Accepted Posters

Category 'I'- Genome Annotation'
Poster I01
AGeS: A Software System for Annotation and Analysis of Genome Sequences
Nela Zavaljevski- US Army Medical Research and Materiel Command
Kamal Kumar (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute); Valmik Desai (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute); Li Cheng (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute); Maxim Khitrov (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute); Deepak Grover (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute); Ravi Vijaya Satya (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute); Chenggang Yu (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute); Jaques Reifman (US Army Medical Research and Materiel Command, Biotechnology HPC Software Applications Institute);
Short Abstract: The software system for Annotation and Analysis of Genome Sequences (AGeS) allows remote users to upload draft genomic sequences from next-generation platforms, annotate genes and proteins, and visualize the annotated sequences with GBrowse. The uploaded sequences and annotated results are stored in a relational database system.
Long Abstract:Click Here

Poster I02
Biofuel Feedstock Genomics Resource - A Comparative Gene and Transcript Annotation Database for Lignocellulosic Feedstock Species
Kevin Childs- Michigan State University
Kranti Konganti (Michigan State University, Plant Biology Department); C. Robin Buell (Michigan State University, Plant Biology Department);
Short Abstract: We have uniformly annotated gene and transcript sequence from biofuel feedstock and model species in order to aid biofuel researchers in the characterization of their genes and sequences of interest. Additionally, data are presented in a comparative fashion so that researchers can easily leverage functional information across taxa.
Long Abstract:Click Here

Poster I03
Scanning genomic data for structurally related RNAs
Linda Stern- The University of Melbourne
Ross Hall (The University of Melbourne, Dept of Computer Science and Software Engineering);
Short Abstract: RNA Template Assisted Secondary Structure Search (RTASSS) identifies
members of RNA families in genomic DNA sequences, using structural
similarity, with bounded variation. Processing time is linear in the
length of the genomic sequence. Experimental validation has been
performed on tRNA and 5.8S ribosomal RNA families from a number of
organisms.
Long Abstract:Click Here

Poster I04
Ciport: A comparative and integrative transporter annotation tool and identification of lignin-related transporters
Patrick Xuechun Zhao- The Samuel Roberts Noble Foundation
Haiquan Li (The Samuel Roberts Noble Foundation, Plant Biology Division); Xinbin Dai (The Samuel Roberts Noble Foundation, Plant Biology Division);
Short Abstract: We develop a systematic computational approach for genome-wide membrane transporter functional characterization which integrates homology search, machine learning and empirical biological rules. In a case study, our comparative analysis between vascular and non-vascular plants identified an interesting transporter family which is likely to relate lignin production.
Long Abstract:Click Here

Poster I05
Genome Annotation Test for Evaluation of CHiP-Seq Peaks
Justin Bedo- NICTA
No additional authors
Short Abstract: Many ChIP-Seq experiments determining the locations of various genome features such as transcription start or transcription factor binding sites. Many such experiments lack techniques for evaluating and fine tuning wet-lab and bioinformatics techniques. We have developed a self consistency test whereby a dataset is tested against itself.
Long Abstract:Click Here

Poster I06
Whole genome characterisation of Francisella orientalis from tilapia
Sridhar Settu- University of Bergen
Animesh Sharma (University of Bergen, institute of informatics); Heidi Kongshaug (University of Bergen, department of biology); Frank Nilsen (University of Bergen, department of biology); Inge Jonassen (University of Bergen, institute of informatics);
Short Abstract: Francisella is a gram negative bacterium highly virulent in fishes and humans. Tilapia fishes are used as food resources and to control undesired aquatic plants. Francisella causing serious problems in Tilapia that leads to mortality. The results of complete genome characterisation of Francisella orientalis strain and comparative analysis is discussed.
Long Abstract:Click Here

