Salk Institute
Integrative Genomics and Bioinformatics Core

Razavi Newman Integrative Genomics and Bioinformatics Core

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Chirs Benner

Chris Benner
Director
Integrative Genomics and Bioinformatics Core

As director of the IGC, Chris brings a wealth of experience using genomics to solve biological problems to the Salk Institute. Chris conducted his Ph.D. studies in Bioinformatics at UCSD, where he played a pioneering role in developing analysis tools for next-generation sequencing technologies. His doctoral work focused on the discovery of genomic features and cis-regulatory codes underlying transcription factor recruitment and transcription initiation. Chris continued as a post doc and project scientist at UCSD where he contributed to genomics projects in over a dozen labs while developing widely adopted analysis software for next-generation sequencing. He joined the Salk in May 2012 to start the Integrative Genomics and Bioinformatics Core.

Selected Publications

Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, et al. Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes. PLoS Genet. 2011 Dec;7(12).

Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity. 2011 Sep 23;35(3):413-25.

Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature. 2011 May 15;474(7351):390-4.

Sullivan AL, Benner C, Heinz S, Huang W, Xie L, Miano JM, Glass CK. Serum response factor utilizes distinct promoter- and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages. Mol Cell Biol. 2011 Feb;31(4):861-75.

Barish GD, Yu RT, Karunasiri M, Ocampo CB, Dixon J, Benner C, Dent AL, Tangirala RK, Evans RM. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev. 2010 Dec 15;24(24):2760-5.

Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, Liu WT, Ohgi KA, Benner C, Garcia-Bassets I, Aggarwal AK, Desai A, Dorrestein PC, Glass CK, Rosenfeld MG. PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature. 2010 Jul 22;466(7305):508-12.

Stender JD, Kim K, Charn TH, Komm B, Chang KC, Kraus WL, Benner C, Glass CK, Katzenellenbogen BS. Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol Cell Biol. 2010 Aug;30(16):3943-55.

Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010 Jul;11(7):635-43.

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010 May 28;38(4):576-89.

 

 


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