Volume 11 Supplement 4

UT-ORNL-KBRIN Bioinformatics Summit 2010

Meeting abstracts

Edited by Eric C Rouchka, Robert M Flight and Claire Rinehart

Funding for the UT-ORNL-KBRIN Summit is provided in part by The Kentucky Biomedical Research Infrastructure Network (KBRIN), the University of Tennessee Molecular Resource Center, The UT-ORNL Science Alliance, The University of Tennessee Center for Integrative and Translational Genomics, and NIH grant P20RR16481.

UT-ORNL-KBRIN Bioinformatics Summit 2010. Go to conference site.

Cadiz, KY, USA19-21 March 2010

Concatenated PDF 11S4

Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010

Authors: Eric C Rouchka, Robert M Flight and Claire Rinehart

Citation: BMC Bioinformatics 2010 11(Suppl 4):I1

Content type: Introduction Published on: 23 July 2010
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Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia

Authors: Peilin Jia and Zhongming Zhao

Citation: BMC Bioinformatics 2010 11(Suppl 4):O1

Content type: Oral presentation Published on: 23 July 2010
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Subsystems-based servers for rapid annotation of genomes and metagenomes

Authors: Ramy Karam Aziz

Citation: BMC Bioinformatics 2010 11(Suppl 4):O2

Content type: Oral presentation Published on: 23 July 2010
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Genomic analysis of a rare human tumor

Authors: Steven JM Jones, Janessa Laskin, Yvonne Y Li, Obi L Griffith, Jianghong An, Mikhail Bilenky, Yaron S Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk…

Citation: BMC Bioinformatics 2010 11(Suppl 4):O3

Content type: Oral presentation Published on: 23 July 2010
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Association of genomewide newborn DNA methylation patterns with maternal and newborn characteristics

Authors: Ronald M Adkins, Julia Krushkal, Steven Zeisel, Chandrika Piyathilake, Fran Tylavsky and Grant Somes

Citation: BMC Bioinformatics 2010 11(Suppl 4):O4

Content type: Oral presentation Published on: 23 July 2010
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Inferring gene coexpression networks for low dose ionizing radiation using graph theoretical algorithms and systems genetics

Authors: Sudhir Naswa, Gary L Rogers Jr., Rachel M Lynch, Stephen A Kania, Suchita Das, Elissa J Chesler, Arnold M Saxton, Brynn H Voy and Michael A Langston

Citation: BMC Bioinformatics 2010 11(Suppl 4):O5

Content type: Oral presentation Published on: 23 July 2010
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Integrating experimental and computational approaches for the proteogenomic characterizations of microbial communities

Authors: Robert L Hettich, Alison L Russell, Nathan C VerBerkmoes, Manesh Shah, Claire Fraser-Liggett and Janet K Jansson

Citation: BMC Bioinformatics 2010 11(Suppl 4):O6

Content type: Oral presentation Published on: 23 July 2010
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High-throughput sequencing of the DBA/2J mouse genome

Authors: Xusheng Wang, Richa Agarwala, John A Capra, Zugen Chen, Deanna M Church, Daniel C Ciobanu, Zhengsheng Li, Lu Lu, Khyobeni Mozhui, Megan K Mulligan, Stanley F Nelson, Katherine S Pollard, Williams L Taylor, Donald B Thomason and Robert W Williams

Citation: BMC Bioinformatics 2010 11(Suppl 4):O7

Content type: Oral presentation Published on: 23 July 2010
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Analysis of equine protein-coding gene structure and expression by RNA-sequencing

Authors: Stephen J Coleman, Zheng Zeng, Jinze Liu and James N MacLeod

Citation: BMC Bioinformatics 2010 11(Suppl 4):O8

Content type: Oral presentation Published on: 23 July 2010
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Epigenetic control of signaling networks involved in interleukin-18-induced cardiac hypertrophy and its attenuation by pan-histone deacetylase inhibitors

Authors: Gipsy Majumdar and Rajendra Raghow

Citation: BMC Bioinformatics 2010 11(Suppl 4):P1

Content type: Poster presentation Published on: 23 July 2010
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Identifying potential drugs that induce QT prolongation using electronic medical records

Authors: Mei Liu, Joshua C Denny, Subramani Mani, Yukun Chen, Yong Hu and Hua Xu

Citation: BMC Bioinformatics 2010 11(Suppl 4):P2

Content type: Poster presentation Published on: 23 July 2010
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Molecular analysis of Trypanosoma cruzi isolates obtained from raccoons in Warren and Barren counties of Kentucky

