Accepted Posters

Category 'D'- Comparative Genomics'
Poster D01
Comparative genomics of cell envelope components in Mycobacteria
Pankaj Vats- Centre for Development of Advanced Computing
Sonal Dahale (Centre for Development of Advanced Computing, Bioinformatics Team); Ruma Banerjee (Centre for Development of Advanced Computing, Bioinformatics Team); Sunitha Manjari Kasibhatla (Centre for Development of Advanced Computing, Bioinformatics Team); Rajendra Joshi (Centre for Development of Advanced Computing, Bioinformatics Team);
Short Abstract: Comparative genomics of 21-mycobacterial genomes with a focus on genes involved in biosynthesis of cell envelope components was carried out using phylogenetic profiling. The genomes were earlier curated to include genes in the context of metabolic pathways using MetaCyc, SSEARCH and PubMed. Novel functional linkages were discovered which correlated with microarray coexpression values.
Long Abstract:Click Here

Poster D02
Context dependent substitution biases vary across the genome
P. Nevarez- Harvey Mudd College
Benjamin Freeland (Harvey Mudd College, Biology); Eliot Bush (Harvey Mudd College, Biology);
Short Abstract: We have developed a method to measure nucleotide substitution biases up to the 5 bp scale, and used it to study the substitution process in humans after the divergence from chimpanzee. We find that substantial context effects exist above 2 bp, and that these effects vary across the genome.
Long Abstract:Click Here

Poster D03
miRConSeq: A microRNA-Seq analysis portal with comparative studies
Namshin Kim- KRIBB
Sanghyuk Lee (KRIBB, KOBIC); Sungsoo Kang (KRIBB, KOBIC); Sang-Yoon Kim (KRIBB, KOBIC); Yong Lee (KRIBB, KOBIC); Hak-Min Kim (KRIBB, KOBIC); Dae-Soo Kim (KRIBB, KOBIC); Woo-Yeon Kim (KRIBB, KOBIC);
Short Abstract: To support microRNA biologists, we developed miRConSeq, a microRNA-Seq analysis portal. It features (1) annotation of known microRNAs including their annotation in miRBase, (2) prediction of novel microRNAs based on their secondary structures from the Vienna RNAFold program, and (3) comparative map of known and novel microRNAs.
Long Abstract:Click Here

Poster D04
Curating the Rat Genome: RGD’s Automated Data Integration Pipelines Maximize Coverage
Marek Tutaj- The Medical College of Wisconsin
Mary Shimoyama (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Elizabeth Worthey (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Jennifer Smith (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Rajni Nigam (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Victoria Petri (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Stan Laulederkind (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Tim Lowry (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Tom Hayman (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Shur-Jen Wang (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Jeff De Pons (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Pushkala Jayaraman (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Weisong Liu (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Diane Munzenmaier (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Melinda Dwinell (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Simon Twigger (The Medical College of Wisconsin, The Human and Molecular Genetics Center); Howard Jacob (The Medical College of Wisconsin, The Human and Molecular Genetics Center);
Short Abstract: RGD's automated data integration pipelines maximize coverage to provide comprehensive genome-wide functional and structural information with minimal human interference on a periodic basis
Long Abstract:Click Here

Poster D05
Correlation between Gene-Gene Functional Association Patterns and Ecological Traits of Prokaryotes
Yaming Lin- Georgia Institute of Technology
Hongwei Wu (Georgia Institute of Technology, School of Electrical and Computer Engineering);
Short Abstract: Gene-gene functional association was first quantified using a stochastic model describing gene arrangements on the chromosome. ANOVA, phylogentic analysis, and prediction tests were then performed to identify those gene pairs whose functional association measures are correlated with certain ecological traits but are independent of the phylogenetic origins of the genomes.
Long Abstract:Click Here

