Accepted Posters
| Poster J01 |
| Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps |
| Jason Tsai- Wellcome Trust Sanger Institute |
| Thomas Otto (Wellcome Trust Sanger Institute, Parasite Genomics); Matthew Berriman (Wellcome Trust Sanger Institute, Parasite Genomics); |
| Short Abstract: Advances in sequencing technology allow genomes to be sequenced at vastly decreased costs. However, the assemblies frequently are highly fragmented with many gaps. We present a practical approach that uses Illumina sequences to improve draft assemblies by aligning sequences against contig ends and performing local assemblies to produce gap-spanning contigs. |
| Long Abstract:Click Here |
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| Poster J02 |
| Towards a Comprehensive Visual Analytics Approach to Genome Browsing |
| Robert Kincaid- Agilent Technologies |
| Amir Ben-Dor (Agilent Technologies, Agilent Laboratories); |
| Short Abstract: We describe a new research prototype for the visual analysis of genomic data with the aim to merge rich genome sequence and annotation browsing with more complete integration of experimental data analysis and visualization. Our long-term goal is to provide broad support for visual analytics of any genome-relevant data. |
| Long Abstract:Click Here |
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| Poster J03 |
| Comparison of methods finding the diversity of microbe communities based on 16S rRNA and metagenome shotgun sequencing |
| Chaochun Wei- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University;Shanghai center for bioinformation technology |
| Peng JIA (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Key Lab of Systems Biology); Kaiye Cai (Shanghai center for bioinformation technology, Pathogen genomics group); Guangyong Zheng (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Key Lab of Systems Biology); Lei Liu (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences;Shanghai center for bioinformation technology, Key Lab of Systems Biology); |
| Short Abstract: We present a comparison of microbe diversity identification methods based on 16S rRNA sequencing and metagenome shotgun sequencing by using a customizable metagenomics simulation system for the next generation sequencing technology. Our results show that diversity of microbe communities can be recovered more accurately with all microbial genomes currently available. |
| Long Abstract:Click Here |
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| Poster J04 |
| ELANDv2 - Fast gapped read mapping for Illumina reads |
| Markus Bauer- Illumina UK Ltd. |
| Anthony J. Cox (Illumina UK Ltd. , Computational Biology Group); Dirk J. Evers (Illumina UK Ltd., Computational Biology Group); |
Short Abstract: One single run on Illumina's HiSeq sequencer generates over one
billion paired-end 100bp reads. We present ELANDv2 which allows fast
gapped mapping of long reads and compare its performance to bwa and
Bowtie. We show that ELANDv2 performs favourably compared to the other programs. |
| Long Abstract:Click Here |
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| Poster J05 |
| Visualizing the next generation of sequencing data |
| Thomas Abeel- VIB-UGent |
| Thomas Van Parys (VIB-UGent, PSB); Yvan Saeys (VIB-UGent, PSB); James Galagan (Boston University, Engineering); Yves Van de Peer (VIB-UGent, PSB); |
| Short Abstract: GenomeView, the next-generation genome browser, enables users to interactively browse high volumes of next-generation sequencing data and whole genome alignments of dozens of genomes with dynamic navigation and zooming. Handling dozens of aligned genomes, thousands of annotation features and millions of short reads is a unique feat. |
| Long Abstract:Click Here |
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| Poster J06 |
| THE RAT GENOME DATABASE GENOME VIEWER |
| Jeffrey De Pons- Medical College of Wisconsin |
| Liz Worthey (Medical College of Wisconsin, Human and Molecular Genetics Center); Mary Shimoyama (Medical College of Wisconsin, Human and Molecular Genetics Center); Jennifer Smith (Medical College of Wisconsin, Human and Molecular Genetics Center); Rajni Nigam (Medical College of Wisconsin, Human and Molecular Genetics Center); Victoria Petri (Medical College of Wisconsin, Human and Molecular Genetics Center); Stan Laulederkind (Medical College of Wisconsin, Human and Molecular Genetics Center); Tim Lowry (Medical College of Wisconsin, Human and Molecular Genetics Center); Tom Hayman (Medical College of Wisconsin, Human and Molecular Genetics Center); Shur-Jen Wang (Medical College of Wisconsin, Human and Molecular Genetics Center); marek tutaj (Medical College of Wisconsin, Human and Molecular Genetics Center); weisong Liu (Medical College of Wisconsin, Human and Molecular Genetics Center); Diane Munzenmaier (Medical College of Wisconsin, Human and Molecular Genetics Center); Melinda Dwinell (Medical College of Wisconsin, Human and Molecular Genetics Center); Simon Twigger (Medical College of Wisconsin, Human and Molecular Genetics Center); Howard Jacob (Medical College of Wisconsin, Human and Molecular Genetics Center); Pushkala Jayaraman (Medical College of Wisconsin, Human and Molecular Genetics Center); |
| Short Abstract: In order to support visualization and analysis of the large volumes of genomic data, there is a need to build and integrate computational and visualization tools that aid in data analysis. One such tool developed at the Rat Genome Database (RGD) is the RGD Web Genome Viewer. |
| Long Abstract:Click Here |
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| Poster J07 |
| Comparative study of compositional symmetry in bacterial genomes using a novel method for replication terminus prediction |
| Nobuaki Kono- Institute for Advanced Biosciences, Keio University |
| Kazuharu Arakawa (Institute for Advanced Biosciences, Keio University, Systems Biology Program); Masaru Tomita (Institute for Advanced Biosciences, Keio University, Systems Biology Program); |
| Short Abstract: We have comprehensively predicted the dif sequences in bacterial genomes, that are used for chromosome dimer resolution and related to replication termination. The positions of dif sequences showed strong correlation with the shift point of genomic base compositional skews, suggesting an effective interplay of DNA replication termination and cell division. |
| Long Abstract:Click Here |
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| Poster J08 |
| BiNGS!SL-Seq: A Computational Analysis Workflow for Whole-Genome RNA Interference Screening Using the Next Generation Sequencing Technology |
| Tzu Lip Phang- University of Colorado Denver |
