Genome Informatics Session 1 DATABASES, DATA MINING, VISUALIZATION AND CURATION WEDNESDAY 10/30/2013, 7:30 PM M. Fiume / C. Bult # lname Title Talk Length 1 Fiume MedSavant—Graphical search engine for genetic variants 15 2 Colak ELASPIC—Combining ensemble learning and structure-based modeling to accurately predict 15 effects on affinity and stability of protein mutations 3 Coraor Galaxy's long-term sustainability—Deployment to the XSEDE system 15 4 Nip jhive—Visual network comparison with differential hive plots 15 Bult No abstract 15 5 Nutter Progress towards a turnkey system for high-throughput variant discovery and interpretation 15 6 Ouellette Data availability and re-usability in the transition from microarray to next-generation 15 sequencing—Can we do better? 7 Smith The Genome Modeling System—An analysis engine for next generation genome sequencing 15 KEYNOTE SPEAKER: Michael Snyder THURSDAY 10/31/2013, 9:00 AM Session 2 TRANSCRIPTOMICS, ALTERNATIVE SPLICING AND GENE PREDICTIONS THURSDAY 10/31/2013, 9:45 AM M. Stanke / C. Burge # lname Title Talk Length 8 Stanke Simultaneous gene finding in aligned genomes 15 9 Ainsley Genome wide characterization of ribosome-bound mRNA from activated dendrites 15 10 Kannan Optimal algorithms and fundamental limits for de novo transcriptome assembly 15 11 Mortazavi A computational pipeline for the validation of canonical RNA editing using ICE-seq 15 Burge No abstract 15 12 Neretti Genome-wide transcriptional landscape of repetitive elements in humans 15 13 Patro Sailfish—RNA-seq expression estimates need not take longer than a cup of coffee 15 14 Sibbesen Probabilistic transcriptome assembly 15 Session 3 POSTER SESSION I THURSDAY 10/31/2013, 2:00 PM # lname Title Talk Length 15 Abolude Human Microbiome Project data analysis and coordination center resources for user-friendly, automated metagenomic analysis 16 Adhikari Genomic analysis of atoxigenic isolates of Aspergillus flavus 17 Aganezov Varying-resolution synteny blocks construction for large-scale phylogenomics 18 Aitken Kinetic signatures—A novel approach to time series expression data analysis Page 1 of 9 19 Akatsuka Informatics for analyzing distribution of oxidative DNA damages across the entire genome in mammalian cells 20 Alameer Modeling complex genetic and environmental influences on ALS and FTD 21 Argimon In silico genome subtraction to simplify the discovery of accessory sequences in microbial genomes 22 Ballouz Characterizing RNA-seq through the meta-analysis of co-expression networks 23 Barrell Ensembl Gene Annotation 2013 24 Beier Assembling barley chromosome 3H by multiplexed Illumina sequencing 25 Benoukraf Visualizing the DNA/DNA interactome using ChromoLens 26 Berthelot Benchmarking ChIP-seq pipelines for non-model species data 27 Blankenberg Wrangling Galaxy’s reference data 28 Bouvier Improving reproducibility using automated testing frameworks 29 Boyle The real effect of SNPs on transcription factor binding 30 Canzar Cutterhead—Recovering low-expressed transcripts from RNA-seq 31 Chan RNA-seq analysis workflow comparison on Ion Torrent data 32 Coffman DGIdb—Mining the druggable genome 33 Colak Novel machine learning approach identifies 30-40% of alternative splicing isoforms as novel functional proteins 34 Criscione RepEnrich—A new method to estimate repetitive element enrichment reveals age-associated changes in retrotransposon expression 35 Daugherty The IGS analysis engine 36 Davila Analysis and characterization of immunoglobulin light chain SMRT™ sequencing data in normal and amyloid samples 37 De Pons Search, visualization, comparison, and annotation of next-gen rat strain sequence at the Rat Genome Database 38 DeBoever Transcriptome sequencing reveals aberrant 3’ splicing and alternative 3’ UTR usage in SF3B1-mutated cancers 39 Denas Deep modeling of gene expression regulation during erythropoiesis 40 Dobin Circular RNA detection and classification using RNA-seq data 41 Erickson ENCODE Project data access via REST API and JSON 42 Ferretti The new ICGC data portal and its underlying scalable software architecture 43 Fortini Optimization of PAR-CLIP and RNA-Seq analysis to give insights into the internal organization and function of a nuclear long noncoding RNA:Protein complex 44 Fourrage Identification and visualization of alternative splicing events in Uveal Melanoma RNA-seq samples using EASANA 45 Frankish Identifying functional ‘nonsense’ across the human genome Page 2 of 9 46 Friedberg Critical assessment of function annotations 2—Lessons learned and the road ahead 47 Fu RNA-Seq based transcriptome assembly, profiling, and polymorphism identification of two alfalfa genotypes 48 Fu Conserved secondary structure prediction for RNA homologs with domain insertions—Dynalign II 49 Ghosh Evaluation