ISMB 2008 ISCB


















Accepted Posters
Category 'J'- Genomics'
Poster J01
Towards investigation of the evolution of nitrogen fixation using condensed matrix method and probing for the unit of selection
Arnab Sen- University of North Bengal
Saubashya Sur (University of North Bengal, NBU Bioinformatics Facility); Asim Bothra (Raiganj College, Chemistry); Uttam Mondal (Raiganj College, Chemistry);
Short Abstract: Evolution of nitrogen fixation has been investigated using condensed matrix method. Findings support polyphyly and lateral gene transfer. Mutation and selection occur at different intensities. nif genes did not evolve as a unit. Positive Darwinian selection controls nif D genes while purifying selection influences nif H and nif K.
Long Abstract: Click Here

Poster J02
Computational Prediction of Genes Regulated by LEC1, LEC2, and WRI1 in Oil Seed Plants
Alain Tchagang- National Research Council Canada
Hugo Bérubé (National Research Council Canada, Knowledge Discovery Group, Institute for Information Technology); Fazel Famili (National Research Council Canada, Knowledge Discovery Group, Institute for Information Technology); Youlian Pan (National Research Council Canada, Knowledge Discovery Group, Institute for Information Technology);
Short Abstract: We present a data mining approach for predicting genes that may be regulated by one of the transcription factors, LEC1, LEC2, and WRI1 in Arabidopsis thaliana. This leads to discovery of potential new components in the gene networks controlling fatty acid metabolism and to the potential improvement of oil production.
Long Abstract: Click Here

Poster J03
Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Martin Kircher- Max-Planck-Institute for evolutionary Anthropology
Udo Stenzel (Max-Planck-Institute for evolutionary Anthropology, Evolutionary Genetics/Bioinformatics); Janet Kelso (Max-Planck-Institute for evolutionary Anthropology, Evolutionary Genetics/Bioinformatics);
Short Abstract: Various approaches to base calling have been proposed for the Illumina high-throughput DNA sequencer, which are either limited in accuracy or too time consuming. We show that fast and accurate base calling can be performed without prior modeling of the sequencing chemistry.
Long Abstract: Click Here

Poster J04
First steps towards Barley Genome Sequencing by second generation sequencing technologies
Marius Felder- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI)
Burkhard Steuernagel (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genome Diversity Group); Daniela Schulte (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genome Diversity Group); Andreas Petzold (Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Genome Analysis Group); Heidrun Gundlach (Helmholtz Center Munich, Information Center for Protein Sequences); Uwe Scholz (Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Genome Diversity Group); Mihaela Martis (Helmholtz Center Munich, Information Center for Protein Sequences); Stefan Taudien (Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Genome Analysis Group); Hana Simková (Institute of Experimental Botany, Olomouc , Laboratory of Molecular Cytogenetics and Cytometry); Eva Hřibová (Institute of Experimental Botany, Olomouc , Laboratory of Molecular Cytogenetics and Cytometry); Andreas Graner (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Genome Diversity Group); Jaroslav Dolezel (Institute of Experimental Botany, Olomouc, Laboratory of Molecular Cytogenetics and Cytometry); Klaus Mayer (Helmholtz Center Munich, Information Center for Protein Sequences); Matthias Platzer (Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Genome Analysis Group); Nils Stein (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Genome Diversity Group);
Short Abstract: Within the GABI-BARLEX project we evaluate the efficiency to achieve part of genetic anchoring by high-throughput second generation sequencing of BAC clones. Towards this end, we combine the physical map construction by fingerprinted BAC libraries with massively parallel sequencing of barcoded BAC pools and sorted chromosomes.
Long Abstract: Click Here

Poster J05
Populus DNA digestion with restriction endonucleases in silico
Viktor Tomilov- SibEnzyme Ltd
Elena Savchkova (SibEnzyme Ltd, ); Danila Gonchar (SibEnzyme Ltd, ); Murat Abdurashitov (SibEnzyme Ltd, ); Sergey Degtyarev (SibEnzyme Ltd, );
Short Abstract: In this work we have performed in silico analysis of populus DNA digestion at recognition sequences of restriction enzymes. Theoretical data have been compared to experimental patterns of total populus DNA hydrolysis with respective restriction enzymes and the correspondence has been observed in the most cases.
Long Abstract: Click Here