| Hyuming Kim (University of Colorado Denver, Department of Biochemistry and Molecular Genetics); Jihye Kim (University of Colorado Denver, Division of Medical Oncology, Department of Medicine); Dexiang Gao (University of Colorado Denver, Department of Biostatistics and Informatics, Colorado School of Public Health); Tiejun Tong (University of Colorado Boulder, Department of Applied Mathematics); Heather Selby (University of Colorado Denver, Division of Medical Oncology, Department of Medicine); Mark A. Gregory (University of Colorado Denver, Department of Biochemistry and Molecular Genetics); James DeGregori (University of Colorado Denver, Department of Biochemistry and Molecular Genetics); Aik Choon Tan (University of Colorado Denver, Division of Medical Oncology, Department of Medicine); |
| Short Abstract: This poster describes the development of BiNGS!SL-seq, a computational workflow on a "genome-wide" shRNA interference-based screen, to identify genes that, when inhibited, sensitize cancer cells to chemotherapeutics and novel targeted therapies. Next Generation Sequencing technology was employed to quantify the relative representation of shRNA on the experimental samples. |
| Long Abstract:Click Here |
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| Poster J09 |
| Transcriptome of embryonic and neonatal mouse cortex by RNA-seq |
| Xinwei Han- Pennsylvania State University |
| Hong Ma (Pennsylvania State University, Biology); |
| Short Abstract: We applied RNA-seq with solexa sequencing to investigate the change in transcriptome between embryonic day 18 and postnatal day 7 of mouse cortex. We found >16,000 genes expressed in the early cortex, 3,758 of which differentially expressed between the two stages, providing clues for further function study. |
| Long Abstract:Click Here |
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| Poster J10 |
| De novo characterization of the transcriptome in mouse cortical neurons using RNA-Seq and ChIP-Seq |
| Martin Hemberg- Children's Hospital Boston |
| Jesse Gray (Harvard Medical School, Neurobiology); Tae-Kyung Kim (Harvard Medical School, Neurobiology); Harrison Gabel (Harvard Medical School, Neurobiology); Gabriel Kreiman (Children's Hospital Boston, Ophthalmology); |
Short Abstract: We present a novel method for detecting transcripts in large mammalian
genomes using high-throughput sequencing data without the use of any
annotation. Our algorithm allows for the discovery and
characterization of thousands of unannotated transcripts. |
| Long Abstract:Click Here |
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| Poster J11 |
| s it possible to detect phenotype determining genome differences using DNA reads from pooled individuals of species with huge haploid genomes? |
| Rikard Erlandsson- Austrian Institute of Technology |
| Ratri Boonruangrod (Austrian Institute of Technology, Health and Environment); Kornel Burg (Austrian Institute of Technology, Health and Environment); Silvia Fluch (Austrian Institute of Technology, Health and Environment); |
| Short Abstract: In an attempt to examine the contribution of genomic factors to Heterobasidion resistance and flushing time in Norway spruce, Picea abies, filtrated pooled genomic DNA was subjected to 454 sequencing. Phenotype specific sequences were determined using a special bioinformatics pipeline. |
| Long Abstract:Click Here |
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| Poster J12 |
| Prioritization of pathogenic variants for monogenic diseases using targeted and exome resequencing data |
| Christian Gilissen- Radboud University Nijmegen Medical Centre |
| Alexander Hoischen (Radboud University Nijmegen Medical Centre, Human Genetics); Kostas Nikopoulos (Radboud University Nijmegen Medical Centre, Human Genetics); Bregje van Bon (Radboud University Nijmegen Medical Centre, Human Genetics); Nienke Wieskamp (Radboud University Nijmegen Medical Centre, Human Genetics); Peer Arts (Radboud University Nijmegen Medical Centre, Human Genetics); Bart van Lier (Radboud University Nijmegen Medical Centre, Human Genetics); Marloes Steehouwer (Radboud University Nijmegen Medical Centre, Human Genetics); Petra de Vries (Radboud University Nijmegen Medical Centre, Human Genetics); Rob Collin (Radboud University Nijmegen Medical Centre, Human Genetics); Hans Scheffer (Radboud University Nijmegen Medical Centre, Human Genetics); Bert de Vries (Radboud University Nijmegen Medical Centre, Human Genetics); Frans Cremers (Radboud University Nijmegen Medical Centre, Human Genetics); Han Brunner (Radboud University Nijmegen Medical Centre, Human Genetics); Joris Veltman (Radboud University Nijmegen Medical Centre, Human Genetics); |
| Short Abstract: We developed a computational pipeline that prioritizes candidate mutations based upon biological relevant information such as functional consequences, evolutionary conservation, and on combining data from multiple patients. This allowed us to rapidly identify TSPAN12 as the causative gene for FEVR and SETBP1 as the causative gene for Schinzel-Giedion Syndrome. |
| Long Abstract:Click Here |
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| Poster J13 |
| Comparative Statistical Analysis on Identifying Differentially Expressed Reads in Next Generation Sequencing Data |
| Dexiang Gao- University of Colorado Denver |
| Jihye Kim (University of Colorado Denver , Division of Medical Oncology, Department of Medicine); Hyunmin Kim (University of Colorado Denver , Department of Biochemistry and Molecular Genetics); Heather Selby (University of Colorado Denver , Division of Medical Oncology, Department of Medicine); Tzu Phang (University of Colorado Denver , Division of Pulmonary Sciences and Critical Care Medicine, Department of medicine); Aik Choon Tan (University of Colorado Denver , Division of Medical Oncology, Department of Medicine); Tiejun Tong (University of Colorado Boulder, Department of Applied Mathematics); |
| Short Abstract: Several statistical packages suitable for analyzing NGS data were evaluated for their performance on genome-wide shRNA screens to identify potential therapeutic targets in several cancer lines. The results show that Negative Binomial models assigned the smallest p-values to the most depleted shRNA sequences in treatment group, which best suits our needs in synthetic lethal screening. |
| Long Abstract:Click Here |
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| Poster J14 |
| Analysis of Genomic Data based on Information Theory |
| Jang Yi- University of Texas Medical Branch |
| Maga Rowicka (University of Texas Medical Branch, Biochemistry & Molecular Biology, Sealy Center for Molecular Medicine, Institute for Translational Sciences, Bioinformatics Programme); |
