 DOI: 10.1093/hmg/ddu607  0.84
2015 Masica DL, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch WM, Chung CH, Karchin R. Predicting survival in head and neck squamous cell carcinoma from TP53 mutation. Human Genetics. 134: 497-507. PMID 25108461 DOI: 10.1007/s00439-014-1470-0  0.84
2014 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. A probabilistic model to predict clinical phenotypic traits from genome sequencing. Plos Computational Biology. 10: e1003825. PMID 25188385 DOI: 10.1371/journal.pcbi.1003825  0.84
2014 Sharma N, Sosnay PR, Ramalho AS, Douville C, Franca A, Gottschalk LB, Park J, Lee M, Vecchio-Pagan B, Raraigh KS, Amaral MD, Karchin R, Cutting GR. Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions. Human Mutation. 35: 1249-59. PMID 25066652 DOI: 10.1002/humu.22624  0.84
2014 Li L, Masica D, Ishida M, Tomuleasa C, Umegaki S, Kalloo AN, Georgiades C, Singh VK, Khashab M, Amateau S, Li Z, Okolo P, Lennon AM, Saxena P, Geschwind JF, ... ... Karchin R, et al. Human bile contains microRNA-laden extracellular vesicles that can be used for cholangiocarcinoma diagnosis. Hepatology (Baltimore, Md.). 60: 896-907. PMID 24497320 DOI: 10.1002/hep.27050  0.84
2014 Carter H, Karchin R. Predicting the functional consequences of somatic missense mutations found in tumors. Methods in Molecular Biology (Clifton, N.J.). 1101: 135-59. PMID 24233781 DOI: 10.1007/978-1-62703-721-1_8  0.84
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, ... ... Karchin R, et al. Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas. Nature Genetics. 45: 1470-3. PMID 24185509 DOI: 10.1038/ng.2813  0.84
2013 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, et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nature Genetics. 45: 1160-7. PMID 23974870 DOI: 10.1038/ng.2745  0.84
2013 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, et al. Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing Science Translational Medicine. 5. PMID 23926200 DOI: 10.1126/scitranslmed.3006200  0.84
2013 Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, ... ... Karchin R, et al. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proceedings of the National Academy of Sciences of the United States of America. 110: 13481-6. PMID 23901115 DOI: 10.1073/pnas.1304227110  0.84
2013 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, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10: 723-9. PMID 23900255 DOI: 10.1038/nmeth.2562  0.84
2013 Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. Identifying Mendelian disease genes with the variant effect scoring tool. Bmc Genomics. 14: S3. PMID 23819870 DOI: 10.1186/1471-2164-14-S3-S3  0.84
2013 Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Human Genetics. 132: 1235-43. PMID 23793516 DOI: 10.1007/s00439-013-1325-0  0.84
2013 Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R. A hybrid likelihood model for sequence-based disease association studies. Plos Genetics. 9: e1003224. PMID 23358228 DOI: 10.1371/journal.pgen.1003224  0.84
2013 Masica DL, Karchin R. Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Research. 73: 1699-708. PMID 23338612 DOI: 10.1158/0008-5472.CAN-12-3122  0.84
2013 Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics (Oxford, England). 29: 647-8. PMID 23325621 DOI: 10.1093/bioinformatics/btt017  0.84
2012 Liang H, Cheung LW, Li J, Ju Z, Yu S, Stemke-Hale K, Dogruluk T, Lu Y, Liu X, Gu C, Guo W, Scherer SE, Carter H, Westin SN, Dyer MD, ... ... Karchin R, et al. Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Research. 22: 2120-9. PMID 23028188 DOI: 10.1101/gr.137596.112  0.84
2012 Woods NT, Mesquita RD, Sweet M, Carvalho MA, Li X, Liu Y, Nguyen H, Thomas CE, Iversen ES, Marsillac S, Karchin R, Koomen J, Monteiro AN. Charting the landscape of tandem BRCT domain-mediated protein interactions. Science Signaling. 5: rs6. PMID 22990118 DOI: 10.1126/scisignal.2002255  0.84
2012 Masica DL, Sosnay PR, Cutting GR, Karchin R. Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Human Mutation. 33: 1267-74. PMID 22573477 DOI: 10.1002/humu.22110  0.84
2012 Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, Sjöblom T. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers. Genes, Chromosomes & Cancer. 51: 480-9. PMID 22302350 DOI: 10.1002/gcc.21935  0.84