Poster J06
INCORPORATING EPIGENOMIC INFORMATION TO STUDY THE TRANSCRIPTIONAL REGULATION OF HUMAN MICRORNAS
Xiaowo Wang- Tsinghua University
Yu Liu (Tsinghua Univ., Automation); Michael Zhang (Cold Spring Harbor Laboratory, CSHL); Yanda Li (Tsinghua Univ., Automation);
Short Abstract: By incorporating the information of promoter predictions, histone modifications, DNAse I hypersensitive sites and comparative genomics, we conducted a systematic analysis of the cis-regulatory region of human miRNAs, and constructed a regulatory network between miRNAs and transcription factors.
Long Abstract: Click Here

Poster J07
De novo assembly of short read sequence data using SASSY
Michael Imelfort- The University of Queensland
Daniel Marshall (Australian center for plant functional genomics, Bioinformatics); Chris Duran (Australian center for plant functional genomics, Bioinformatics); David Edwards (Australian center for plant functional genomics, Bioinformatics); Ping Zhang (Australian center for plant functional genomics, Bioinformatics);
Short Abstract: Second generation sequencing (SGS) technology will provide fast cheap genome sequencing. Most SGS projects have focussed on re-sequencing however the majority of organisms have no available reference sequence. We have developed novel algorithms for the de-novo assembly of short read sequence data and we have produced software which implements these algorithms.
Long Abstract: Click Here

Poster J08
Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast
Michael Fernandez- Kyushu Institute of Technology
Satoshi Fujii (Kyushu Institute of Technology (KIT), Department of Bioscience and Bioinformatics); Hidetoshi Kono (Japan Atomic Energy Agency, Computational Biology Group); Akinori Sarai (Kyushu Institute of Technology, Department of Bioscience and Bioinformatics);
Short Abstract: We calculated intramolecular interaction energies of DNA by threading DNA sequences around crystal structures of nucleosomes. The strength of the intramolecular energy oscillations at frequency ~10 bps for dinucleotides was in agreement with previous nucleosome models. The intramolecular energy calculated along yeast genome positively correlated with nucleosome positioning experimentally measured.
Long Abstract: Click Here

Poster J09
Evolutionary histories of gene clusters in primate genomes
Tomas Vinar- Comenius University Bratislava
Brona Brejova (Comenius University Bratislava, Computer Science); Webb Miller (Penn State University, Center for Comparative Genomics and Bioinformatics ); Adam Siepel (Cornell University, Biological Statistics and Computational Biology);
Short Abstract: Complex gene clusters are hotspots of evolutionary innovation andcontain many biomedically important gene families. We propose thatthese clusters should be analyzed in the context of theirduplication histories. We show novel methods forreconstructing the duplication histories from genomic sequences ofmultiple species and use them to analyze several biomedicallyinteresting human gene clusters.
Long Abstract: Click Here

Poster J10
The Mouse Genomes Project Pilot: Short-read sequencing and de novo assembly of chromosome 17 from two inbred mouse strains: A/J and CAST/EiJ
James Stalker- Wellcome Trust Sanger Institute
Ian Sudbery (WTSI, Mouse cancer group); Jared Simpson (WTSI, Informatics); Thomas Keane (WTSI, Informatics); Ian Jackson (MRC Human Genetics Unit, Molecular Genetics); Laura Reinholdt (Jackson Laboratory, Reproductive Genomics); Leah Rae Donahue (Jackson Laboratory, Genetic Resources); Steve Brown (MRC Harwell, Mammalian Genetics Unit); Jonathan Flint (Wellcome Trust Centre for Human Genetics , Neurogenetics & Psychiatric Genetics); Ewan Birney (EMBL-EBI, Informatics); Allan Bradley (WTSI, Mouse Genetics); Zemin Ning (WTSI, Informatics); Richard Durbin (WTSI, Genome Informatics); David Adams (WTSI, Mouse cancer group);
Short Abstract: The Mouse Genomes Project aims to sequence 17 inbred strains to generate complete maps of the nucleotide and structural variation, and ultimately de novo genome assemblies, of each strain. Here we present the pilot sequencing, analysis, and assembly of chromosome 17 from two strains: A/J (domesticus) and CAST/EiJ (castaneus).
Long Abstract: Click Here