Poster I07
Ensembl genome annotation for gorilla
Amy Tang- Wellcome Trust Sanger Institute
Bronwen Aken (Wellcome Trust Sanger Institute, Informatics); Susan Fairley (Wellcome Trust Sanger Institute, Informatics); Julio Fernandez-Banet (European Bioinformatics Institute, Microarray Informatics); Magali Ruffier (Wellcome Trust Sanger Institute, Informatics); Aylwyn Scally (Wellcome Trust Sanger Institute, Informatics); Jan-Hinnerk Vogel (Wellcome Trust Sanger Institute, Informatics); Simon White (Wellcome Trust Sanger Institute, Informatics); Amonida Zadissa (Wellcome Trust Sanger Institute, Informatics); Stephen Searle (Wellcome Trust Sanger Institute, Informatics); Richard Durbin (Wellcome Trust Sanger Institute, Informatics); Tim Hubbard (Wellcome Trust Sanger Institute, Informatics);
Short Abstract: Ensembl has annotated the gorGor3 gorilla genome assembly. Our release 58 gorilla annotation includes 20949 protein-coding genes based on evidence from human, gorilla and other vertebrates. We also provide 33515 RNA-Seq transcript models built from gorilla transcriptome data, allowing users to compare RNA-Seq models with Ensembl gene models.
Long Abstract:Click Here

Poster I08
Ensembl genome annotation for low- and high-coverage genomes
Magali Ruffier- Wellcome Trust Sanger Institute
Bronwen Aken (WEllcome Trust Sanger Institute, Informatics); Susan Fairley (WEllcome Trust Sanger Institute, Informatics); Jan-Hinnerk Vogel (WEllcome Trust Sanger Institute, Informatics); Steve Searle (WEllcome Trust Sanger Institute, Informatics); Simon White (WEllcome Trust Sanger Institute, Informatics); Amonida Zadissa (WEllcome Trust Sanger Institute, Informatics); Amy Tang (WEllcome Trust Sanger Institute, Informatics); Julio Fernandez Banet (European Bioinformatics Institute, Microarray); Michael Schuster (European Bioinformatics Institute, Ensembl Helpdesk); Kevin Howe (Cancer Research UK Cambridge Research Institute, Cancer Research UK); Tim Hubbard (Wellcome Trust Sanger Institute, Informatics);
Short Abstract: Gene annotation on low-coverage genome assemblies is difficult because genes can be split across sequence fragments. Ensembl has a pipeline to annotate low-coverage genomes. The quality of our pipeline will be assessed using elephant and rabbit, two species that were sequenced initially to low-coverage and then to high-coverage.
Long Abstract:Click Here

Poster I09
The comparative annotation and analysis platform at Canada's National Microbiology Laboratory
Philip Mabon- Public Health Agency of Canada
Gary Van Domselaar (Public Health Agency of Canada, National Microbiology Laboratory); Heather Kent (Public Health Agency of Canada, National Microbiology Laboratory);
Short Abstract: GenDB is an automatic web-based prokaryotic genome annotation platform that facilitates review and manual curation of annotations. We are currently working on our own distribution based on the GenDB framework with new functionality that allows for more rapid annotation of multiple genomes in parallel and analytical tools for comparative genomics.
Long Abstract:Click Here

Poster I10
ISGA - An Intuitive Web Server for Prokaryotic Genome Annotation and Other Analyses
Christopher Hemmerich- Indiana University
Aaron Buechlein (Indiana University, Center for Genomics and Bioinformatics);
Short Abstract: Integrative Services for Genomic Analysis (ISGA), a web-based prokaryotic genome annotation server, leverages the Ergatis workflow system. ISGA provides an intuitive web interfaces for biologists to customize and execute bioinformatics pipelines, and integrates standalone tools. ISGA is designed to be installed at genomics core facilities and used directly by biologists.
Long Abstract:Click Here

Poster I11
A linear-time algorithm for reconstructing zero-recombinant haplotype con?guration on pedigree with a small number of loops
Tao Jiang- University of California, Riverside
En-Yu Lai (National Yang-Ming University, Institute of Biomedical Informatics); Wei-Bung Wang (University of California, Riverside, Department of Computer Science); Kun-Pin Wu (National Yang-Ming University , Institute of Biomedical Informatics);
Short Abstract: This work is aimed to efficiently infer haplotypes from genotypes of individuals related by a pedigree assuming that the hereditary process was free of mutations and recombinants. We modeled the haplotype inference problem as a system of linear equations and developed a loop-tolerant extension of the linear time algorithm.
Long Abstract:Click Here

