| Poster D02 |
| cn.FARMS - a probabilistic model to detect DNA copy numbers |
| Djork Clevert- Johannes Kepler University Linz |
| Djork-Arné Clevert (Johannes Kepler University Linz, Institute of Bioinformatics); Marianne Tuefferd (Johnson & Johnson Pharmaceutical Research & Development, Pharmaceutical Research & Development); An De Bondt (Johnson & Johnson Pharmaceutical Research & Development, Pharmaceutical Research & Development); Willem Talloen (Johnson & Johnson Pharmaceutical Research & Development, Pharmaceutical Research & Development); Hinrich W.H. Göhlmann (Johnson & Johnson Pharmaceutical Research & Development, Pharmaceutical Research & Development); Sepp Hochreiter (Johannes Kepler University Linz, Institute of Bioinformatics); |
| Short Abstract: High-density oligonucleotide microarrays, and in particular Affymetrix Mapping or SNP arrays offer the opportunity to get a genome-wide view on copy number alterations and are increasingly used in oncology. We present a probabilistic latent variable model, called cn.FARMS, that takes probe level information to model the the correlation in the observed data. |
| Long Abstract: Click Here |
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| Poster D05 |
| HCOP: A one stop orthology shop |
| Michael Lush- European Bioinformatics Institute, |
| Susan Gordon (European Bioinformatics Institute,, HGNC); Ruth Seal (European Bioinformatics Institute,, HGNC); Matt Wright (European Bioinformatics Institute,, HGNC); Elspeth Bruford (European Bioinformatics Institute,, HGNC); |
| Short Abstract: The HUGO Gene Nomenclature Committee (HGNC) promotes the use of the samename and symbol for orthologous genes in other species. We have developedthe HCOP search tool, which allows rapid survey of orthology assertionsfor a given gene or group of genes . |
| Long Abstract: Click Here |
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| Poster D06 |
| Microbial genome sequence analysis in a high-speed process |
| Jessica Schneider- Center for Biotechnology (CeBiTec) |
| Jochen Blom (Center for Biotechnology, Computational Genomics); Eva Trost (Center for Biotechnology, Systems Biology of Regulatory Networks); Andreas Tauch (Center for Biotechnology, Systems Biology of Regulatory Networks); Alexander Goesmann (Center for Biotechnology, Computational Genomics); |
| Short Abstract: New sequencing strategies provide ultrafast access to microbial genome sequences. For their interpretation an efficient bioinformatics pipeline based on comparative genome approaches is required. Starting with the assembly and annotation of a new sequenced genome using GenDB, the software tools CARMEN and EDGAR facilitate further functional and comparative genome analysis. |
| Long Abstract: Click Here |
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| Poster D07 |
| Phylogenomic inference of functional divergence |
| Tom Williams- Trinity College Dublin |
| Brian E. Caffrey (Trinity College Dublin, Smurfit Institute of Genetics); Xiaowei Jiang (Trinity College Dublin, Smurfit Institute of Genetics); Christina Toft (Trinity College Dublin, Smurfit Institute of Genetics); Mario A. Fares (Trinity College Dublin, Smurfit Institute of Genetics); |
| Short Abstract: The identification of proteins under functional divergence is of broad interest. We present a fast new method for detecting these changes at the whole-genome level across a complex phylogenetic tree. We demonstrate the usefulness of the method through application to the evolution of pathogenicity in divergent bacterial lineages. |
| Long Abstract: Click Here |
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| Poster D08 |
| Comparative Analysis of the Burkholderia pseudomallei Core Genome |
| Tannistha Nandi- Genome Institute of Singapore |
| Catherine Ong Ee Ling (Defense Medical and Environmental Research Institute, Infectious Diseases); Hui Hoon Chua (Genome Institute of Singapore, Infectious Diseases); Jason Kriesberg (Genome Institute of Singapore, Infectious Diseases); Patrick Tan (Genome Institute of Singapore, Infectious Diseases); Paul Keim (Northern Arizona University, Center for Microbial Genetics and Genomics); Talima Ross Pearson (Northern Arizona University, Center for Microbial Genetics and Genomics); William Nierman (J. Craig Venter Institute (JCVI), Infectious Diseases); |
| Short Abstract: Multi-genome comparison of Burkholderia pseudomallei strains. This often causes a fatal disease called meliodosis in humans, endemic in Southeast Asia and Northern Australia. |
| Long Abstract: Click Here |
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| Poster D09 |
| Evolution of structure and sequence in alternatively spliced Drosophila genes |
| Ekaterina Ermakova- Institute for Information Transmission Problems (The Kharkevich Institute) |
| Dmitry Malko (State Research Institute of Genetics and Selection of Industrial Microorganisms, Laboratory of Bioinformatics); Mikhail Gelfand (Institute for Information Transmission Problems (The Kharkevich Institute), Research and Training Center on Bioinformatics); |
| Short Abstract: Gain and loss of introns, constitutive and alternatively spliced coding regions, and nucleotide substitutions in constitutively and alternatively spliced coding regions were considered in twelve Drosophila genomes. The rearrangement rates may differ dramatically even in recently diverged species. The substitution rates depend on the type of alternative regions. |
| Long Abstract: Click Here |
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| Poster D12 |
| The ABCG tranporter proteins in Plasmodium: Phylogenomic Analises |
| Ricardo Gonzalez Mendez- University of Puerto Rico School of Medicine |
| Adelfa Serrano (University of Puerto Rico School of Medicine, Microbiology); Hugh Nicholas, Jr. (Pittsburgh Supercomputing Center, National Resource for Biomedical Supercomputing); Alexander Ropelewski (Pittsburgh Supercomputing Center, National Resource for Biomedical Supercomputing); Roxana Cintron Moret (University of Georgia, Department of Cellular Biology); |