Poster D06
Biologically applied filter level interpretation of lung cancer data reveals markers for onset and progression
Kevin Thompson- UNC-Charlotte
No additional authors
Short Abstract: We have implemented the BaFL pipeline for the publically available Bhattacharjee lung cancer dataset. The pipeline identifies putative confounding factors for the probe-transcript hybridization reaction, and thereby eliminates false reactions and biological variation not correlated with the disease. This facilitates the robustness of statistical analysis and experimental conformation.
Long Abstract:Click Here

Poster D07
RECOG: Research Environment for Comparative Genomics
Ikuo Uchiyama- National Institute for Basic Biology
Mikihiko Kawai (National Institute for Basic Biology, Laboratory of Genome Informatics);
Short Abstract: RECOG is a general comparative genomics tool based on large-scale ortholog table. In RECOG, various comparative analysis functions such as phylogenetic pattern analysis are performed through ortholog table operations including filtering, sorting, and coloring. RECOG also contains several unique features particularly useful for closely related genome comparison and metagenomic analysis.
Long Abstract:Click Here

Poster D08
The Rat Genome Database – Genome Browser
Pushkala Jayaraman- Medical College of Wisconsin
Elizabeth Worthey (Medical College of Wisconsin, The Human and Molecular Genetics Center); Mary Shimoyama (Medical College of Wisconsin, The Human and Molecular Genetics Center); Jennifer Smith (Medical College of Wisconsin, The Human and Molecular Genetics Center); Rajni Nigam (Medical College of Wisconsin, The Human and Molecular Genetics Center); Victoria Petri (Medical College of Wisconsin, The Human and Molecular Genetics Center); Stan Laulederkind (Medical College of Wisconsin, The Human and Molecular Genetics Center); Tim Lowry (Medical College of Wisconsin, The Human and Molecular Genetics Center); Tom Hayman (Medical College of Wisconsin, The Human and Molecular Genetics Center); Shur-Jen Wang (Medical College of Wisconsin, The Human and Molecular Genetics Center); Jeff DePons (Medical College of Wisconsin, The Human and Molecular Genetics Center); Marek Tutaj (Medical College of Wisconsin, The Human and Molecular Genetics Center); Weisong Liu (Medical College of Wisconsin, The Human and Molecular Genetics Center); Diane Munzenmaier (Medical College of Wisconsin, The Human and Molecular Genetics Center); Melinda Dwinell (Medical College of Wisconsin, The Human and Molecular Genetics Center); Simon Twigger (Medical College of Wisconsin, The Human and Molecular Genetics Center); Howard Jacob (Medical College of Wisconsin, The Human and Molecular Genetics Center);
Short Abstract: This presentation conveys the importance of the Genome Browser at the Rat Genome Database not only as a visualization tool but also a means of comparative analysis. New data tracks will simplify the analysis of strain specific data to further the users' insight into the relationship between genotype and phenotype
Long Abstract:Click Here

Poster D09
Gene Order Comparison With Contigs And Scaffolds
Adriana Munoz- University of Ottawa
Qian Zhu (Princeton University, Computer Science); Victor Albert (University at Buffalo, Biological Sciences); Chunfang Zheng (Universite de Montreal, DIRO); Steve Rounsley (University of Arizona, School of Plant Sciences and BIO5 Institute); David Sankoff (University of Ottawa, Mathematics and Statistics);
Short Abstract: The trend toward publishing genomes in rough draft form only undermines comparative genomics based on complete gene order data. We show how to use comparative data to insert missing genes into scaffold gaps and to assemble scaffolds into larger assemblages, approaching full chromosomes. This is applied to the castor bean/grapevine comparison.
Long Abstract:Click Here

Poster D10
Hybrid assembly of bacterial genomes using optical map, 454 and Illumina sequences
William Hsiao- Institute for Genome Sciences
Art Delcher (University of Maryland, College Park, Center for Bioinformatics and Computational Biology); Elliott Drabek (University of Maryland, Baltimore, Institute for Genome Sciences); Claire Fraser-Liggett (University of Maryland, Baltimore, Institute for Genome Sciences);
Short Abstract: We have developed a suite of tools to assemble bacterial genomes using sequences from 454 and Illumina platforms, assisted by optical maps. In the case of three Bacteroides thetaiotaomicron genomes, despite limited long-paired-end data, we have been able to produce a single scaffold covering, on average, >95% of the chromosome.
Long Abstract:Click Here