2012 Karchin R, Ochs MF, Stuart JM, Bader JS. Identification of aberrant pathway and network activity from high-throughput data 17th Pacific Symposium On Biocomputing, Psb 2012. 1-6.  0.84
2011 Wu J, Jiao Y, Dal Molin M, Maitra A, de Wilde RF, Wood LD, Eshleman JR, Goggins MG, Wolfgang CL, Canto MI, Schulick RD, Edil BH, Choti MA, Adsay V, Klimstra DS, ... ... Karchin R, et al. Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proceedings of the National Academy of Sciences of the United States of America. 108: 21188-93. PMID 22158988 DOI: 10.1073/pnas.1118046108  0.84
2011 Tyekucheva S, Marchionni L, Karchin R, Parmigiani G. Integrating diverse genomic data using gene sets. Genome Biology. 12: R105. PMID 22018358 DOI: 10.1186/gb-2011-12-10-r105  0.84
2011 Guthrie VB, Allen J, Camps M, Karchin R. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. Plos Computational Biology. 7: e1002184. PMID 21966264 DOI: 10.1371/journal.pcbi.1002184  0.84
2011 Lee D, Karchin R, Beer MA. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research. 21: 2167-80. PMID 21875935 DOI: 10.1101/gr.121905.111  0.84
2011 Liu Y, Woods NT, Kim D, Sweet M, Monteiro AN, Karchin R. Yeast two-hybrid junk sequences contain selected linear motifs. Nucleic Acids Research. 39: e128. PMID 21785140 DOI: 10.1093/nar/gkr600  0.84
2011 Zhang X, Reis M, Khoriaty R, Li Y, Ouillette P, Samayoa J, Carter H, Karchin R, Li M, Diaz LA, Velculescu VE, Papadopoulos N, Kinzler KW, Vogelstein B, Malek SN. Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia. Leukemia. 25: 1908-10. PMID 21701494 DOI: 10.1038/leu.2011.163  0.84
2011 Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics (Oxford, England). 27: 2147-8. PMID 21685053 DOI: 10.1093/bioinformatics/btr357  0.84
2011 Goes FS, Rongione M, Chen YC, Karchin R, Elhaik E, Potash JB. Exonic DNA sequencing of ERBB4 in bipolar disorder. Plos One. 6: e20242. PMID 21637803 DOI: 10.1371/journal.pone.0020242  0.84
2011 Allen JM, Simcha DM, Ericson NG, Alexander DL, Marquette JT, Van Biber BP, Troll CJ, Karchin R, Bielas JH, Loeb LA, Camps M. Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic Acids Research. 39: 7020-33. PMID 21622658 DOI: 10.1093/nar/gkr157  0.84
2011 Masica DL, Karchin R. Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Research. 71: 4550-61. PMID 21555372 DOI: 10.1158/0008-5472.CAN-11-0180  0.84
2011 Sosnay PR, Castellani C, Corey M, Dorfman R, Zielenski J, Karchin R, Penland CM, Cutting GR. Evaluation of the disease liability of CFTR variants. Methods in Molecular Biology (Clifton, N.J.). 742: 355-72. PMID 21547743 DOI: 10.1007/978-1-61779-120-8_21  0.84
2011 Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, ... ... Karchin R, et al. The genetic landscape of the childhood cancer medulloblastoma. Science (New York, N.Y.). 331: 435-9. PMID 21163964 DOI: 10.1126/science.1198056  0.84
2011 Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics (Oxford, England). 27: 441-8. PMID 21159622 DOI: 10.1093/bioinformatics/btq695  0.84
2011 Ochs MF, Karchin R, Ressom H, Gentleman R. Identification of aberrant pathway and network activity from high-throughput data-workshop introduction Pacific Symposium On Biocomputing 2011, Psb 2011. 364-368. PMID 21121064  0.84
2011 Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Letter to the editor Protein Science. 20: 4-5. DOI: 10.1002/pro.555  0.84
2010 Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA. Accumulation of driver and passenger mutations during tumor progression Proceedings of the National Academy of Sciences of the United States of America. 107: 18545-18550. PMID 20876136 DOI: 10.1073/pnas.1010978107  0.84
2010 Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Science : a Publication of the Protein Society. 19: 2110-21. PMID 20799350 DOI: 10.1002/pro.491  0.84
2010 Carter H, Samayoa J, Hruban RH, Karchin R. Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer Biology & Therapy. 10: 582-7. PMID 20581473 DOI: 10.4161/cbt.10.6.12537  0.84
2009 Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T. Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Research. 37: 5959-68. PMID 19661281 DOI: 10.1093/nar/gkp634  0.84
2009 Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R. Cancer-specific high-throughput annotation of somatic mutations: Computational prediction of driver missense mutations Cancer Research. 69: 6660-6667. PMID 19654296 DOI: 10.1158/0008-5472.CAN-09-1133  0.84