| Short Abstract: We present an analytic method for determining the amount of biologically meaningful information of a set of genes typically arising from a genomic experiment, utilizing divergence measures used in information theory for comparing probability distributions. |
| Long Abstract:Click Here |
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| Poster J15 |
| Statistical Analysis of Nondisjunction Assays in Drosophila |
| Hua Li- Stowers Institute for Medical Research |
| Yong Zeng (University of Missouri at Kansas City, Department of Mathematics and Statistics); Scott Hawley (Stowers Institute for Medical Research, Hawley Lab); William Gilliland (DePaul University, Department of Biological Sciences); |
| Short Abstract: The estimation of error rates for X chromosome nondisjunction during female meiosis is complicated by the fact that half of the nondisjunctional oocytes are lost due to lethal aneuploidy after fertilization. We show that statistical properties of the widely used estimator for the nondisjunction rate, and derive its asymptotic distribution. |
| Long Abstract:Click Here |
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| Poster J16 |
| The Bonobo de novo Genome Assembly Generated by CABOG |
| Jason Miller- JCVI |
| Brian P. Walenz (JCVI, Informatics); Sergey Koren (JCVI, Informatics); Granger Sutton (JCVI, Informatics); |
| Short Abstract: A de novo genome assembly of the great ape Pan paniscus was generated from pyrosequencing data produced by the Bonobo Sequencing Consortium. The large data set was tackled with the Best Overlap Graph (BOG) algorithm as implemented in the CABOG variant of Celera Assembler. |
| Long Abstract:Click Here |
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| Poster J17 |
| Gramene: A Database Platform For Comparative Genomics in Plants |
| Joshua Stein- Cold Spring Harbor Laboratory |
| Immanuel Yap (Cornell University, Department of Plant Breeding); Jon Zhang (Cornell University, Department of Plant Breeding); Terry Casstevens (Cornell University, Department of Plant Breeding); Charles Chen (Cornell University, Department of Plant Breeding); Genevieve DeClerck (Cornell University, Department of Plant Breeding); Susan McCouch (Cornell University, Department of Plant Breeding); Edward Bucker (Cornell University, Institute for Genomic Diversity); Ken Youens-Clark (Cold Spring Harbor Laboratory, Ware Laboratory); Sharon Wei (Cold Spring Harbor Laboratory, Ware Laboratory); Jim Thomason (Cold Spring Harbor Laboratory, Ware Laboratory); Shulamit Avraham (Cold Spring Harbor Laboratory, Ware Laboratory); Liya Ren (Cold Spring Harbor Laboratory, Ware Laboratory); Doreen Ware (Cold Spring Harbor Laboratory, Ware Laboratory); Gina Bono (Oregon State University, Department of Botany and Plant Pathology); Pankaj Jaiswal (Oregon State University, Department of Botany and Plant Pathology); William Spooner (Cold Spring Harbor Laboratory, Ware Laboratory); |
| Short Abstract: Gramene (http://www.gramene.org) is a curated resource for comparative genomics in plants. The database integrates information about genomic sequence, annotation, QTL, traits, and population diversity with comparative information from phylogenetic trees and whole genome alignments. The 31st build was released in spring 2010. Gramene is supported by NSF grant #0703908. |
| Long Abstract:Click Here |
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| Poster J18 |
| BioHDF: A Data Storage Solution for Next-Generation Sequencing |
| Dana Robinson- The HDF Group |
| Mike Folk (The HDF Group, Software Development); Todd Smith (Geospiza, Inc., Software Development); Mark Welsh (Geospiza, Inc., Software Development); |
| Short Abstract: BioHDF is an open source data storage package for storing next-generation sequencing data in HDF5 files. We describe the current state of BioHDF and the design and capabilities of the production library and tools. |
| Long Abstract:Click Here |
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| Poster J19 |
| A normalization technique for next generation sequencing experiments |
| Günter Klambauer- Johannes Kepler Universität Linz |
| Karin Schwarzbauer (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 for normalization of read counts of next generation sequencing experiments.
Normalizing makes experiments comparable even if they stem from different labs and have different quality. After normalization local models based on Poisson distributions can be fitted. |
| Long Abstract:Click Here |
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| Poster J20 |
| Identification of protein disorder in Corynebacterium pseudotuberculosis proteome using phage display data |
| Sintia Almeida- Federal University of Minas Gerais |
| Vívian D'Afonseca (UFMG, General Biology); Siomar Soares (UFMG, General Biology); Anne Pinto (UFMG, General Biology); Nubia Seyffert (UFMG, General Biology); Carlos Prudencio (UFU, Nanobiotechnology Laboratory); Fabiana Almeida (UFU, Nanobiotechnology Laboratory); Anderson Santos (UFMG, General Biology); Cassio Faria (UFMG, General Biology); Jeronimo Ruiz (Rene Rachoud Institute, Fiocruz); Robert Moore (CSIRO, Australian Animal Health Laboratory); Anderson Miyoshi (UFMG, General Biology); Luiz Goulart (UFU, Nanobiotechnology Laboratory); Vasco Azevedo (UFMG, General Biology); |
| Short Abstract: The biopanning (using phage display) or procedure of election is made by the incubation of the peptides displayed in phages against a target and to select recombinant peptides directly related to related to Corynebacterium pseudotuberculosis, and together with disorder prediction we find candidate to the vaccine development. |
| Long Abstract:Click Here |
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| Poster J21 |
| Generalized Random Sets for Functional Enrichment Analysis Using Primary Genomics Datasets |
| Johannes Freudenberg- University of Cincinnati College of Medicine |
| Siva Sivaganesan (University of Cincinnati, Mathematical Sciences Department); Mukta Phatak (University of Cincinnati, Department of Environmental Health); Kaustubh Shinde (University of Cincinnati, Department of Environmental Health); Mario Medvedovic (University of Cincinnati, Department of Environmental Health); |
| Short Abstract: Functional analysis using primary genomics datasets is an emerging approach for functional enrichment analysis of newly generated genomics data. We developed and validated a new statistical framework, Generalized Random Set analysis, for identifying pairs of genomics datasets with concordant signatures that, for the first time, does not require gene categorization. |
| Long Abstract:Click Here |