Poster D11
Evolution of Regulation in Primates
Nathan Sheffield- Program in Computational Biology and Bioinformatics
Yoichiro Shibata (Duke University, Institute for Genome Sciences and Policy); Olivier Fedrigo (Duke University, Institute for Genome Sciences and Policy); Greg Wray (Duke University, Institute for Genome Sciences and Policy); Greg Crawford (Duke University, Institute for Genome Sciences and Policy); Terry Furey (Duke University, Institute for Genome Sciences and Policy);
Short Abstract: We explored regulation and expression in 3 primate species through matched-sample DNase-seq and DGE-tag expression experiments. We compared DNase hypersensitivity, expression, and selection differences among the species. We found species-specific DNase-hypersensitive gains and losses in all 3 species, preferentially located in intergenic and intronic regions.
Long Abstract:Click Here

Poster D12
Detecting rare copy number variations (CNVs) with sparse coding
Andreas Mitterecker- Johannes Kepler University
Djork-Arné Clevert (Johannes Kepler University, Bioinformatics); Andreas Mayr (Johannes Kepler University, Bioinformatics); An De Bondt (Johnson & Johnson Pharmaceutical Research & Development, Janssen Pharmaceutica); Willem Talloen (Johnson & Johnson Pharmaceutical Research & Development, Janssen Pharmaceutica); Hinrich Göhlmann (Johnson & Johnson Pharmaceutical Research & Development, Janssen Pharmaceutica); Sepp Hochreiter (Johannes Kepler University, Bioinformatics);
Short Abstract: We generalize the copy number variation (CNV) detection method cn.FARMS for Affymetrix genotyping arrays to Laplacian distribution of CNVs. The Laplacian distribution captures also cases where only few variants are present in a cohort. On the HapMap datasets we confirm most known CNVs, found new ones, but also identified many false positives.
Long Abstract:Click Here

Poster D13
Detection of gene orthology from gene co-expression and protein interaction networks
Fadi Towfic- Bioinformatics and Computational Biology Graduate Program/Iowa State University
Susan VanderPlas (Iowa State University, Bioinformatics and Computational Biology Graduate Program); Casey Oliver (Susquehanna University, Department of Mathematical Sciences); Oliver Couture (Iowa State University, Department of Animal Science); Christopher Tuggle (Iowa State University, Department of Animal Science); M. Heather West-Greenlee (Iowa State University, Department of Biomedical Sciences); Vasant Honavar (Iowa State University, Department of Computer Science);
Short Abstract: Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across divergent organisms. We exploit features derived from the alignment of protein-protein interaction and gene-coexpression networks to reconstruct KEGG orthologs for fly, yeast, mouse, human and pig networks using 5 different machine learning classifiers.
Long Abstract:Click Here

Poster D14
cn.FARMS - a probabilistic model to detect DNA copy numbers
Djork-Arne Clevert- Johannes Kepler University Linz
Djork-Arné Clevert (Johannes Kepler University Linz, Institute of Bioinformatics); Marianne Tuefferd (Johnson & Johnson , Pharmaceutical Research & Development); An De Bondt (Johnson & Johnson , Pharmaceutical Research & Development); Willem Talloen (Johnson & Johnson , Pharmaceutical Research & Development); Hinrich W.H. Göhlmann (Johnson & Johnson , Pharmaceutical Research & Development); Robert Burger (Johannes Kepler University Linz, Institute of Bioinformatics); Sepp Hochreiter (Johannes Kepler University Linz, Institute of Bioinformatics);
Short Abstract: High-density oligonucleotide genotyping microarrays, especially Affymetrix SNP6 chips, are widely used for high-resolution copy number analysis (CN) and are extremely relevant in medical research. In order to identify copy number variations (CNVs) more reliable, we have developed a Maximum a posteriori factor analysis model called cn.FARMS.
Long Abstract:Click Here