of methods to analyze isoform expression from RNA-Seq data generated by the Ion Torrent *Proton platform 50 Ghosh Two-step alignment for optimal ION *Proton RNA-Seq analysis 51 Giardine Using workflows for consistent analysis of ChIP-seq and RNA-seq data 52 Goecks Understanding cancer genomes using Galaxy 53 Gonnella Harlekin—Effective and scalable homopolymer error correction for NGS data 54 Gonzalez Increasing the GENCODE mouse lncRNA gene repertoire using RNAseq data 55 Gout Transcriptome analysis reveals novel gene coding variants and fusion transcripts in infant acute lymphoblastic leukemia 56 Gupta GABox—A "white-box" genome annotation pipeline 57 Gurtowski An improved method for hybrid correction of long-read, low-identity sequencing data 58 Haberman Ziv Ileal transcriptome analysis in treatment naïve pediatric Crohn’s disease supports age-related immune maturation that is associated with induction and pathogenesis of disease in the ileum 59 hajirasouliha A combinatorial approach for constructing ancestral history of tumors, using inferred mutational frequencies in deep sequenced genomes 60 Halpern Use of known variants within the iSAAC variant calling pipeline, with evaluation using the Platinum Genomes resource 61 Hansen BARD—Detection of copy number alterations in next-generation sequence from tumors and matched normal samples 62 Hayes Transitioning phytozome genome visualization to JBrowse 63 Herrero Genome assembly assessment based on single copy genes 64 Hong Draft genome sequence of three Pseudomonas sp. strain H1, H5-1 and H5-2, analysis revealing genes for caprolactam degradation 65 Hou Detecting pico-inversions using multi-species alignment 66 Imai New genome assembly algorithm using only PacBio continuous long reads for genomes larger than bacterial genomes 67 Isomoto Population based discovery of tobacco-smoking-related differential DNA methylation 68 Jacobsen Systematic analysis of microRNA target interactions across diverse cancer types 69 Jain SBRI—A sampling based quantitative index to evaluate ChIP-Seq reproducibility 70 Janga Dissecting the expression landscape of RNA-binding proteins implicated in human cancers 71 Janin Versatile cloud-based genomics with compressed text indexes Page 3 of 9 72 Janky Detecting master regulators and cis-regulatory interactions in human cancer related gene networks 73 Jex The draft Trichuris suis genome 74 Jiao Maize Pan-genome construction by short reads assembly 75 Jose Functional annotation of transcriptomes assembled de-novo from RNA-Seq data using random walk with return 76 JUNG Bacterial community structure and yield of the red pepper, Capsicum annum L., under different cropping systems via 454-pyrosequencing 77 Katayama Histogram Clustering approach for ChIP-seq data across multiple samples 78 Khalfan DNA subway—Genomics, DNA barcoding, and RNA-seq bringing cutting-edge biology into the classroom 79 Kim TopHat3—Faster and more sensitive spliced alignment 80 Kucukural Flexible pipeline generation platform for HPC systems 81 Kumari Emergence—Data-driven pipeline discovery interface integrating multiple bioinformatics platforms 82 Kyriazopoulou Integrating gene expression and sequence data with existing biological knowledge to model context-specific gene regulation 83 Lam Mapping of a non-canonical secondary structure, the G-quadruplex, in the mammalian genome 84 Layer Efficient and accurate DNA classification without sequence alignment 85 Layer LUMPY—A probabilistic framework for structural variant discovery 86 Lederman General purpose and customized random-permutations-based mappers 87 Lederman Using the long-range “independence” property of DNA for read mapping 88 Li Oshell—A comprehensive work environment for NGS analysis 89 Li A regression model for assessing factors that affect the reproducibility of high-throughput experiments 90 Liseron-Monfils The dynamic of regulatory network based on transcription factors and miRNAs during plant development and response to stresses 91 Liu Linear time de novo detection of transposable elements with sequence variation 92 Loraine Visualizing RNA-Seq data with Integrated Genome Browser 7.0 93 MARSHALL The future of the Samtools software package 94 Marshall Exome sequencing 1000 individuals with extreme bone density—Rare variant discovery and Validation 95 Martin Collared flycatcher genome annotation 96 Middleton NoFold—RNA structure characterization without folding or alignment 97 Minot Evaluating novel metagenomic classification algorithms for forensic microbial detection Page 4 of 9 98 Mirmomeni Increasing genome assembly quality using high performance computing 99 Monaco Gramene—A resource for comparative plant genomics 100 Moore The antecedents of higher-order chromatin—Insights from integrative modelling