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| Poster J22 |
| Conserved G-quadruplexes May Regulate NF1 Gene Expression at Translational and Polyadenylation levels |
| Rami Alrabaa- Ramapo College of New Jersey |
| Lawrence D'Antonio (Ramapo College of New Jersey, Department of Bioinformatics); Paramjeet Bagga (Ramapo College of New Jersey, Department of Bioinformatics); |
| Short Abstract: Mutations in the NF1 gene cause Neurofibromatosis which is characterized by peripheral nervous system tumors. G-quadruplex structures in the RNA are known to be involved in important biological function. Our phylogenetic analysis strongly suggests that G-quadruplexes play a role in the regulation of the NF1 gene expression at multiple levels. |
| Long Abstract:Click Here |
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| Poster J23 |
| Alternative splicing of MECP2 gene involved in autism and related mental retardation syndromes may be regulated by G-quadruplex motifs |
| Joetsaroop Bagga- John P Stevens High School, Edison, NJ |
| Lawrence D'Antonio (Ramapo College of New Jersey, Mathematics); Paramjeet Bagga (Ramapo College of New Jersey, Bioinformatics); |
| Short Abstract: Mutations in the MECP2, which regulates gene transcription in early development of the brain, have been linked to autism. We have identified conserved G-quadruplexes near the alternate splice sites of the MECP2 pre-mRNA. Our findings suggest that G-quadruplexes are involved in regulated alternative splicing in the MECP2 gene. |
| Long Abstract:Click Here |
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| Poster J24 |
| GENOME-WIDE DISTRIBUTION OF G-QUADRUPLEXES SUGGESTS THEIR ROLE IN REGULATED SPLICING |
| Paramjeet Bagga- Ramapo College of New Jersey |
| Viktor Vasilev (Ramapo College of New Jersey, Computer Science); Lawrence D'Antonio (Ramapo College of New Jersey, Mathematics); |
| Short Abstract: G-quadruplex structures can play significant biological roles in cellular processes and human disease. We have used a bioinformatics approach to study G-quadruplex distribution patterns in >17,000 human protein coding genes, including alternatively processed genes. Our findings strongly suggest that G-quadruplexes play a regulatory role in splicing of the human pre-mRNAs. |
| Long Abstract:Click Here |
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| Poster J25 |
| Estimation of DNA Fragment Size Distribution and Reconstruction of DNA-binding Profiles from ChIP-seq Data |
| Shouyong Peng- Harvard Medical School |
| Arteom A. Alekseyenko (Harvard Medical School, Genetics); Mitzi I. Kuroda (Harvard Medical School, Genetics); Peter J. Park (Harvard Medical School, Genetics); |
Short Abstract: ChIP-seq is a technique for genome-wide profiling of DNA-binding proteins.
We propose a method for estimating the distribution of fragment sizes and use this information to more accurately reconstruct DNA-binding profile. We validate our approach by a paired-ends ChIP-seq experiment and qPCR data. |
| Long Abstract:Click Here |
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| Poster J26 |
| Using RNAi and RNA-Seq to Identify Alternative Exons Regulated by Individual RNA Binding Proteins and their Associated Regulatory Motifs |
| Angela Brooks- University of California, Berkeley |
| Li Yang (University of Connecticut Health Center, Genetics and Developmental Biology); Michael Duff (University of Connecticut Health Center, Genetics and Developmental Biology); Kasper Hansen (University of California, Berkeley, Division of Biostatistics); Sandrine Dudoit (University of California, Berkeley, Division of Biostatistics); Steven Brenner (University of California, Berkeley, Plant and Microbial Biology); Brenton Graveley (University of Connecticut Health Center, Genetics and Developmental Biology); |
| Short Abstract: To identify splicing regulatory sequence elements in the Drosophila melanogaster genome, we are individually depleting RNA binding proteins by RNAi; sequencing the transcriptomes (RNA-seq); and using statistical methods and informatics to identify exons regulated by each RNA binding protein and the sequence motifs present near co-regulated exons. |
| Long Abstract:Click Here |
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| Poster J27 |
| Graphical Analyser of Contig for all Sequencers generation - G4ALL |
| Rommel Ramos- Federal University Of Pará |
| Adriana Carneiro (Federal University Of Pará, Institute of Biological Sciences); Paula Schneider (Federal University Of Pará, Institute of Biological Sciences); Vasco Azevedo (Federal University Of Minas Gerais, Institute of Biological Sciences); Jeronimo Ruiz (FIOCRUZ, Rene Rachou Research Center); Artur Silva (Federal University Of Pará, Institute of Biological Sciences); |
| Short Abstract: G4ALL is a tool that use the local alignment results to order and orient the ab initio contigs, allowing for the visualisation and editing of the contigs and generates reports of the contigs that were selected by manual curation and makes them available in a multifasta archive. |
| Long Abstract:Click Here |
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| Poster J28 |
| Preliminary comparative analysis of four novel Mycoplasma genomes |
| Iddo Friedberg- Miami University |
| Mitchell Balish (Miami University, Microbiology); Lucinda Fulton (Wasington University, Genome Sequencing Center); Rachel Pritchard (Miami University, Microbiology); Jennifer Hatchel (Miami University, Microbiology); Richard Wilson (Washington University St. Louis, Genome Sequencing Center); |
| Short Abstract: Four genomes of mycoplasma have been sequenced, partially assembled and the results are presented here. Due to their small genome size, even partial assembly provides major insights into comparative genome analysis. We discuss our ability to perform comparative genomics form partially assembled sequences, and discuss initial findings |
| Long Abstract:Click Here |
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| Poster J29 |
| Indel detection using guided reassembly of unaligned paired-end reads |
| Ole Schulz-Trieglaff- Illumina Cambridge Ltd. |
| Bret Barnes (Illumina US, Computational Biology); Anthony Cox (Illumina UK, Computational Biology); Keira Cheetham (Illumina UK, Computational Biology); Russell Grocock (Illumina UK, Computational Biology); Lisa Murray (Illumina UK, Computational Biology); Christopher Saunders (Illumina USA, Computational Biology); Wendy Wong (Illumina UK, Computational Biology); Dirk Evers (Illumina UK, Computational Biology); |
Short Abstract: We present GROUPER, an algorithm for the detection of insertions and deletions (indels) from paired-end DNA reads.