Poster D15
Bacterial whole-genome probabilistic alignment
Colin Dewey- University of Wisconsin-Madison
Farzad Rastegar (University of Wisconsin-Madison, Computer Sciences);
Short Abstract: We present a novel method for whole genome probabilistic alignment that simultaneously models the events of substitution, insertion, deletion, rearrangement, and duplication. The method is capable of aligning pairs of bacterial-sized genomes, learns its parameters from the input data, and provides estimates of confidence on components of the alignment.
Long Abstract:Click Here

Poster D16
Expression profiling of oilseeds using next-generation sequencing
Xia Cao- Michigan State University
Nicholas Thrower (Michigan State University, GLBRC); Curtis Wilkerson (Michigan State University, Plant Biology); John Ohlrogge (Michigan State University, Plant Biology);
Short Abstract: We studied reproducibility of next-generation sequencing from replicates for both model and non-model plant oilseeds, and investigated the effect of oligo dT primer and random priming on expression profiling of transcriptome. The results show sequencing data are highly reproducible but random priming poses potential problems for quantitative analysis of transcription.
Long Abstract:Click Here

Poster D17
Identifying copy number variations based on next generation sequencing data by a mixture of Poisson model
Karin Schwarzbauer- Johannes Kepler Universität Linz
Günter Klambauer (Johannes Kepler Universität Linz, Institute of Bioinformatics); Andreas Mayr (Johannes Kepler Universität Linz, Institute of Bioinformatics); Sepp Hochreiter (Johannes Kepler Universität Linz, Institute of Bioinformatics);
Short Abstract: We present an algorithm to identify copy number variations (CNVs) in HapMap samples
based on next generation sequencing data. A mixture of Poisson
model extracts locations on the chromosome with high variation of read
counts which are associated with CNVs. Our method is in agreement
with array based detection methods.
Long Abstract:Click Here

Poster D18
Potential drug targets in Mycobacterium tuberculosis through comparative genome analysis of three KZN strains.
Alan Christoffels- University of the Western Cape
Ruben Cloete (University of the Western Cape, South African National Bioinformatics Institute); Ekow Oppon (Medical Research Council of South Africa, Biomedical Informatics and Research Division);
Short Abstract: We have downloaded the whole genome sequences for 3 South Africa multi-drug resistant strains of TB, KZN605, MDR-KZN1435, and DS-KZN 4207. Drug resistance metabolic pathways of first and second-line anti-TB drugs were identified. We describe the selection of 6 genes as novel targets and application of homology modeling.
Long Abstract:Click Here

Poster D19
Microbial Variome Database: All Genetic Variations in a Species at One Glance.
Sujay Chattopadhyay- University of Washington
Scott Weissman (University of Washington, Microbiology); Fred Taub (University of Washington, Microbiology); Evgeni Sokurenko (University of Washington, Microbiology);
Short Abstract: Detecting adaptive polymorphisms in strains of a bacterial species is crucial to understanding virulence evolution and selecting novel therapeutic targets. To address this need, we establish Microbial Variome Database – a species-specific genomic resource database, applying population genomics to experimental research, clinical diagnostics, epidemiology, and environmental control of human pathogens.
Long Abstract:Click Here

Poster D20
Bacterial Phylogenomics
Robert Stones- FERA
No additional authors
Short Abstract: Advances in next generation DNA sequencing, enabling rapid sequencing of complete bacterial genomes, has given tremendous opportunities for whole comparative genomics studies; important to clinical and regulatory science agencies.

