Volume 12 Supplement 1

Beyond the Genome 2011

Meeting abstracts

Beyond the Genome 2011. Go to conference site.

Washington, DC, USA19-22 September 2011

Concatenated PDF 12S1

Page 2 of 3

InSilico DB: an online platform to collaboratively structure and export publicly available datasets from the Gene Expression Omnibus database

Authors: A Coletta, C Molter, R Duqué, D Steenhoff, J Taminau, V de Schaetzen, C Lazar, S Meganck, A Nowé, H Bersini and D Weiss

Citation: Genome Biology 2011 12(Suppl 1):P33

Content type: Poster presentation Published on: 19 September 2011
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Introducing the non-B DNA Motif Search Tool (nBMST)

Authors: Regina Z Cer, Kevin H Bruce, Duncan E Donohue, Alpay N Temiz, Albino Bacolla, Uma S Mudunuri, Ming Yi, Natalia Volfovsky, Brian T Luke, Jack R Collins and Robert M Stephens

Citation: Genome Biology 2011 12(Suppl 1):P34

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Integrating GWAS with gene expression data to dissect the genetic architecture of triple-negative breast cancer

Authors: Chindo Hicks, Ranjit Kumar, Antonio Pannuti and Lucio Miele

Citation: Genome Biology 2011 12(Suppl 1):P35

Content type: Poster presentation Published on: 19 September 2011
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Novel purification reagents for the study of the human microbiome

Authors: George R Feehery, Eileen Dimalanta and Sriharsa Pradhan

Citation: Genome Biology 2011 12(Suppl 1):P36

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An amalgamated risk estimation model (REM) and assay integration into future REMs

Authors: Peter Cartwright, Erica Ramos, India Bradley and Eric Hanson

Citation: Genome Biology 2011 12(Suppl 1):P37

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G-CODE: enabling systems medicine through innovative informatics

Authors: Subha Madhavan, Yuriy Gusev, Michael A Harris, David M Tanenbaum, Robinder Gauba, Krithika Bhuvaneshwar, Andrew Shinohara, Kevin Rosso, Lavinia A Carabet, Lei Song, Rebecca B Riggins, Sivanesan Dakshanamurthy, Yue Wang, Stephen W Byers, Robert Clarke and Louis M Weiner

Citation: Genome Biology 2011 12(Suppl 1):P38

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Timing chromosomal abnormalities using mutation data

Authors: Steffen Durinck, Christine Ho, Nicholas J Wang, Wilson Liao, Lakshmi R Jakkula, Eric A Collisson, Jennifer Pons, Sai-Wing Chan, Ernest T Lam, Catherine Chu, Kyunghee Park, Sung-woo Hong, Joe S Hur, Nam Huh, Isaac M Neuhaus, Siegrid S Yu…

Citation: Genome Biology 2011 12(Suppl 1):P39

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RNA-Seq-based transcriptional map of the bovine respiratory disease pathogen Histophilus somni 2336

Authors: Ranjit Kumar, Mark L Lawrence, James Watt, Amanda Cooksey, Shane C Burgess and Bindu Nanduri

Citation: Genome Biology 2011 12(Suppl 1):P40

Content type: Poster presentation Published on: 19 September 2011
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On using optical maps for genome assembly

Authors: Henry Lin and Mihai Pop

Citation: Genome Biology 2011 12(Suppl 1):P41

Content type: Poster presentation Published on: 19 September 2011
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Utilizing whole genome sequences to study population genomics of gene networks: a case study of the Arabidopsis thaliana immune-signaling network

Authors: Mridu Middha, Yungil Kim, Peter Morrell, Chad Myers and Fumiaki Katagiri

Citation: Genome Biology 2011 12(Suppl 1):P42

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Genomes or exomes: evaluation of cost, time and coverage

Authors: Sumit Middha, Jeanne L Theis, Adele H Goodloe, Timothy M Olson and Jean-Pierre A Kocher

Citation: Genome Biology 2011 12(Suppl 1):P43

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Integrating whole transcriptome sequence data and public databases for analysis of somatic mutations in tumors

Authors: Amin A Momin, Brian P James, Thomas C Motter, Humam N Kadara, Garth Powis and Ignacio I Wistuba

Citation: Genome Biology 2011 12(Suppl 1):P44

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Effective detection of rare variants in pooled DNA samples using cross-pool tail-curve analysis

Authors: Tejasvi S Niranjan, Abby Adamczyk, Hector Corrada Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry and Tao Wang

Citation: Genome Biology 2011 12(Suppl 1):P45

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A comprehensive transcriptomic and biochemical evaluation of a differentiation inducing anti-leukemic principle isolated from Momordica charantia