Poster J11
Bayesian multiple QTL approach for detecting completely imprinted QTL loci in outbred F2 families
Virpi Ahola- Univerisity of Helsinki
Johanna Vilkki (MTT Agrifood Research Finland, Biotechnoloy and food research); Mikko Sillanpää (University of Helsinki, Department of Mathematics and Statistics);
Short Abstract: The phenomenon called genomic imprinting leads to different expression of a particular allele depending on the parent from which it is inherited. We developed a Bayesian method for detecting imprinted QTL loci in outbred F2 families. The results suggest that the method can flexibly test complete paternal and maternal imprinting.
Long Abstract: Click Here

Poster J12
Analysis of alternative splicing of 3'UTRs defines modules of functional motifs
Fabrizio Ferrè- Università Sapienza
Paolo Marcatili (Università Sapienza, Biochemical Sciences); Domenico Raimondo (Università Sapienza, Biochemical Sciences);
Short Abstract: The generation of alternative 3'UTRs regulates the fate of mRNAs, modulating the presence of motifs (e.g. miRNA binding sites). The distribution of motifs suggests the presence of regulatory modules in which different regulatory regions act in a concerted fashion to govern transcript processes such as translation efficiency, localization, and stability.
Long Abstract: Click Here

Poster J13
In-Silico Analysis of Prospective African Strains of Algae for Bio-Diesel Production
Ijeoma Dike- Covenant University
Conrad Omonhinmin (covenant university, biological science); Ezekiel Adebiyi (covenant university, Computer and Information Sciences); Angela Eni (covenant university, biological science); Shalom Chinedu (covenant university, biological science); Frank Ibikunle (covenant university, Electrical and Information Engineering); Itunu Ekwejobi (covenant university, Computer and Information Sciences); Olubanke Ogulana (covenant university, biological science);
Short Abstract: The rise in fuel rates, projected depletion of oil reserves and mounting environmental pollution, indicates the need for alternate energy sources, of which algae is of priority. Through in-silico genetic analysis, establishment of optimum nutrient supply and environmental conditions, efficient and higher oil-storing capacity of algae will be triggered.
Long Abstract: Click Here

Poster J14
Structure and functions study of human PMS2-related genes and products of their expression
Elena Shematorova- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
Dmitry Shpakovski (Shemyakin-Ovchinnikov Institute Of Bioorganic Chemistry, Russian Academy of Science); George V. Shpakovski (Shemyakin-Ovchinnikov Institute Of Bioorganic Chemistry, Russian Academy of Science);
Short Abstract: Using bioinformatics and experimental approaches all main stages of the molecular evolution of PMS2-related sequences in the Primates lineage were deciphered and direct correlation between amplification and diversification of the PMS2-related genes and the main steps of the higher Primates evolution have been established.
Long Abstract: Click Here

Poster J15
Integration of summary-level gene expression and genetic association data
Johan Rung- EMBL-EBI
Misha Kapushesky (EMBL - EBI, Microarray Informatics group); Maria Krestyaninova (EMBL - EBI, Microarray Informatics group); Alvis Brazma (EMBL - EBI, Microarray Informatics group);
Short Abstract: In genetical genomics, the aim is to discover regulatory mechanisms behind various sample conditions when both genotype and gene expression data have been measured. We present a method to integrate publicly available results from gene expression and genetic association studies to discover such effects even when measured on different samples.
Long Abstract: Click Here