We have developed analytical tools/pipelines to compare bacterial genomes, and construct phylogenies of whole genomes.
Long Abstract:Click Here

Poster D21
A global network of coexisting microbes from environmental and whole-genome sequence data
Samuel Chaffron- University of Zurich
Hubert Rehrauer (UZH - ETH, Functional Genomics Center Zurich); Jakob Pernthaler (UZH, Limnological Station of the Institute of Plant Biology); Christian von Mering (UZH, IMLS);
Short Abstract: Environmental preferences and ecological interdependencies of microorganisms remain difficult to assess. Here we present a global co-occurrence analysis of previously sampled microbial lineages. Naturally occurring microbes indeed exhibited numerous, significant inter-lineage associations. Genomes from coexisting microbes tended to be more similar, both with respect to pathway content and genome size.
Long Abstract:Click Here

Poster D22
GC-wave correction algorithm for microarray-based comparative genomic hybridization
Angela Leo- Genzyme
Andrew Walker (Genzyme, Research and Development); Minggeng Gao (Genzyme, Research and Development); Thomas Scholl (Genzyme, Research and Development); Viatcheslav R Akmaev (Genzyme, Research and Development);
Short Abstract: aCGH data has artifacts or 'waves' caused by individual probe log ratios deviating from zero in diploid regions. We developed a GC-wave correction algorithm to normalize the log ratios, thereby reducing the waves. Our correction allows aberration detection methods to detect smaller aberrant regions with increased confidence and reproducibility.
Long Abstract:Click Here

Poster D23
Function conservation in diverged noncoding elements
Leila Taher- NCBI/NLM/NIH
David McGaughey (Johns Hopkins Medical Institute, McKusick-Nathans Institute for Genetic Medicine); Samantha Maragh (Johns Hopkins Medical Institute, McKusick-Nathans Institute for Genetic Medicine); Marcelo Nobrega (The University of Chicago, Human Genetics); Andrew McCallion (Johns Hopkins Medical Institute, McKusick-Nathans Institute for Genetic Medicine); Ivan Ovcharenko (NIH, NCBI/NLM);
Short Abstract: Lack of evolutionary sequence conservation does not necessarily imply lack of function. To uncover functional identity of diverged regulatory regions, we model genomic sequences as arrangements of transcription factor binding sites. We apply our method to reveal hidden ancestral relationships among 300 pairs of noncoding human and zebrafish sequences.
Long Abstract:Click Here

Poster D24
Detecting Between-Pathway Model conservation across S. cerevisiae and S. pombe yeast species
Daniel Malmer- Tufts University
Benjamin Hescott (Tufts University, Computer Science); Lenore Cowen (Tufts University, Computer Science); Mark Leiserson (Tufts University, Computer Science);
Short Abstract: The Between-Pathway Model (BPM) motif identifies pairs of fault-tolerant gene pathways in the yeast interactome. Algorithms have been used to find BPMs in the Saccharomyces cerevisiae and Schizosaccharomyces pombe species of yeast. Here we identify and apply a method for finding conservation of BPMs across these two species.
Long Abstract:Click Here

Poster D25
POLYMORPHISM ANALYSIS OF WHEAT RUST FUNGI
Sharadha Sakthikumar- Broad Institute of MIT and Harvard
Manfred Grabherr (Broad Institute of MIT and Harvard, GSAP); David Heiman (Broad Institute of MIT and Harvard, GSAP); Evan Mauceli (Broad Institute of MIT and Harvard, GSAP); Zehua Chen (Broad Institute of MIT and Harvard, GSAP); Sarah Young (Broad Institute of MIT and Harvard, GSAP); Qiandong Zeng (Broad Institute of MIT and Harvard, GSAP); Bruce Birren (Broad Institute of MIT and Harvard, GSAP); Guus Bakkeren (Agriculture & Agri-Food Canada, -); Xianming Chen (USDA-ARS, Wheat Genetics, Quality, Physiology, and Disease Research Unit); John Fellers (USDA-ARS, -); Scot Hulbert (Washington State University, Plant Pathology); Les Szabo (Univ. of Minnesota, Cereal Disease Laboratory); Christina Cuomo (Broad Institute of MIT and Harvard, GSAP);
Short Abstract: Polymorphic analysis and characterization of the variation of virulent rust fungi strains may help identify factors that are responsible for overcoming the stem rust resistance genes of wheat.
Long Abstract:Click Here