Authors: Punit Prabha and Aparna Dixit

Citation: Genome Biology 2011 12(Suppl 1):P46

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Microbial community function and biomarker discovery in the human microbiome

Authors: Nicola Segata, Sahar Abubucker, Johannes Goll, Alyxandria M Schubert, Jacques Izard, Brandi L Cantarel, Beltran Rodriguez-Mueller, Levi Waldron, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T Kelley, Barbara Methé, Patrick D Schloss, Wendy S Garrett…

Citation: Genome Biology 2011 12(Suppl 1):P47

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A high-throughput-sequence analysis infrastructure technology investigation framework for the evaluation of next-generation sequencing software

Authors: Xiaoyu Liu, Sumit Middha, Steven Hart, Asha Nair, Ahmed Hadad, Patrick Duffy and Jean-Pierre Kocher

Citation: Genome Biology 2011 12(Suppl 1):P48

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Analysis of 2,440 human exomes highlights the evolution and functional impact of rare coding variation

Authors: Joshua Akey

Citation: Genome Biology 2011 12(Suppl 1):I1

Content type: Invited speaker presentation Published on: 19 September 2011
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Citation: Genome Biology 2011 12(Suppl 1):I2

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Are clinical genomes already becoming semi-routine for patient care?

Authors: Mark Boguski

Citation: Genome Biology 2011 12(Suppl 1):I3

Content type: Invited speaker presentation Published on: 19 September 2011
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Interrogating the architecture of cancer genomes

Authors: Peter Campbell

Citation: Genome Biology 2011 12(Suppl 1):I4

Content type: Invited speaker presentation Published on: 19 September 2011
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Genome-forward oncology: how do we get there?

Authors: Matthew Ellis

Citation: Genome Biology 2011 12(Suppl 1):I5

Content type: Invited speaker presentation Published on: 19 September 2011
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Citation: Genome Biology 2011 12(Suppl 1):I6

Content type: Invited speaker presentation Published on: 19 September 2011
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Microbial reference genomes for human metagenomics

Authors: Sarah K Highlander

Citation: Genome Biology 2011 12(Suppl 1):I7

Content type: Invited speaker presentation Published on: 19 September 2011
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Citation: Genome Biology 2011 12(Suppl 1):I8

Content type: Invited speaker presentation Published on: 19 September 2011
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Next-generation clinical sequencing in a children’s hospital

Authors: Stephen Kingsmore

Citation: Genome Biology 2011 12(Suppl 1):I9

Content type: Invited speaker presentation Published on: 19 September 2011
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A glimpse at tumor genome evolution

Authors: Elaine R Mardis

Citation: Genome Biology 2011 12(Suppl 1):I10

Content type: Invited speaker presentation Published on: 19 September 2011
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Citation: Genome Biology 2011 12(Suppl 1):I11

Content type: Invited speaker presentation Published on: 19 September 2011
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Comparative genomic analysis of mouse and human mammary tumors

Authors: Charles M Perou

Citation: Genome Biology 2011 12(Suppl 1):I12

Content type: Invited speaker presentation Published on: 19 September 2011
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Reconstructing microbial communities

Authors: Mihai Pop

Citation: Genome Biology 2011 12(Suppl 1):I13

Content type: Invited speaker presentation Published on: 19 September 2011
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Next-generation human genetics

Authors: Jay Shendure

Citation: Genome Biology 2011 12(Suppl 1):I14

Content type: Invited speaker presentation Published on: 19 September 2011
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Metatranscriptomics of the human gut microbiome

Authors: Thomas Sichertz Pontén

Citation: Genome Biology 2011 12(Suppl 1):I15

Content type: Invited speaker presentation Published on: 19 September 2011
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De novo mutations in mental retardation

Authors: Joris A Veltman

Citation: Genome Biology 2011 12(Suppl 1):I16

Content type: Invited speaker presentation Published on: 19 September 2011
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Comparative analysis of the vaginal microbiome in health and disease

Authors: Bryan A White, Andres M Gomez, Mengfei Ho, Margret Berg Miller, Susan M Thomas, Carl J Yeoman, Suleyman Yildirim, Douglas J Creedon, Tony L Goldberg, Steven R Leigh, Karen E Nelson, Rebecca M Stumpf and Brenda A Wilson

Citation: Genome Biology 2011 12(Suppl 1):I17

Content type: Invited speaker presentation Published on: 19 September 2011
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The Joint Center for Structural Genomics: exploration of the human gut microbiome

Authors: Ian Wilson

Citation: Genome Biology 2011 12(Suppl 1):I18

Content type: Invited speaker presentation Published on: 19 September 2011
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RNA-Seq methods for imperfect samples: development, evaluation and applications