Poster J16
Explore human housekeeping genes with a manually-curated microarray database
Cheng-Wei Chang- National Tsing Hua University
Wei-Chung Cheng (National Tsing Hua University, Biomedical Engineering and Environmental Science); Chaang-Ray Chen (National Tsing Hua University, Biomedical Engineering and Environmental Science); Ming-Lung Tsai (National Tsing Hua University, Biomedical Engineering and Environmental Science); Ian C. Hsu (National Tsing Hua University, Biomedical Engineering and Environmental Science);
Short Abstract: We obtained HK gene lists using 1,714 Affymetrix microarray data of 28 normal human tissues, by analyzing the gene expression with both intensity and present call after raw data were uniformly normalized. Several selection criteria were adjusted to obtain various HK gene lists which were then analyzed by Gene Ontology.
Long Abstract: Click Here

Poster J17
Transcript Quantification with RNA-Seq Data
Regina Bohnert- Friedrich Miescher Laboratory Of The Max Planck Society
Gunnar Rätsch (Friedrich Miescher Laboratory Of The Max Planck Society, Machine Learning in Biology);
Short Abstract: High-throughput sequencing technologies opens exciting new approaches to transcriptome profiling. For the important task of inferring transcript abundances from RNA-Seq data, we developed a new technique based on linear programming. Combined with ab initio gene finding, our method is also a powerful tool to reveal and quantify novel (alternative) transcripts.
Long Abstract: Click Here

Poster J18
Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies
Kenny Daily- University of California, Irvine
Pierre Baldi (University of California, Irvine, Department of Computer Science, Institute for Genomics and Bioinformatics, Department of Biological Chemistry); Xiaohui Xie (University of California, Irvine, Department of Computer Science, Institute for Genomics and Bioinformatics); Paul Rigor (University of California, Irvine, Department of Computer Science, Institute for Genomics and Bioinformatics); Scott Christley (University of California, Irvine, Department of Computer Science, Department of Mathematics);
Short Abstract: The amount of data produced by high throughput sequencing technologies creates significant challenges to store and share these data. We have developed new data structures and entropy coding algorithms for the efficient storage, retrieval, and transmission of the data with factors in the 10-400 range.
Long Abstract: Click Here

Poster J19
DNA methylation status at CpG islands are characterized by histone codes
Inkyung Jung- Korea Advanced Institute Of Science And Technology
No additional authors
Short Abstract: We propose several plausible mechanisms for precise controlling of DNA methylation status at CpG islands. We utilized Bayesian network to construct regulatory network and found several meaningful relationships supported by previous studies. Based on those findings we predicted the status of methylation level at CpG islands with high accuracy.
Long Abstract: Click Here

Poster J20
2d Gaussian convolution identifies a network of co-operating DNA copy number losses.
Christiaan Klijn- Netherlands Cancer Institute
Jan Bot (Delft University of Technology, Information and Communication Theory); David Adams (Wellcome Trust Sanger Institute, Experimental Cancer Genetics); Marcel Reinders (Delft University of Technology, Information and Communication Theory); Lodewyk Wessels (Netherlands Cancer Institute, Molecular Biology); Jos Jonkers (Netherlands Cancer Institute, Molecular Biology);
Short Abstract: In order to develop cancer, multiple simultaneous mutations are necessary. We have analyzed copy number mutation data to find simultaneously occurring changes in the DNA of tumors. Using a genome-wide scoring framework we are able to identify known and novel interacting copy number changes that are related to cancer.
Long Abstract: Click Here

Poster J21
Dynamics in genome organisation during cell differentiation
Wouter Meuleman- Netherlands Cancer Institute / Delft University of Technology
Daan Peric Hupkes (Netherlands Cancer Institute, Gene Regulation); Marcel Reinders (Delft University of Technology, Bioinformatics); Lodewyk Wessels (Netherlands Cancer Institute, Molecular Biology); Bas van Steensel (Netherlands Cancer Institute, Gene Regulation);
Short Abstract: Our data provide a genome-wide view on the spatial reorganisation of the mouse genome during differentiation. We quantify changes in organisation using a statistical test and find they often encompass exactly one gene, reflect cellular state and are strongly linked to changes in gene expression.
Long Abstract: Click Here