Poster D26
Identification of gene transfers and duplications in closely related bacterial pathogens
Joshua Earl- Allegheny-Singer Research Institute
Maureen Stolzer (Carnegie Mellon University, Biological Sciences); Benjamin Vernot (Carnegie Mellon University, Biological Sciences); Luisa Hiller (Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences); Garth Ehrlich (Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences); Dannie Durand (Carnegie Mellon University, Biological and Computer Sciences);
Short Abstract: We investigate horizontal transfer and gene duplication in 23
strains of Streptococcus pneumoniae, a biofilm-forming pathogen,
through genome-scale comparison of gene and strain trees using
Notung. Strain trees were created through sequence comparison of
core gene families and phylogenetic profiling of distributed
families.
Long Abstract:Click Here

Poster D27
N-gram Analysis of 970 Microbial Organisms Reveals Presence of Biological Language Model
Hatice Osmanbeyoglu- University of Pittsburgh
Thahir Mohamed (University of Pittsburgh, Intelligent Systems Program); Madhavi Ganapathiraju (University of Pittsburgh, Biomedical Informatics);
Short Abstract: Biological language modeling using n-grams has been suggested to reveal genome signatures. Our analysis on 970 microbial organisms illustrates that unigram distribution of amino acids shows a genus-level signature. Further a statistical measure called cross-perplexity has been found to be predictive of genus level branch distance on evolutionary tree.
Long Abstract:Click Here

Poster D28
Comparative genomics of dormancy regulation in Mycobacteriaceae and Nocardiaceae
Anna Gerasimova- Lawerence Berkeley National Laboratory
Alexey Kazakov (Institute for Information Transmission Problems , RAS); Adam Arkin (Lawrence Berkeley National Laboratory, Physical Biosciences Division); Inna Dubchak (Lawrence Berkeley National Laboratory, Physical Biosciences Division); Mikhail Gelfand (Institute for Information Transmission Problems, RAS);
Short Abstract: In response to hypoxia Mycobacterium cells become dormant. In M. tuberculosis dormancy is well-characterized, and it was shown to be regulated by DevR. We described the DevR-regulon in nine Mycobacteriaceae, two Nocardiaceae and S.erythraea; predicted new regulon members and carried out functional evolutionary analysis of large families of regulated proteins.
Long Abstract:Click Here

Poster D29
Evidence of Widespread Stop Codon Readthrough in Drosophila
Irwin Jungreis- MIT
Irwin Jungreis (MIT, Computer Science and Artificial Intelligence Laboratory);
Short Abstract: Comparative genomics suggests hundreds of Drosophila genes undergo translational stop codon readthrough. This was suggested in our 2007 Genome Research paper in which we compared genomes of 12 species of Drosophila to determine protein coding regions. One of our findings was that for 149 genes the ORF following the stop codon has a protein-coding conservation signature, suggesting possible translational stop codon readthrough. Although readthrough was known to occur for isolated genes in various species, it had not previously been thought to be so widespread in any species.

We have returned to this observation armed with an improved higher-resolution comparative genomics metric for detecting coding regions, and other computational tools. We have expanded the list of Drosophila genes that display this phenomenon to 283, found additional evidence that these post-stop codon regions are protein coding, and ruled out alternative explanations including alternative splicing, dicistronic translation, and RNA editing. We have also found 19 examples that appear to be double readthrough.

Various properties distinguish our readthrough candidates from other genes:
- Unusual 4-base stop codon context distribution.
- Stop codon is extremely well conserved.
- They are longer and have longer 3'- and 5'-UTRs.
- A few have conserved stem loops soon after the stop codon.

Other insects show the signature of readthrough for several of the Drosophila candidate genes. We have found isolated examples in mammals and nematodes, but not the widespread readthrough exhibited by Drosophila.

Finally, we consider the likely amino acid sequence produced when the readthrough genes are translated.
Long Abstract:Click Here

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