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

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

Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 2009 Jun 1;25(11):1431-2. doi: 10.1093/bioinformatics/btp242. Epub 2009 Apr 15. PMID: 19369493; PMCID: PMC6276889.

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.

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.

Karchin R. (2009) Next generation tools for the annotation of human SNPs. Briefing in Bioinformatics. 10(1):35-52