GROUPER uses the information from reads spanning the indel region and reconstructs the indel sequence using a de Bruijn graph approach. We compare our algorithm to existing tools on real and simulated data. |
| Long Abstract:Click Here |
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| Poster J30 |
| De novo Coral Genome Assembly by Short-Read Sequencing |
| Arthur Hsu- The Walter and Eliza Hall Institute |
| Deniz Koellhofer (Australian Genome Research Facility, Australian Genome Research Facility); Tony Papenfuss (The Walter and Eliza Hall Institute, Bioinformatics); Kirby Siemering (Australian Genome Research Facility, Australian Genome Research Facility); |
| Short Abstract: We sequenced and assembled the most common reef builder coral in the Great Barrier Reef –Acropora millepora entirely by short read sequencing. This puts coral genome among the first eukaryotic genomes being sequenced entirely of short-reads. Three popular assembly programs: Velvet, ABySS and SOAPdenovo were compared in this work. |
| Long Abstract:Click Here |
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| Poster J31 |
| Identification of combinatorial epigenetic patterns associated with functional DNA elements in human genome |
| Duygu Ucar- Postdoctoral Fellow |
| No additional authors |
| Short Abstract: Epigenetic markers, such as post-translational modifications to histone proteins, are central players in regulating gene expression. The unified hypothesis on 'histone code' points to combinatorial patterns that led to the same biological and functional outcome on the genome. We propose a scalable clustering algorithm to capture frequently repeating combinatorial patterns. |
| Long Abstract:Click Here |
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| Poster J32 |
| Comparative Epigenomic Analysis of Repetitive DNA Elements |
| Fabian Mueller- Broad Institute / Max Planck Institute for Informatics |
| No additional authors |
| Short Abstract: We present a method for globally analyzing and comparing DNA methylation and chromatin marks of mammalian repetitive element prototypes and families in multiple samples. Our results suggest protection of genome integrity by specific DNA methylation of abundant, CpG-rich and young prototypes. |
| Long Abstract:Click Here |
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| Poster J33 |
| AltAnalyze: Assessing Functional Implications of Alternative Splicing on a Genome-Wide Scale |
| Nathan Salomonis- Gladstone Institutes |
| Laura Pereira (University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics); Christine Wahlquist (Burnham Institute for Medical Research, Neuroscience, aging and stem cell); Alexandre Colas (Burnham Institute for Medical Research, Neuroscience, aging and stem cell); Eva Samal (Gladstone Institutes, Cardiovascular Disease); Mark Mercola (Burnham Institute for Medical Research, Neuroscience, aging and stem cell); Bradley Merrill (University of Illinois at Chicago, Department of Biochemistry and Molecular Genetics); Dorothea Emig (Max Planck Institute for Informatics, Computational Biology and Applied Algorithmics); Mario Albrecht (Max Planck Institute for Informatics, Computational Biology and Applied Algorithmics); Bruce Conklin (Gladstone Institutes, Cardiovascular Disease); |
| Short Abstract: To understand the functional consequences of mRNA isoform variation, we developed a new open-source bioinformatics tool, named AltAnalyze (http://www.AltAnalyze.org). Analysis of exon and exon-exon junction array data led to functional predictions on microRNA binding site exclusion and protein domain modification by alternative splicing, that were experimentally verified. |
| Long Abstract:Click Here |
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| Poster J34 |
| Graphical quasi-species analyses of a deep sequencing sample of avian influenza A (H5N1) virus |
| Lars Steinbrück- Max Planck Institute for Informatics |
| Dirk Höper (Friedrich-Loeffler-Institut, Institute of Diagnostic Virology); Bernd Hoffmann (Friedrich-Loeffler-Institut, Institute of Diagnostic Virology); Martin Beer (Friedrich-Loeffler-Institut, Institute of Diagnostic Virology); Alice McHardy (Max Planck Institute for Informatics, Computational Genomics and Epidemiology); |
| Short Abstract: 454 sequencing enables the analysis of viral quasi-species within a given host. Based on error-corrected reads we provide a graph-based visualization of the intra-host population for an avian influenza A (H5N1) virus and analyze high-quality SNPs with regard to their potential impact on viral proteins for all genome segments. |
| Long Abstract:Click Here |
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| Poster J35 |
| Applying normalization and phylogenetic information in estimating distance metrics for metagenomes |
| Huai-Kuang Tsai- Academia Sinica |
| Chien-Hao Su (National Taiwan University, Department of Computer Science and Information Engineering); Daryi Wang (Academia Sinica, Biodiversity Research Center); |
| Short Abstract: Discriminating the differences between microbial communities is important in metagenomics. However, the strengths and limitations of current distance metrics are still unclear. We analyzed three distance metrics and our results on clustering samples using real and synthetic datasets suggested that incorporating suitable normalizations and phylogenetic information yield significant improvements. |
| Long Abstract:Click Here |
|
| Poster J36 |
| Short read assembly of subtelomeric regions and multi-gene families in Plasmodium falciparum |
| Sammy Assefa- Wellcome Trust Sanger Institute |
| Thomas Otto (Wellcome Trust Sanger Institute , Parasite Genomics); Chris Newbold (Wellcome Trust Sanger Institute; 2Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford., -); Matthew Berriman (Wellcome Trust Sanger Institute, Parasite Genomics); |
| Short Abstract: We present an iterative walking approach based on conserved motifs as a better way to assemble the most difficult parts of the P. falciparum genome. The results of this approach show significant improvements over simple de novo and comparative assemblies in lab adapted and field samples. |
| Long Abstract:Click Here |
|
| Poster J37 |
| Large scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing |
| Graziano Pesole- University Of Bari |
| Ernesto Picardi (University of Bari, Dipartimento di Biochimica E Biologia Molecolare); David Horner (University of Milan, Dipartimento di Scienze Biomolecolari e Biotecnologie); Matteo Chiara (University of Milan, Dipartimento di Scienze Biomolecolari e Biotecnologie); Riccardo Schiavon (University of Padua, CRIBI); Giorgio Valle (University of Padua, CRIBI); |