Poster I12
Unique identifiers for alternative splicing isoforms
Alberto Riva- University of Florida
Graziano Pesole (University of Bari, Italy, Department of Biochemistry and Molecular Biology);
Short Abstract: When we insert a CD in our computer's CD-ROM drive, the titles of its tracks automatically appear after a few seconds. How does the player program recognize the record? And, what does this have to to with alternative splicing? The answers to these questions will hopefully become clear by the end of this presentation. We have developed an algorithm that assigns a simple, unique identifier, called isoform signature, to the exon/intron structure of a primary gene transcript, suitable to be used as a key in databases of alternatively spliced isoforms, or to compare alternative splicing predictions produced by different methods. We will present the algorithm to calculate isoform signatures, discuss the importance of unique isoform identifiers in genomic research, and describe a web-based service we developed to compute isoform signatures and use them in database searches. And finally, we will explain about those CDs...
Long Abstract:Click Here

Poster I13
The potential functional role of chimeric transcripts in higher eukaryotes
Milana Frenkel-Morgenstern- Spanish National Cancer Research Centre (CNIO)
Alfonso Valencia (Spanish National Research Centre (CNIO), Structural Biology and BioComputing);
Short Abstract: Chimeric RNAs are produced by trans-splicing of two distinct transcripts, have been reported in different organisms.However, how the trans-splicing machinery can be used to design new functional proteins remains unclear. We found that chimeric RNAs resulting from trans-splicing, if they are translated, might produce the dominant negative effect in cells.
Long Abstract:Click Here

Poster I14
MaxExon: A tool for selecting maximum number and length of exons for DNA sequencing enrichment strategies
James Cavalcoli- University of Michigan
Zachary Wright (University of Michigan, Center for Computational Medicine and Bioinformatics);
Short Abstract: We present a web-based tool to generate custom genomic regions for sequence enrichment protocols using gene (known and predicted) tracks (UCSC). The tool returns the longest coordinates of all possible exons among all transcripts and gene prediction models. The output format can be modified for different enrichment strategies.
Long Abstract:Click Here

Poster I15
GBrowse and Next Generation Sequencing Data
Scott Cain- Ontario Institute for Cancer Research
Dave Clements (NESCent, GMOD); Lincoln Stein (Ontario Institute for Cancer Research, Informatics and Biocomputing);
Short Abstract: There is a need for displaying NGS data in a way that researchers can visualize it. The Bio::DB::Sam adaptor allows GBrowse to present data from a BAM database. Here we present examples of GBrowse with E. coli resequencing data using GBrowse as a NGS browser.
Long Abstract:Click Here

Poster I16
Fungal genome annotation with multi-genome Gnomon pipeline
Alexandre Souvorov- NCBI
Boris Kiryutin (NCBI, National Center for Biotechnology Information); Vyacheslav Chetvernin (NCBI, National Center for Biotechnology Information); Barbara Robbertse (NCBI, National Center for Biotechnology Information); Leonid Zaslavsky (NCBI, National Center for Biotechnology Information); Tatiana Tatusova (NCBI, National Center for Biotechnology Information); David Lipman (NCBI, National Center for Biotechnology Information);
Short Abstract: A novel multi-genome annotation method developed at NCBI has been applied to eight Aspergillus genomes. The proposed method is an iterative process that starts from single genome gene
Gnomon predictions and uses predicted proteins to gradually improve
the annotation. The annotations are tremendously improved compared to the single-genome annotation method.
Long Abstract:Click Here

Poster I17
Transcriptomics Platform Integration for Expression and Splice Variant Detection
John Van Hemert- Iowa State University
Alberto Ferrarini (University of Verona, Italy, Science and Technology); Mario Pezzotti (University of Verona, Italy, Science and Technology); Massimo Delledonne (University of Verona, Italy, Science and Technology); Julie Dickerson (Iowa State University, Electrical and Computer Engineering);
Short Abstract: We have developed a method for transcriptomics platform integration
that represents data in four levels: a genome, base-specific
expression levels, gene models, and functional annotation. Different
platforms are integrated into "meta-probes" on the genome and
quantified with respect to underlying gene models for biological
interpretation including alternatively spliced genes.
Long Abstract:Click Here