Poster J22
Probing M. tuberculosis through transcriptomic data
Luke Yancy Jr- Morehouse College
Robert Riley (Broad Institute of MIT/Harvard, Computational Biology); Brian Weiner (Broad Institute of MIT/Harvard, Computational Biology); Bruce Birren (Broad Institute of MIT/Harvard, Computational Biology);
Short Abstract: Newly accessible gene expression data from Mycobacterium tuberculosis presents an opportunity to learn more about the biological basis of TB. Here, we applied both a biclustering, and a traditional clustering algorithm to Mtb expression data in hopes to eventually produce a global regulatory network for Mtb.
Long Abstract: Click Here

Poster J23
Looking for chromosome spatial organization rules in microarray gene expression data
Teresa Szczepińska- Nencki Institute of Experimental Biology
No additional authors
Short Abstract: Evidence supports that the basic nuclear functions are structurally integrated. We have used the human data and rat hippocampi gene expression data to explore relations between gene expression and genomic context. We identified and functionally annotated statistically higher than random number of distant genomic clusters within co-expression clusters.
Long Abstract: Click Here

Poster J24
ACT: Aggregation and Correlation Tool
Justin Jee- Yale
Joel Rozowsky (Yale, MBB); Robert Bjornson (Yale, CS); Guoneng Zhong (Yale, MBB); Zhengdong Zhang (Yale, MBB); Mark Gerstein (Yale, MBB);
Short Abstract: We have created a tool which facilitates the analysis of genomic signal data, such as ChIP-Seq, providing an aggregate signal profile across annotated positions (such as TSS’s) or calculates the correlation between a set of signal tracks as a means of determining their phylogenetic relationship.
Long Abstract: Click Here

Poster J25
Cross Platform Data Integration applied to Ageing Studies
Erik van den Akker- Leiden University Medical Centre / Delft University of Technology
Bas Heijmans (Leiden University Medical Centre, Molecular Epidemiology); Marian Beekman (Leiden University Medical Centre, Molecular Epidemiology); Joost Kok (Leiden University Medical Centre, Molecular Epidemiology); Marcel Reinders (Delft University of Technology, Information and Communication Theory Group); Pieternella Slagboom (Leiden University Medical Centre, Molecular Epidemiology);
Short Abstract: Classical gene set enrichment tests can be improved by weighting gene contributions according to the amount of supporting evidence. We aim to develop a statistical framework which allows for both the incorporation of weights derived from gene network topology as well as additional experimental evidence.
Long Abstract: Click Here

Poster J26
Prediction of Prokaryotic Transcription Units from Microarray Data Revisited
Ulrich Bodenhofer- Johannes Kepler University
Wilhelm Lichtberger (Johannes Kepler University, Institute of Bioinformatics); Frank Klawonn (University of Applied Sciences Braunschweig-Wolfenbuettel, Data Analysis and Pattern Recognition Lab);
Short Abstract: We propose a framework for inferring hypotheses about prokaryotic transcription units from expression microarray data. Upon summarization with the FARMS algorithm, support vector machines are employed to determine possible interrelations between genes using intergenic distances and a specifically designed correlation measure. The approach is validated on E.coli data.
Long Abstract: Click Here

Poster J27
Identification of Mammalian Polyadenylation Sites Using Logistic Regression
Eric Ho- Rutgers University
Samuel Gunderson (Rutgers University, Molecular Biology & Biochemistry);
Short Abstract: Our goal is to identify less-understood polyadenylation cis-acting elements, and to predict polyA sites. Singular value decomposition is used to locate and identify putative cis-acting elements flanking polyA sites. These features are incorporated into our logistic regression classifier. Sensitivity-specificity assessment has shown that our classifier achieves greater than 90% in performance.
Long Abstract: Click Here