| Short Abstract: RNA editing by C-to-U modification has been investigated at genomic scale in the grapevine mtDNA by RNA deep-sequencing. Millions of short reads from Solexa/Illumina and ABI SOLiD platforms provided statistically significant support for 401 C-to-U conversions in mitochondrial coding regions giving the opportunity to investigate the RNA editing tissue specificity. |
| Long Abstract:Click Here |
|
| Poster J38 |
| Wobble Patterns in Plants and Animals |
| Tatiana Tatarinova- University of Glamorgan |
| Tatiana Tatarinova (University of Glamorgan, Faculty of Advanced Technology); Nickolai Alexandrov (Ceres, inc, Computational Biology); Kenneth Feldmann (University of Arizona, School of Plant Sciences); |
| Short Abstract: Our findings suggest that genes with high levels of GC3 represent a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC3 bimodality: biased gene conversion, transcriptional/translational advantage and gene methylation. |
| Long Abstract:Click Here |
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| Poster J39 |
| Using GPU programming for short read mapping |
| Tobias Jakobi- Computational Genomics |
| Alexander Goesmann (Computational Genomics, Institute for Bioinformatics, Center for Biotechnology, Bielefeld University); Sebastian Jaenicke (Computational Genomics, Institute for Bioinformatics, Center for Biotechnology, Bielefeld University); Jochen Blom (Computational Genomics, Institute for Bioinformatics, Center for Biotechnology, Bielefeld University); Daniel Doppmeier (Bioinformatics of Signaling Networks, Institute for Bioinformatics, Center for Biotechnology, Bielefeld University); |
| Short Abstract: We are presenting an exact and complete approach to map short reads of next generation sequencing techniques against microbial reference genomes using modern graphics hardware. Compared to other tools available we are able deal with gapped alignments while furthermore finding all possible mapping positions in an adequate running time. |
| Long Abstract:Click Here |
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| Poster J40 |
| A computational study of cross-hybridizing stable loop structures in oligonucleotide sequences. |
| D. Andrew Carr- Accelerated Technology Laboratories |
| Saeed Khoshnevis (University of North Carolina Charllote, Bioinformatics); Jennifer Weller (University of North Carolina Charllote, Bioinformatics); |
| Short Abstract: Many genomics assays use hybridization of a short nucleotide fragment to a longer target fragment as an essential processing step. If stable looped target structures are included in the search space the degree to which some of the probes cross-hybridize is considerably greater than is currently recognized. |
| Long Abstract:Click Here |
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| Poster J41 |
| Architecturally driven alternative splicing |
| Rileen Sinha- University of Freiburg |
| Klemens Hertel ( University of California, Irvine, CA, Department of Microbiology and Molecular Genetics); Rolf Backofen (University of Freiburg, Institute of Computer Science, Bioinformatics Group, Freiburg, Germany); |
| Short Abstract: Our analyses based on the architecture of pre-mRNA (1) showed that not only short, but also long exons are enriched in alternative splicing(AS), (2) yielded sets of intron- and exon-definition elements, (3) found that unusually long exons are depleted in ESEs, and (4) identified a subset of length-dependent AS exons. |
| Long Abstract:Click Here |
|
| Poster J42 |
| Dynamics and evolution of genome – nuclear lamina interactions |
| Wouter Meuleman- Delft University of Technology |
| Daan Peric-Hupkes (Netherlands Cancer Institute, Gene Regulation); Marcel Reinders (Delft University of Technology, Delft Bioinformatics Lab); Lodewyk Wessels (Netherlands Cancer Institute, Molecular Biology); Bas van Steensel (Netherlands Cancer Institute, Gene Regulation); |
| Short Abstract: We present high-resolution maps of the interaction of human and mouse genomes with the nuclear lamina, providing detailed views of the spatial organization of interphase chromosomes. These maps reveal substantial refolding of chromosomes during differentiation, but also indicate that a cell-type independent backbone of lamina-interactions is highly conserved. |
| Long Abstract:Click Here |
|
| Poster J43 |
| Quality guided correction and filtration of errors in short reads |
| David Kelley- University of Maryland, College Park |
| No additional authors |
| Short Abstract: We introduce a program named Quake to correct errors in Illumina sequencing reads. By using read quality values and the different rates at which nucleotides are called as errors to different nucleotides, Quake achieves near perfect accuracy on simulated data. We also Quake's ability to improve assembly and SNP detection. |
| Long Abstract:Click Here |
|
| Poster J44 |
| De Novo Transcriptome Assembly Using 454 Sequencing |
| Daniel Fasulo- 454 Life Sciences |
| Miroslav Kukricar (454 Life Sciences, Bioinformatics Development); Mohammed Mohiuddin (454 Life Sciences, Genomics); James Knight (454 Life Sciences, Research and Development); Chinnappa Kodira (454 Life Sciences, Genomics); Stephen Hutchison (454 Life Sciences, Research and Development); |
| Short Abstract: We describe algorithmic modifications to the 454 gsAssembler software to support de novo assembly of transcriptomes from cDNA sequencing reads. We demonstrate the performance of our de novo transcriptome assembler using results from 454 whole transcriptome sequence data for yeast, Neurospora, and Drosophila. |
| Long Abstract:Click Here |
|
| Poster J45 |
| Discovery and characterization of chromatin states for systematic annotation of the human genome. |
| Jason Ernst- MIT/Broad Institute |
| Manolis Kellis (MIT/Broad Institute, CSAIL); |
Short Abstract: A plethora of epigenetic modifications have been described in the human
genome and associated with diverse functional roles. We developed a method
based on a multivariate Hidden Markov Model to systematically discover and
characterize recurrent spatially coherent and biologically meaningful
chromatin mark combinations, or chromatin states and study their dynamics. |
| Long Abstract:Click Here |
|
| Poster J46 |
| Knowing when to stop: A framework for threshold selection in gene family classification |
| Jacob Joseph- Carnegie Mellon University |
| Greg Smith (Carnegie Mellon University, Biological Sciences); Michael Livstone (Princeton University , Lewis-Sigler Institute for Integrative Genomics ); Dannie Durand (Carnegie Mellon University, Computer Science, Biological Sciences); |
Short Abstract: We seek automated methods to identify homologous sequence families.