Poster I18
Finding Frameshifts in 1100+ Prokaryotic Genomes
Ivan Antonov- Georgia Institute of Technology
Mark Borodovsky (Regents' Professor, Department of Biomedical Engineering and Division of Computational Science and Engineering);
Short Abstract: A new frameshift prediction program GeneTack was applied to 1,102 prokaryotic genomes. It has identified 206,991 potential frameshifts subsequently validated by BLASTp and Pfam and grouped into orthologous clusters. Most confident predictions include 5,523 sequencing errors and 19,182 conserved frameshift mutations many of which are likely to be programmed frameshifts.
Long Abstract:Click Here

Poster I19
The Oak Ridge National Lab Genome Annotation Pipeline Workflow
Daniel Quest- Oak Ridge National Lab
Loren Hauser (Oak Ridge National Lab, Biological Sciences Division); Doug Hyatt (Biological Sciences Division, Oak Ridge National Lab); Janet Yun-Juan Chang (Oak Ridge National Lab, Biological Sciences Division); Frank Larimer (Oak Ridge National Lab, Biological Sciences Division); Cynthia Jeffries (Oak Ridge National Lab, Biological Sciences Division); Thomas Brettin (Oak Ridge National Lab, Biological Sciences Division); Miriam Land (Oak Ridge National Lab, Biological Sciences Division); Robert Cottingham (Oak Ridge National Lab, Biological Sciences Division);
Short Abstract: This work prototypes a next generation genome annotation engine using workflow technology and Symantec Web data representations. The resulting system streamlines conventional annotation systems by increasing process interoperability, reduces dependencies, and separates work processes from the underlying hardware and software implementations.
Long Abstract:Click Here

Poster I20
CAFA: a Community Driven Effort to Assess Protein Function Predicitons
Iddo Friedberg- Miami University
Predrag Radivojac (Indiana University, Informatics and Computing);
Short Abstract: We will assess the quality of current computational techniques in an unbiased manner via a set of presented protocols we term CAFA: Critical Assessment of (protein) Functional Annotations. We call upon the community of computational function predictors to submit their predictions of several thousand gene targets we will provide.
Long Abstract:Click Here

Poster I21
Functional Gene Ontology Annotation across Species using PAINT
Pascale Gaudet- Northwestern University
Eduardo Lee (Lawrence Berkeley National Lab , Berkeley Bioinformatics); Michael Livstone (Princeton University, Lewis-Sigler Institute for Integrative Genomics); Kara Dolinski (Princeton University, Lewis-Sigler Institute for Integrative Genomics); Suzanna Lewis (Lawrence Berkeley National Lab, Berkeley Bioinformatics); Paul Thomas (University of Southern California, Preventive Medicine);
Short Abstract: Genes sharing a common ancestor often function similarly. We have developed PAINT, a Phylogenetic Annotation and INference Tool that exploits evolutionary relationships between proteins to transfer Gene Ontology annotations more precisely than other methods. PAINTing GO annotations across genomes provides opportunities to improve primary annotations, consistency, and ontology structure.
Long Abstract:Click Here

Poster I22
GENCODE: Producing the Reference Human Gene Set for ENCODE
Adam Frankish- Wellcome Trust Sanger Institute
Tyler Alioto (Centre for Genomic Regulation, Bioinformatics and Genomics); Bronwen Aken (Wellcome Trust Sanger Institute, Ensembl Group); Philip Cayting (Yale University, Department of Molecular Biophys. and Biochem); Thomas Derrien (Centre for Genomic Regulation, Bioinformatics and Genomics); Mark Diekhans (UCSC, Center for Biomolecular Science and Engineering); Rachel Harte (UCSC, Center for Biomolecular Science and Engineering); Cedric Howald (University of Lausanne, Center for Integrative Genomics); Felix Kokocinski (Wellcome Trust Sanger Institute, Bioinformatics); Mike Lin (Broad Institute, MIT Computer Science and AI Laboratory); Michael Tress (Spanish National Cancer Research Centre (CNIO), Structural and Computational Biology); Jeltje van Baren (Washington University, Lab. for Comp. Genomics and Dept. of CS); James Gilbert (Wellcome Trust Sanger Institute, Bioinformatics); Michael Brent (Washington University, Lab. for Comp. Genomics and Dept. of CS); Mark Gerstein (Yale University, Department of Molecular Biophys. and Biochem); Roderic Guigó (Centre for Genomic Regulation-, Bioinformatics and Genomics); Manolis Kellis (Broad Institute, MIT Computer Science and AI Laboratory); Alexandre Reymond (University of Lausanne, Center for Integrative Genomics); Steve Searle (Wellcome Trust Sanger Institute, Ensembl Group); Jennifer Harrow (Wellcome Trust Sanger Institute, HAVANA group); Tim Hubbard (Wellcome Trust Sanger Institute, Bioinformatics);
Short Abstract: The GENCODE consortium is producing the reference human gene set for the ENCODE project using manual annotation, computational prediction and experimental validation. This geneset is available through the UCSC genome browser where annotated genes are assigned to one of three confidence levels based on their provenance and validation.
Long Abstract:Click Here