Authors: Xian Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko, Nathalie Pochet, Aaron Berlin, Sarah Young, Gad Getz, Aviv Regev, Chad Nusbaum, Andreas Gnirke and Joshua Z Levin

Citation: Genome Biology 2011 12(Suppl 1):P1

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Viral diversity in children with diarrhea in Gambia

Authors: Irina Astrovskaya, Bo Liu and Mihai Pop

Citation: Genome Biology 2011 12(Suppl 1):P2

Content type: Poster presentation Published on: 19 September 2011
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COSMIC: the catalogue of somatic mutations in cancer

Authors: Nidhi Bindal, Simon A Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Chai Yin Kok, Mingming Jia, Sally Bamford, Charlotte Cole, Sari Ward, Jon Teague, Michael R Stratton, Peter Campbell and Andrew P Futreal

Citation: Genome Biology 2011 12(Suppl 1):P3

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A novel functional variant in 8q24 is associated with regulation of prostate stem cell antigen (PSCA) gene expression and bladder cancer risk

Authors: Yi-Ping Fu, Indu Kohaar, Adam Mumy, Wei Tang, Brian Muchmore, Patricia Porter-Gill, Luyang Liu, Jonine Figueroa, Montserrat Garcia-Closas, Dalsu Baris, Mark Purdue, Michael Thun, Demetrius Albanes, Nuria Malats, Francisco X Real, Manolis Kogevinas…

Citation: Genome Biology 2011 12(Suppl 1):P4

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Evaluating short-read sequence data from the highly redundant, novel transcriptome of Polarella glacialis

Authors: Theodore R Gibbons, Gregory T Concepcion, Tsvetan R Bachvaroff and Charles F Delwiche

Citation: Genome Biology 2011 12(Suppl 1):P5

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A cost-effective and universal strategy for complete prokaryotic genome sequencing proposed by computer simulation

Authors: Jingwei Jiang, Jun Li and Frederick C Leung

Citation: Genome Biology 2011 12(Suppl 1):P6

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Functional exploration of CCNE1splicing forms as a possible link to bladder cancer susceptibility

Authors: Indu Kohaar, Alexandra Scott-Johnson, Yi-Ping Fu, Patricia Porter-Gill and Ludmila Prokunina-Olsson

Citation: Genome Biology 2011 12(Suppl 1):P7

Content type: Poster presentation Published on: 19 September 2011
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ScaffViz: visualizing metagenome assemblies

Authors: Sergey Koren, Todd Treangen and Mihai Pop

Citation: Genome Biology 2011 12(Suppl 1):P8

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Systems biology of bacteriophage proteins and new dimensions of the virus world discovered through metagenomics

Authors: David M Kristensen, Arcady R Mushegian and Eugene V Koonin

Citation: Genome Biology 2011 12(Suppl 1):P9

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Genetic basis of common human disease: insight into the role of nonsynonymous SNPs from genome-wide association studies

Authors: Lipika R Pal and John Moult

Citation: Genome Biology 2011 12(Suppl 1):P10

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Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Authors: Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen and Mihai Pop

Citation: Genome Biology 2011 12(Suppl 1):P11

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Citation: Genome Biology 2011 12(Suppl 1):P12

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Massively parallel sequencing identifies a previously unrecognized X-linked disorder resulting in lethality in male infants owing to amino-terminal acetyltransferase deficiency

Authors: Alan F Rope, Kai Wang, Rune Evjenth, Jinchuan Xing, Jennifer J Johnston, Jeffrey J Swensen, W Evan Johnson, Barry Moore, Chad D Huff, Lynne M Bird, John C Carey, John M Opitz, Cathy A Stevens, Christa Schank, Heidi Deborah Fain, Reid Robison…

Citation: Genome Biology 2011 12(Suppl 1):P13

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Citation: Genome Biology 2011 12(Suppl 1):P14

Content type: Poster presentation Published on: 19 September 2011
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Prostate stem cell antigen (PSCA) and risk of bladder cancer: linking genotypes to functional mechanisms

Authors: Adam Mumy, Indu Kohaar, Patricia Porter-Gill, Wei Tang, Yi-Ping Fu and Ludmila Prokunina-Olsson

Citation: Genome Biology 2011 12(Suppl 1):P15

Content type: Poster presentation Published on: 19 September 2011
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Metabolic pathways are affected differently in Saccharomyces cerevisiae thiol peroxidase mutants during redox stress with hydrogen peroxide

Authors: Amy L Olex, Brian M Westwood, Leslie B Poole and Jacquelyn S Fetrow

Citation: Genome Biology 2011 12(Suppl 1):P16

Content type: Poster presentation Published on: 19 September 2011
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Beyond the Genome 2011

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