Though methodology exists to evaluate classifiers using curated data,
this yields little guidance for a priori threshold selection with
novel data. We introduce a framework for performing and evaluating
family classification, using intrinsic organization, models of family
evolution, and curated data. |
| Long Abstract:Click Here |
|
| Poster J47 |
| Multiple Sequence Realignment-Enhanced Detection of Short Germline and Somatic Indels |
| Andrey Sivachenko- Broad Institute |
| Eric Banks (Broad Institute, Medical and Population Genetics); Matthew Meyerson (Broad Institute, Cancer Program); Eric Lander (Broad Institute, ); Stacey Gabriel (Broad Institute, Cancer Program); Mark DePristo (Broad Institute, Medical and Population Genetics); Gad Getz (Broad Institute, Cancer Program); |
| Short Abstract: Algorithms and tools for indel discovery in next-generation sequencing data (Illumina) are presented with the accuracy assessed by large-scale Sequenom validation. Multiple sequence realignment in the regions exhibiting signatures of suboptimal initial alignments is shown to be important for recovery of additional evidence for an indel overlooked by single-read aligners. |
| Long Abstract:Click Here |
|
| Poster J48 |
| Sequence variability is reflected in nucleosome occupancy profiles in the human genome |
| Michael Tolstorukov- Harvard Medical School |
| Natalia Volfovsky (SAIC-Frederick, National Cancer Institute at Frederick, Advanced Biomedical Computing Center); Robert Stephens (SAIC-Frederick, National Cancer Institute at Frederick, Advanced Biomedical Computing Center); Peter Park (Harvard Medical School, Center for Biomedical Informatics); |
| Short Abstract: Using a high-confidence collection of human indels and SNPs we analyzed how variation in genomic sequence affects primary structure of chromatin. Our results indicate stronger conservation of the sequences associated with epigenetically modified nucleosomes as compared to nucleosomal DNA in bulk, highlighting complex organization of the human genome. |
| Long Abstract:Click Here |
|
| Poster J49 |
| Integrative analysis of gene expression and epigenomic data in stem cells, progentiors and cancer stem cells |
| Amit Sinha- Dana-Farber Cancer Institute |
| Nan Zhu (Children's Hospital Boston, Hematology/Oncology); Tobias Neff (Children's Hospital Boston, Hematology/Oncology); Scott Armstrong (Children's Hospital Boston, Hematology/Oncology); |
| Short Abstract: We analyzed histone modifications marks H3K4me3, H3K27me3 and H3K79me2 in hematopoietic stem cells (HSC), progenitor cells – granulocyte macrophage progenitors (GMP) and leukemic stem cells (LSC). By integrating gene expression data with epigenomic data, we identified important genesets could not be identified by using either data alone. |
| Long Abstract:Click Here |
|
| Poster J50 |
| Online Quantitative Transcriptome Analysis |
| Regina Bohnert- Friedrich Miescher Laboratory Of The Max Planck Society |
| Jonas Behr (Friedrich Miescher Laboratory, Max Planck Society); André Kahles (Friedrich Miescher Laboratory, Max Planck Society); Géraldine Jean (Friedrich Miescher Laboratory, Max Planck Society); Gunnar Rätsch (Friedrich Miescher Laboratory, Max Planck Society); |
Short Abstract: The current revolution in sequencing technologies allows us to obtain
a much more detailed picture of transcriptomes via RNA-Sequencing. We present the first integrative online platform for quantitatively analyzing RNA-Seq experiments. It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation. |
| Long Abstract:Click Here |
|
| Poster J51 |
| Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts |
| Philipp Drewe- Friedrich Miescher Laboratory of the Max Planck Society |
| Oliver Stegle (Max Planck Institute for Developmental Biology, Machine Learning & Computational Biology Research Group ); Regina Bohnert (Friedrich Miescher Laboratory of the Max Planck Society, Machine Learning in Biology ); Karsten Borgwardt (Max Planck Institute for Developmental Biology, Machine Learning & Computational Biology Research Group ); Gunnar Rätsch (Friedrich Miescher Laboratory of the Max Planck Society, Machine Learning in Biology); |
Short Abstract: We present two novel statistical tests for differential abundances of RNA
transcripts: a 'gene structure sensitive' Poisson test when the transcript structure of a gene is
known, and a kernel-based test when it is unknown.
We show that both approaches perform better than testing for differential expression by first quantifying the transcript abundance. |
| Long Abstract:Click Here |
|
| Poster J52 |
| gee_fu: a RESTful web-services database for next-generation sequencing data |
| Dan MacLean- The Sainsbury Laboratory |
| Ricardo Ramirez-Gonzalez (Genome Analysis Centre, department Bioinformatics); |
| Short Abstract: gee_fu is a Ruby-on-Rails based RESTful web-service application for genome feature data and is designed for use with high-throughput sequencing experiments. It is easily extended into bespoke web apps and interfaces with next-gen viewports like AnnoJ easily. |
| Long Abstract:Click Here |
|
| Poster J53 |
| A Validation Framework for Next-Generation Resequencing Data, Utilizing a High-Confidence Set of HuRef Genomic Variants |
| Charles Scafe- Life Technologies |
| Chantal Roth (Life Technologies, Bioinformatics); Fiona Hyland (Life Technologies, Bioinformatics); Asim Siddiqui (Life Technologies, Bioinformatics); |
| Short Abstract: We frequently update our analysis framework for next-generation genomic resequencing and whole transcriptome applications. A pipeline to validate system data quality and software performance was applied to HuRef resequencing results at 33x coverage. We report high specificity and sensitivity of SNP calling against orthogonal genotype data. |
| Long Abstract:Click Here |
|
| Poster J54 |
| The mutation spectrum revealed by paired genome sequences from a lung cancer patient |
| William Lee- Genentech, Inc. |
| William Lee (Genentech, Inc., Bioinformatics and Computational Biology); |
| Short Abstract: Lung cancer is the leading cause of cancer-related mortality worldwide, with non-small cell lung carcinomas in smokers being the predominant form of the disease. While previous studies have identified important common somatic mutations in lung cancers, they primarily have focused on a limited set of genes and hence provide a constrained view of the mutational spectrum. Recent cancer sequencing efforts have leveraged next-generation sequencing technologies to provide a genome-wide view of mutations in leukemia, breast cancer, and cancer cell lines. Here we present the first complete sequences of a primary lung tumor (60x coverage) and adjacent normal tissue (46x). Comparing the two genomes, we identified a wide variety of somatic variations, including >50,000 high-confidence single nucleotide variations (SNVs). We validated 530 somatic SNVs in this tumor, including one in the KRAS proto-oncogene and 391 others in coding regions, as well as 43 large-scale structural variations. These constitute a large set of novel somatic mutations and yield an estimated 17.7 per Mb genome-wide somatic mutation rate. Interestingly, we observe a distinct pattern of selection against mutations within expressed genes compared to non-expressed genes and in promoter regions up to 5 kb upstream of all protein-coding genes. Additionally, we observe a higher rate of amino acid-changing mutations in kinase genes. This report presents the most comprehensive view of somatic alterations in a single lung tumor, and provides the first picture of distinct selective pressures present within the tumor environment. |