Poster I23
Purine degradation capacity of the human gut microbiome
Riccardo Percudani- University of Parma
Riccardo Percudani (University of Parma, Biochemistry and molecular biology); Vincenzo Puggioni (University of Parma, Biochemistry and molecular biology);
Short Abstract: In many animals part of the nitrogen waste is transferred in the form of oxidized purines to the intestine, constituting a potential nutrient source for microorganisms. Analysis of the human gut metagenome suggests the existence of a pathway for purine degradation with unknown molecular components.
Long Abstract:Click Here

Poster I24
DNA Annotation Induction: Intra- and Cross-Species in-silico Transcription Start Site Predictions
Justin Bedo- NICTA, Victoria Research Laboratory
Albin Steininger (University of Applied Sciences Technikum Wien, Department of Biomedical Engineering); Izhak Haviv (The Alfred Medical Research and Education Precinct, Baker Medical Research, Dept. of Biochemistry and Molecular Biology of The University of Melbourne); Adam Kowalczyk (NICTA, Victoria Research Laboratory, Dept. of Electrical and Electronic Engineering);
Short Abstract: We have shown that the knowledge of DNA sequences and functional annotation locations of
transcription start sites of a small part of the whole genome (one chromosome or less) is sufficient to
build models capable of robust prediction of genome-wide sites intra- and cross-species.
Long Abstract:Click Here

Poster I25
Detecting Trans-Splicing Events and Non-co-Linear Transcripts in Transcriptome Assemblies
Inanc Birol- Genome Sciences Centre BC Cancer Agency
Inanc Birol (BC Genome Sciences Centre, Bioinformatics);
Short Abstract: Most methods to study transcriptome sequencing data from high throughput sequencing technologies are based on alignment of the reads to a reference genome or transcriptome. Two of the limitations of this approach are the requirement of a good reference genome and its proper annotation. However, even for the well-studied genomes, alignment-based analysis is a biased approach, with the null hypothesis of the experimental sequence being identical to the sequence of the reference genome; hence they tend to miss large scale events, such as novel transcripts or splicing. In this work, we describe an assembly-based analysis method as an unbiased discovery tool, with a special emphasis on trans-splicing events and non-co-linear transcripts.
Ever since its inception, the central dogma of molecular biology has been under revision, and lately, there is building evidence against the tidy co-linear splicing paradigm being the only route to building mature transcripts. Although exceptions to it were accepted to be common phenomena in nematode and kineoplastid transcriptomes resequencing experiments on mammalian transcriptomes using high throughput sequencing technologies all but ignored them, mostly due to their difficult-to-decipher signature in short read alignments. We report that improved specificity of alignment gained by assembled contigs makes the analysis of transcriptome sequencing data more potent, and helps us detect novel transcription events, including trans-splicing and non-co-linear transcription.
Long Abstract:Click Here

Poster I26
Automated Gene-Model Curation using Global Discriminative Learning
Axel Bernal- University of Pennsylvania
Koby Crammer (Technion. Israel Institute of Technology, Electrical Engineering); Fernando Pereira (University of Pennsylvania, Google Inc., Computer and Information Sciences);
Short Abstract: Gene-model curation exploits multiple sources of evidence to construct annotations. Manual curation gives the best results still, but it is a slow and costly process. Here we present eCRAIG, an automated gene-model curator that improves significantly over the best gene predictors and annotation pipelines on nGASP, eGASP and other datasets.
Long Abstract:Click Here

Accepted Posters


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