Authors: LiPeng Bi, Chad Groce and Cheryl Davis

Citation: BMC Bioinformatics 2010 11(Suppl 4):P3

Content type: Poster presentation Published on: 23 July 2010
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SNPlotz: a generic genome plot tool to aid the SNP association studies

Authors: Zhi-Liang Hu, Rex Fernando, Dorian Garrick and James M Reecy

Citation: BMC Bioinformatics 2010 11(Suppl 4):P4

Content type: Poster presentation Published on: 23 July 2010
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Slim-Prim: an integrated data system for clinical and translational research

Authors: Teeradache Viangteeravat, Ian M Brooks, Somchan Vuthipadadon, Emin Kuscu, Naga Nagisetty, Ebony Smith, Ramin Homayouni and Chanchai S McDonald

Citation: BMC Bioinformatics 2010 11(Suppl 4):P5

Content type: Poster presentation Published on: 23 July 2010
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Phylotree – a toolkit for computing experiments with distance-based methods for genome coevolution

Authors: Elissaveta Arnaoudova, Jerzy W Jaromczyk, Neil Moore, Christopher L Schardl and Ruriko Yoshida

Citation: BMC Bioinformatics 2010 11(Suppl 4):P6

Content type: Poster presentation Published on: 23 July 2010
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Comparative functional genomic study of substrate specificity evolution of the SABATH family of methyltransferases in plants

Authors: Nan Zhao, Jean-Luc Ferrer, Xiaofeng Zhuang and Feng Chen

Citation: BMC Bioinformatics 2010 11(Suppl 4):P7

Content type: Poster presentation Published on: 23 July 2010
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In silico analysis of a family of extracellular polysaccharide deacetylases involved in virulence of pathogenic gram-positive cocci

Authors: Ramy Karam Aziz

Citation: BMC Bioinformatics 2010 11(Suppl 4):P8

Content type: Poster presentation Published on: 23 July 2010
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Experimenting with database segmentation size vs time performance for mpiBLAST on an IBM HS21 blade cluster

Authors: Daniel Harris, Jerzy W Jaromczyk and Christopher L Schardl

Citation: BMC Bioinformatics 2010 11(Suppl 4):P9

Content type: Poster presentation Published on: 23 July 2010
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WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit

Authors: Dexter Duncan, Naresh Prodduturi and Bing Zhang

Citation: BMC Bioinformatics 2010 11(Suppl 4):P10

Content type: Poster presentation Published on: 23 July 2010
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Bioinformatic analysis of gene regulation in the metal-reducing bacterial family Geobacteraceae

Authors: Julia Krushkal, Ronald M Adkins, Yanhua Qu, Jeanette Peeples, Sreedhar Sontineni, Ching Leang, Peter Brown, Nelson D Young, Toshiyuki Ueki, Katy Juarez and Derek R Lovley

Citation: BMC Bioinformatics 2010 11(Suppl 4):P11

Content type: Poster presentation Published on: 23 July 2010
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Integrating neighbor clustering, coexpression clustering and subsystems analysis to define dynamic changes in regulatory networks associated with group A streptococcal sociomicrobiology and niche adaptation

Authors: Ramy K Aziz, Bruce J Aronow, William L Taylor, Sarah L Rowe, Rita Kansal, Mark J Walker and Malak Kotb

Citation: BMC Bioinformatics 2010 11(Suppl 4):P12

Content type: Poster presentation Published on: 23 July 2010
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Pleiotropy of tumor necrosis factor-α in C2C12 myotubes: in vitro studies on genes, networks and pathways involved in TNF-α induced skeletal muscle atrophy

Authors: Shephali Bhatnagar, Siva K Panguluri, Robert F Lundy and Ashok Kumar

Citation: BMC Bioinformatics 2010 11(Suppl 4):P13

Content type: Poster presentation Published on: 23 July 2010
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Developing measures for microbial genome assembly quality control

Authors: Rachel M Adams, Jason B Harris, Jeremy J Jay, Beth G Johnson, Miriam L Land and Loren J Hauser

Citation: BMC Bioinformatics 2010 11(Suppl 4):P14

Content type: Poster presentation Published on: 23 July 2010
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Sequence and annotation of the Wizard007 mycobacterium phage genome

Authors: Ejike Anyanwu, Kaitlyn Cole, Karlee Driver, Anthony Falcone, Elizabeth Farnsworth, Benjamin Howard, Brittney Howard, Courtney Howard, Rodney King, Jordan Olberding, Mackenzie Perkins, Claire Rinehart, Heidi Sayre, Tyler Scaff, Sarah Schrader, Prasanna Tamarapu Parthasarathy…

Citation: BMC Bioinformatics 2010 11(Suppl 4):P15

Content type: Poster presentation Published on: 23 July 2010
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Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine antibiotic resistance genotypes