Poster J28
Detecting Copy Number Variation With Ultra Short Reads
Paul Medvedev- University of Toronto
Michael Brudno (University of Toronto, Computer Science); Marc Fiume (University of Toronto, Computer Science); Seunghak Lee (University of Toronto, Computer Science); Tim Smith (University of Toronto, Computer Science); Adrian Dalca (University of Toronto, Computer Science);
Short Abstract: We develop a paired-end mapping method that combines depth-of-coverage information with a novel interpretation of matepair information to detect CNVs with ultra-short NGS reads. We use our method to detect CNVs within an individual, making a total of 9909 calls.
Long Abstract: Click Here

Poster J29
Function-based analysis of microarray data via l1-l2 regularization
Tiziana Sanavia- University of Padua
Annalisa Barla (University of Genova, Department of Computer and Information Science); Barbara Di Camillo (University of Padua, Department of Information Engineering); Sofia Mosci (University of Genova, Department of Computer and Information Science); Gianna Toffolo (University of Padua, Department of Information Engineering);
Short Abstract: A method is presented to integrate functional annotation with feature selection based on l1-l2 double optimization in microarray high-throughput studies. Our approach is able to increase the biological interpretability of gene signatures by defining subsets of genes annotated with groups of GO terms with similar functional meaning.
Long Abstract: Click Here

Poster J30
PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls
Joel Rozowsky- Yale University
ghia Euskirchen (Yale, MCDB); Raymond Auerbach (Yale, CBB); zhengdong zhang (Yale, MBB); Theodore Gibson (Yale, MBB); Robert Bjornson (Yale, CS); Nicholas Carriero (Yale, CS); Michael Snyder (Yale, MCDB); Mark Gerstein (Yale, CBB);
Short Abstract: We develop a methodology for analyzing ChIP-seq data. Our method use a two-pass approach to identify potential target binding sites compensating for variability in genomic mappability, and then to filter these regions in order to identify sites that are significantly enriched compared to an appropriately normalized control sample.
Long Abstract: Click Here

Poster J31
Development of a new Fungal Model, Holleya Sinecauda, by Paired End Solexa Sequencing
Pankaj Agarwal- Duke University
Fred Dietrich (Duke University, Department of Molecular Genetics and Microbiology);
Short Abstract: Development of a new fungal model, Holleya Sinecauda, using data from paired end Solexa sequencing, is presented. The sequencing data was assembled and the resulting contigs were analyzed computationally to characterize this organism. Results from this work and future experimental and computational work to further characterize the organism are presented.
Long Abstract: Click Here

Poster J32
Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies
Kenny Daily- University of California, Irvine
Xiaohui Xie (University of California, Irvine, Department of Computer Science, Institute for Genomics and Bioinformatics); Paul Rigor (University of California, Irvine, Department of Computer Science, Institute for Genomics and Bioinformatics); Pierre Baldi (University of California, Irvine, Department of Computer Science, Institute for Genomics and Bioinformatics, Department of Biological Chemistry); Scott Christley (University of California, Irvine, Department of Computer Science, Department of Mathematics);
Short Abstract: HTS technologies are driving profound, revolutionary, changes in biology and medicine, while generating massive amounts of data. We have developed new data structures and entropy coding algorithms for the efficient storage, retrieval, and transmission of the data with compression factors in the 10-400 range.
Long Abstract: Click Here

Poster J33
Whole Genome Sequencing of a Glioblastoma Multiforme Cell Line
Brian O'Connor- UCLA
Michael Clark (UCLA, Human Genetics); Nils Homer (UCLA, Human Genetics); Hane Lee (UCLA, Human Genetics); Barry Merriman (UCLA, Human Genetics); Zugen Chen (UCLA, Human Genetics); Stanley Nelson (UCLA, Human Genetics);
Short Abstract: Due to its morbidity, understanding glioblastoma multiforme (GBM) genetic etiology is of great interest. Here we report the full genome sequencing of U87MG, a well-studied GBM cell line. Greater than 25x average genomic coverage was generated using the ABI SOLiD Sequencer platform and a novel 50 base paired end strategy.
Long Abstract: Click Here



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