| Long Abstract:Click Here |
|
| Poster J55 |
| Towards a multi-scale and formalized representation of protein sequence-structure-function relationships – the nsLTP family as a case of study |
| Cécile Fleury- INRA/CIRAD |
| Marie-Françoise Gautier (INRA/CIRAD, UMR DAP); Pierre Larmande (CNRS/CIRAD, UMR DAP); Sabine Peres (CNRS, SysDiag); Frederic de Lamotte (INRA/CIRAD, UMR DAP); Franck Molina (CNRS, SysDiag); Manuel Ruiz (CIRAD, UMR DAP); |
| Short Abstract: We are developing a new information system which will propose a multi-scale and formalized representation of proteins sequence-structure-function relationships. In this context, we performed a structural study of the plant non-specific lipid transfer protein family. The results show correlations between nsLTP sequences, cysteine connectivities, three-dimensional structures and lipid binding properties. |
| Long Abstract:Click Here |
|
| Poster J56 |
| ExpressionPlot: A web-based framework for the comparative analysis of gene expression and RNA processing data from exon array and RNA-Seq platforms |
| Brad Friedman- Harvard University |
| No additional authors |
| Short Abstract: In recent years exon array and RNA-Seq platforms have emerged as important tools for detecting differences in gene expression as well as RNA processing in biological samples. Given the complexity of both approaches, the diversity of available data, and the needs of non-specialist biologists, we have developed a software package called ExpressionPlot that can automatically process both data types and provides an easy-to-use exploratory web-based interface. Web users can view reads or probe intensities on a genome browser, generate plots comparing changes in gene expression or RNA processing events, and browse dynamic tables of significant changes. We will present a case study in which we used ExpressionPlot to discover relationships between gene expression data sets related to the neurodegenerative disease ALS. The software will be available for download through the website friedman-lab.com. |
| Long Abstract:Click Here |
|
| Poster J57 |
| Histone modification levels are predictive for gene expression |
| Martin Vingron- Max-Planck-Institut fur Molekulare Genetik |
| Rosa Karlic (Max-Planck-Institut fur Molekulare Genetik, Computational Molecular Biology); Ho-Ryun Chung (Max-Planck-Institut fur Molekulare Genetik, Computational Molecular Biology); Julia Lasserre (Max-Planck-Institut fur Molekulare Genetik, Computational Molecular Biology); Kristian Vlahovicek (Faculty of Science, Zagreb University, Bioinformatics Group); |
| Short Abstract: Histones are frequently decorated with covalent modifications, which are involved in various chromatin-dependent processes. To elucidate the relationship between histone modifications and transcription, we derived quantitative models to predict expression levels of genes from histone modification levels. We found that histone modification levels and gene expression are highly correlated and showed that only a small number of histone modifications are necessary to accurately predict gene expression. We show that different sets of histone modifications are necessary to predict gene expression driven by high CpG content promoters (HCPs) or low CpG content promoters (LCPs). Quantitative models using H3K4me3 and H3K79me1 are the most predictive for expression of LCPs, whereas HCPs require H3K27ac and H4K20me1. We show that the connections between histone modifications and gene expression seem to be general, as we were able to predict gene expression levels of one cell type using a model trained on another one. |
| Long Abstract:Click Here |
|
| Poster J58 |
| Applying histone modification information to genome-wide prediction of transcription factor binding sites |
| Kyoungjae Won- University Of California, San Diego |
| Bing Ren (UCSD, Ludwig Institute for Cancer Research); Wei Wang (UCSD, Chemistry & Biochemistry); |
| Short Abstract: We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of a transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNAi knockdown) experiments. Capturing characteristics of multi-dimensional epigenetic signatures within the states of hidden Markov models, Chromia, identified functional binding sites associated with histone signatures. |
| Long Abstract:Click Here |
|
| Poster J59 |
| Entangled Mate Sequencing |
| Frederick Roth- Harvard Medical School |
| Yong Lu (Harvard Medical School, Biological Chemistry & Molecular Pharmacology); |
| Short Abstract: Progress in DNA sequencing technology is rapidly changing the field of biology and medicine. Most widely used DNA sequencing platforms read out one base from a template molecule for each sequencing cycle. We propose use of two priming sites in each template molecule, thus enabling simultaneous readout of the 'entangled' mixture of two bases in one sequencing cycle via synchronous extension of both primers. For de novo sequencing of template with a uniform mononucleotide distribution, the proposed 'entangled mate sequencing' (EMS) method can increase information gain by 62.5% compared with conventional (unentnagled) methods. For resequencing or tag-counting applications, we show that EMS can nearly double the information gained. Several challenges must be tackled for the proposed EMS method to work: 1. Prepare EMS-capable sequencing libraries; 2. Call bases from entangled raw signal; 3. 'Disentangle' and map reads to a reference sequence. We designed library protocols to address the first problem, implemented a base caller that calls entangled bases, and devised a novel dynamic programming algorithm for mapping reads. We demonstrated our approach on an Illumina GAII sequencer, and successfully applied EMS to two applications: DNA tag-counting in yeast and resequencing of a genome of Salmonella enterica serotype typhimurium. EMS has the advantage that it can be readily applied with minimal modification of the existing Illumina pipeline, and is potentially useful. In addition, EMS has the potential to keep achieving the 2x gain as DNA sequencing technology evolves. |
| Long Abstract:Click Here |
|
| Poster J60 |
| WebGBrowse - A Web Server for GBrowse |
| Ram Podicheti- Center for Genomics and Bioinformatics, Indiana University |
| Rajesh Gollapudi (Indiana University, Informatics); Qunfeng Dong (University of North Texas, Biology); |
| Short Abstract: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser and visualize the configured genomic features with the integrated GBrowse software. For molecular biologists, WebGBrowse relieves both the burden of installing GBrowse and the need to learn the configuration semantics. WebGBrowse brings Genome Browser to personal level and thus a lot closer to the molecular biology community. |
| Long Abstract:Click Here |
|
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