2009 Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics (Oxford, England). 25: 1431-2. PMID 19369493 DOI: 10.1093/bioinformatics/btp242  0.84
2009 Karchin R. Next generation tools for the annotation of human SNPs. Briefings in Bioinformatics. 10: 35-52. PMID 19181721 DOI: 10.1093/bib/bbn047  0.84
2009 Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD, Rodarte RS, Vaz DC, Monteiro VA, Manoukian S, Colombo M, Ripamonti CB, Rosenquist R, Suthers G, Borg A, et al. Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutation Research. 660: 1-11. PMID 18992264 DOI: 10.1016/j.mrfmmm.2008.09.017  0.84
2009 Mankoo PK, Sukumar S, Karchin R. PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations. Proteins. 75: 499-508. PMID 18951408 DOI: 10.1002/prot.22265  0.84
2009 Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 37: D347-54. PMID 18948282 DOI: 10.1093/nar/gkn791  0.84
2009 Cutting G, Sosnay P, Karchin R, Zielenski J, Penland C, Castellani C. CFTR2: Defining the clinical and functional consequences of CFTR mutations Pediatric Pulmonology. 44: 161-162.  0.84
2008 Karchin R, Agarwal M, Sali A, Couch F, Beattie MS. Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. Cancer Informatics. 6: 203-16. PMID 19043619  0.84
2008 Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, ... ... Karchin R, et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science (New York, N.Y.). 321: 1801-6. PMID 18772397 DOI: 10.1126/science.1164368  0.84
2008 Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, ... ... Karchin R, et al. An integrated genomic analysis of human glioblastoma multiforme. Science (New York, N.Y.). 321: 1807-12. PMID 18772396 DOI: 10.1126/science.1164382  0.84
2008 Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K. PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics (Oxford, England). 24: 2453-9. PMID 18757875 DOI: 10.1093/bioinformatics/btn438  0.84
2007 Kelly L, Karchin R, Sali A. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 51-63. PMID 17990484  0.84
2007 Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, ... ... Karchin R, et al. The genomic landscapes of human breast and colorectal cancers. Science (New York, N.Y.). 318: 1108-13. PMID 17932254 DOI: 10.1126/science.1145720  0.84
2007 Carvalho MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF, Urmenyi TP, Rondinelli E, Silva R, Gayol L, Baumbach L, Sutphen R, Pickard-Brzosowicz JL, Nathanson KL, Sali A, et al. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Research. 67: 1494-501. PMID 17308087 DOI: 10.1158/0008-5472.CAN-06-3297  0.84
2007 Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A. Functional impact of missense variants in BRCA1 predicted by supervised learning. Plos Computational Biology. 3: e26. PMID 17305420 DOI: 10.1371/journal.pcbi.0030026  0.84
2006 Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research. 34: D291-5. PMID 16381869 DOI: 10.1093/nar/gkj059  0.84
2005 Karplus K, Karchin R, Shackelford G, Hughey R. Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics (Oxford, England). 21: 4107-15. PMID 16123115 DOI: 10.1093/bioinformatics/bti629  0.84
2005 Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics (Oxford, England). 21: 2814-20. PMID 15827081 DOI: 10.1093/bioinformatics/bti442  0.84
2005 Karchin R, Kelly L, Sali A. Improving functional annotation of no n-s yno no mo us s nps with information theory Proceedings of the Pacific Symposium On Biocomputing 2005, Psb 2005. 397-408. PMID 15759645  0.84
2004 Karchin R, Cline M, Karplus K. Evaluation of local structure alphabets based on residue burial. Proteins. 55: 508-18. PMID 15103615 DOI: 10.1002/prot.20008  0.84
2003 Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins. 53: 491-6. PMID 14579338 DOI: 10.1002/prot.10540  0.84
2003 Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins. 51: 504-14. PMID 12784210 DOI: 10.1002/prot.10369  0.84
2002 Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics (Oxford, England). 18: 147-59. PMID 11836223  0.84
2001 Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R. What is the value added by human intervention in protein structure prediction? Proteins. 86-91. PMID 11835485 DOI: 10.1002/prot.10021  0.84
1998 Karchin R, Hughey R. Weighting hidden Markov models for maximum discrimination Bioinformatics. 14: 772-782. PMID 9918947  0.84
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