Authors: Leon Dent, Dana Marshall, Robert Hulette and Siddharth Pratap

Citation: BMC Bioinformatics 2010 11(Suppl 4):P16

Content type: Poster presentation Published on: 23 July 2010
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A Bayesian change-point algorithm for detecting copy number alteration

Authors: Fridtjof Thomas and Stanley Pounds

Citation: BMC Bioinformatics 2010 11(Suppl 4):P17

Content type: Poster presentation Published on: 23 July 2010
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A two-step approach to qPCR experimental design and software for data analysis

Authors: Huazhang Guo, Larry Tague, Ramesh Ray and Gabor Tigyi

Citation: BMC Bioinformatics 2010 11(Suppl 4):P18

Content type: Poster presentation Published on: 23 July 2010
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Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection

Authors: Jesse D Ziebarth, Bao Li, Isao Miyairi and Yan Cui

Citation: BMC Bioinformatics 2010 11(Suppl 4):P19

Content type: Poster presentation Published on: 23 July 2010
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The HHMI National Genomics Research Initiative at Western Kentucky University

Authors: Rodney A King, Claire Rinehart and Prasanna Tamarapu Parthasarathy

Citation: BMC Bioinformatics 2010 11(Suppl 4):P20

Content type: Poster presentation Published on: 23 July 2010
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Graph algorithms for machine learning: a case-control study based on prostate cancer populations and high throughput transcriptomic data

Authors: Gary L Rogers, Pablo Moscato and Michael A Langston

Citation: BMC Bioinformatics 2010 11(Suppl 4):P21

Content type: Poster presentation Published on: 23 July 2010
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Understanding molecular recognition and epitope prediction from Information Theoretic approach

Authors: Indranil Mitra and Yan Cui

Citation: BMC Bioinformatics 2010 11(Suppl 4):P22

Content type: Poster presentation Published on: 23 July 2010
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Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes

Authors: Hung-Chung Huang, Siyuan Zheng and Zhongming Zhao

Citation: BMC Bioinformatics 2010 11(Suppl 4):P23

Content type: Poster presentation Published on: 23 July 2010
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Serendipitous discoveries in microarray analysis

Authors: Sally R Ellingson, Charles A Phillips, Randy Glenn, Douglas Swanson, Thomas Ha, Daniel Goldowitz and Michael A Langston

Citation: BMC Bioinformatics 2010 11(Suppl 4):P24

Content type: Poster presentation Published on: 23 July 2010
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The UofL Microarray Facility: merger and new location

Authors: S Waigel, Xiaohong Li, Yinlu Chen, Vennila Arumugam, Nigel GF Cooper and Wolfgang Zacharias

Citation: BMC Bioinformatics 2010 11(Suppl 4):P25

Content type: Poster presentation Published on: 23 July 2010
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Growth hormone induces proliferation in the zebrafish inner ear

Authors: Michael E Smith, Huifang Sun, Julie B Schuck and Shunsuke Moriyama

Citation: BMC Bioinformatics 2010 11(Suppl 4):P26

Content type: Poster presentation Published on: 23 July 2010
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Development of tools for the automated analysis of spectra generated by tandem mass spectrometry

Authors: Sally Ellingson, Joe Hughes, Dylan Storey, Rick Weber and Nathan VerBerkmoes

Citation: BMC Bioinformatics 2010 11(Suppl 4):P27

Content type: Poster presentation Published on: 23 July 2010
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Do pathogenic bacteria encode more secreted proteins than their non-pathogenic relatives?

Authors: Ahmed Abo-Bakr Mahmoud and Ramy Karam Aziz

Citation: BMC Bioinformatics 2010 11(Suppl 4):P28

Content type: Poster presentation Published on: 23 July 2010
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Enabling proteomics-based identification of human cancer variations

Authors: Jing Li, Zeqiang Ma, Robbert JC Slebos, David L Tabb, Daniel C Liebler and Bing Zhang

Citation: BMC Bioinformatics 2010 11(Suppl 4):P29

Content type: Poster presentation Published on: 23 July 2010
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Statistical analysis of multiple significance test methods for differential proteomics

Authors: Bing Wang, Fahim Mohammad, Jun Zhang, Xinmin Yin, Eric Rouchka and Xiang Zhang

Citation: BMC Bioinformatics 2010 11(Suppl 4):P30

Content type: Poster presentation Published on: 23 July 2010
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Design of a DNA-based shift register

Authors: Christy M Gearheart, Eric C Rouchka and Benjamin Arazi

Citation: BMC Bioinformatics 2010 11(Suppl 4):P31

Content type: Poster presentation Published on: 23 July 2010
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