Category: 2011

Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia S

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. 25(12):1908-10

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Discriminative prediction of mammalian enhancers from DNA sequence D

Lee D, Karchin R, Beer M. (2011) Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research. 21(12):2167-80

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Integrating diverse genomic data using gene sets I

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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Yeast two-hybrid junk sequences contain selected linear motifs Y

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

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Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories N

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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Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication R

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

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CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer C

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

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Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival C

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

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Exonic DNA sequencing of ERBB4 in bipolar disorder E

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

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Using bioinformatics to predict the functional impact of SNVs U

Cline MS and Karchin R (2011) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. Feb 15;27(4):441-8. Dec 15

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