From Chasm Software Wiki
Primary Publications
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 PubMed
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 PubMed
Publications that have used CHASM
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
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. Feb 3. [Epub ahead of print].
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]
The Cancer Genome Atlas Research Network (2011) Integrated genomic analysis of ovarian carcinoma Nature. 2011;474:609-615 PubMed
Masica DL and Karchin R (2011) Correlation among somatic mutation expression identifies genes important in human glioblastoma progression and survival Cancer Research. Jul 1;71(13):4550-61 PubMed
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 PubMed
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 PubMed
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. PNAS. Oct 26;107(43):18545-50. PubMed
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) PubMed