| Short Abstract: The ATP-binding cassette, subfamily G (ABCG family), has five members. Sequence analyses and phylogenetic studies were done in Plasmodium species. These analyses show that the ABCG protein found in Plasmodium is a member of the ABCG1 subfamily. These results have important implications for the theories of drug resistance in Plasmodium. |
| Long Abstract: Click Here |
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| Poster D13 |
| In-Silico Development of PCR Primers for Detection of Endogenous Para-Retroviruses & Episomal Viral Sequences |
| Angela Eni- Covenant University |
| Ijeoma Dike (Covenant University, Biological Sciences); Conrad Omonhinmin (Covenant University, Biological Sciences); Shalom Chinedu (Covenant University, Biological Sciences); Olubanke Ogulana (Covenant University, Biological Sciences); Segun Fatumo (Covenant University, Computer and Information Sciences); Ezekiel Adebiyi (Covenant University, Computer and Information Sciences); Abiodun Adebayo (Covenant University, Biological Sciences); |
| Short Abstract: Dioscorea spp serve as food for millions of West-Africans yet yam-viruses are a constraint to yam production. In-silico PCR-primer designing employing sequences of the conserved regions for the detection of EPRVs and episomal badnavirus sequences is proposed and will be implemented using ClustalX, Expression software and primer efficiency tested In-Silico. |
| Long Abstract: Click Here |
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| Poster D14 |
| Human microRNAs with similarity to box H/ACA small nucleolar RNAs |
| Michelle Scott- University of Dundee |
| Fabio Avolio (Univeristy of Dundee, GRE); Motoharu Ono (Univeristy of Dundee, GRE); Angus I Lamond (Univeristy of Dundee, GRE); Geoffrey J Barton (Univeristy of Dundee, BCDD); |
| Short Abstract: By computational analysis, we identified miRNA precursors with significant similarity to snoRNAs, both on the level of their genomic context and predicted folded structure. Some of these miRNA precursors bind dyskerin, a protein that functionally associates with snoRNAs, strengthening the possibility of an evolutionary relationship between some miRNAs and snoRNAs. |
| Long Abstract: Click Here |
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| Poster D18 |
| Structure-function conservation of steroidogenic systems of plants and animals: phylogeny of the main components |
| George Shpakovski- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences |
| Irina N. Berdichevets (Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Laboratory of Molecular Genetics); Nikolai A. Kartel (Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Laboratory of Molecular Genetics); Elena K. Shematorova (Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Laboratory of Mechanisms of Gene Expression); Dmitry G. Shpakovski (Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Laboratory of Mechanisms of Gene Expression); Svetlana G. Spivak (Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 3Laboratory of Lipids Chemistry); |
| Short Abstract: Phylogenetic analysis of all main components of sterol biogenesis in plants and animals was used to uncover the common stages and catalysed reactions. Steroid-5[alpha]-reductase, 3[beta]-hydroxysteroiddehydrogenase/[delta]5-4isomerase, 11[beta] |
| Long Abstract: Click Here |
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| Poster D22 |
| Benchmarking of Methods for the Identification of Orthologs |
| Sabine Thuss- Heinrich Heine Universitaet Duesseldorf |
| Nina Levar (Heinrich Heine Universitaet Duesseldorf, - ); Christian Esser (Heinrich Heine Universitaet Duesseldorf , Institut fuer Botanik III ); Dr. Tal Dagan (Heinrich Heine Universitaet Duesseldorf , Institut fuer Botanik III ); Prof. Dr. Martin J. Lercher (Heinrich Heine Universitaet Duesseldorf, Lehrstuhl fuer Bioinformatik); |
| Short Abstract: We compare four methods for the identification of orthologous genes. A non-standard application of the Markov Cluster Algorithm (MCL), as well as a method combining sequence similarity and synteny, lead to many more complete clusters and fewer singletons than the other tested methods. |
| Long Abstract: Click Here |
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| Poster D23 |
| A High Performance E-Cluster BLAST System |
| Tae-Kyung Kim- Chungbuk National University |
| Chi-Whan Choi (Chungbuk National University, Bioinformatics); Hun-Gi Kim (Chungbuk National University, Bioinformatics); Wan-Sup Cho (Chungbuk National University, MIS/BK21 Team); |
| Short Abstract: We propose a novel BLAST cluster architecture on top of E-Cluster, which consists of dynamic number of PCs. We adopt a logical partitioning and intra-query parallelism on E-Cluster. A proposed BLAST is much superior to conventional grid or cluster BLAST systems in terms of manageability, performances and expenses. |
| Long Abstract: Click Here |
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| Poster D24 |
| Visual and Statistical Comparison of Metagenomes with MEGAN 3 |
| Suparna Mitra- Center for Bioinformatics (ZBIT), Tuebingen University |
| Daniel Richter (Center for Bioinformatics (ZBIT), Tuebingen University, Computer Science Department); Alexander Auch (Center for Bioinformatics (ZBIT), Tuebingen University, Computer Science Department); Stephan Schuster (Center for Comparative Genomics, Center for Infectious Disease Dynamics, PennState University); Daniel Huson (Center for Bioinformatics (ZBIT), Tuebingen University, Computer Science Department); |
| Short Abstract: MEGAN (MEtaGenome Analyzer) is a powerful computer program that allows laptop analysis of large metagenomics datasets providing taxonomic and functional analysis. It has an interactive and fully customizable chart viewer and also allows visual and statistical comparative analysis of different metagenomes. |
| Long Abstract: Click Here |
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