|
Presenting Author |
Abstract Title |
Talk/Poster |
|
Aboukhalil, R. |
Ginkgo—Interactive analysis and quality assessment of single-cell CNV data |
talk |
|
Abyzov, A. |
Comprehensive profiling of somatic mosaicism in human brain |
poster |
|
Ahn, J. |
Decoupling array CGH sample-reference hybridization pairs for normalization of log ratio artefacts. |
poster |
|
Alzbutas, G. |
5-hydroxymethylcytosine in Daphnia pulex |
poster |
|
Amar, D. |
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets |
poster |
|
Arce, J. |
Optimization of de novo transcriptome assembly and differential expression analysis of salt tolerance genes in the halophyte Suaeda fruticosa |
poster |
|
Aswad, L. |
Molecular delineation of two major oncogenic pathways governing invasive ductal breast cancer development |
poster |
|
BAE, S. |
A genetic analysis of a complex trait in a “genetically intractable” gut microbe |
talk |
|
Balasubramanian, G. |
Detection of pathogen integration sites in cancer |
poster |
|
Ballouz, S. |
AuPairWise—Biologically focused RNA-seq quality control using co-expression |
poster |
|
Bao, R. |
Integrated genomic analysis suggests inherited predisposition to cancer in therapy-related acute lymphoblastic leukemia (tr-ALL) |
poster |
|
Blankenberg, D. |
From the ground to the cloud in just minutes—Building a customized Galaxy analysis server using only a web browser |
poster |
|
Bowman, M. |
A modified MAKER structural genome annotation method reveals novel gene predictions of high and low GC content in rice |
poster |
|
Breitwieser, F.P. |
A novel software tool and pipeline for the classification of meta-genomics sequencing data, and their application to the diagnosis of neuropathological infections of the nervous system |
talk |
|
Brumm, R. |
A software tool for data integration in a diagnostic laboratory |
poster |
|
Cain, S. |
GMOD in the Cloud 2.0 |
poster |
|
Cech, M. |
Galaxy Tool World Progression—Happier developers, happier users |
poster |
|
Chen, J. |
slncky—A software and novel approach for annotation and evolutionary analysis of LncRNAs |
poster |
|
Chen, T. |
PickArmSite, investigate the preference of using one arm for miRNAs |
poster |
|
Chen, Z. |
Abundant Inverted Duplicates in the Human and Mouse Genomes as Functional Regulatory elements evolving under sex-related selection |
poster |
|
Chiang, C. |
Detection and interpretation of genome structural variation in GTEx samples |
talk |
|
Chilton, J.M. |
Building more expressive Galaxy workflows |
poster |
|
Chin, J. |
Diploid genome assembly and comprehensive haplotype sequence reconstruction |
talk |
|
Chougule, K.M. |
Assessing new tools and best practices for RNA seq data analysis and visualization with iPlant cyberinfrastructure |
poster |
|
Church, D.M. |
The Rumsfeldian challenges of developing clinical sequencing tests |
talk |
|
Cooke, D. |
Haplotype-based somatic mutation calling in heterogeneous cancer samples |
talk |
|
Cremer, C. |
Deconvolving gene expression profiles for tumor populations with prior frequency information |
poster |
|
Criscione, S.W. |
Comparison of chromosome structure across conditions using a three dimensional chromosome browser |
poster |
|
Dabdoub, S. |
Computational analysis of disease-associated functional shifts in the periodontal microbiome |
talk |
|
Dale, R. |
Wrangling data into track hub visualizations with hubward |
poster |
|
Das Roy, R. |
Identification of differentially expressed genes of developing mouse tooth within their genomic locations |
poster |
|
Dashnow, H.H. |
Comparing algorithms to genotype short tandem repeats in next-generation sequencing data |
poster |
|
Davila, J. |
The impact of RNA degradation on the ability to detect fusions using TruSeq RNA library Preparation |
poster |
|
Davis, A.R. |
Additional variants among the MH-GRID cohort discovered after alignment to an ancestry specific reference genome |
poster |
|
De, S. |
SASE-hunter—A computational method to detect signatures of accelerated somatic evolution in non-coding regions of cancer genomes |
talk |
|
Derr, A. |
ESAT—A new tool for analyzing end-sequencing RNA-Seq data |
poster |
|
Deshwar, A.G. |
Reconstructing the evolutionary history of tumours |
poster |
|
Dobin, A. |
Precision-STAR—Unbiased allele aware mapping of RNA-seq reads to personal genomes |
poster |
|
Dunn, N.A. |
Apollo—A platform for collaborative genome curation and analysis |
poster |
|
Ence, D.D. |
Assembly-free comparative genomics of Trichomonas vaginalis and three other trichomonads |
poster |
|
Eng, S.W. |
Biologically based disease classification for childhood arthritis |
poster |
|
Escaliere, B. |
TuneSim—Tunable variant set Simulator for NGS reads |
poster |
|
Fang, H. |
Scikit-ribo—Accurate A-site prediction and robust modeling of translation control from Riboseq and RNAseq data |
talk |
|
Foltz, S.M. |
Genomic region and sample selection strategy for variant discovery and association analysis |
poster |
|
Freeberg, M. |
Transcriptome states identified by probabilistic modeling of CLIP-seq datasets in yeast |
poster |
|
Friedberg, I. |
A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins |
talk |
|
Frieden, A. |
Orthogonal sequencing of the human exome |
poster |
|
Garcia, G. |
K-mer spectra filters to assemble high quality, contiguous, collapsed mosaics from non-model heterozygous genomes |
poster |
|
Gazzo, A.M. |
DIDA—A first digenic diseases database |
poster |
|
Gingeras, T. |
PIPES—A tool for classifying long RNA reads |
poster |
|
Girgis, H.Z. |
Red—An intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale |
poster |
|
Goldfarb, T. |
RefSeq annotation of functional elements on the human and mouse reference genomes |
poster |
|
Goldstein, L.D. |
Structural alteration of transcript isoforms in human cancers |
poster |
|
Gonnella, G. |
MeTavGen—A Taverna-based pipeline for the analysis of shotgun metagenomic data |
poster |
|
Gorthi, A. |
Characterization of DNA damage response and R-loops in Ewing sarcoma |
poster |
|
Gouin, A. |
Improvement of the assembly of heterozygous genomes of non-model organisms |
poster |
|
Grabowska, E. |
Concordance and contamination checker for WGS and WES matched sample studies |
poster |
|
Greene, C.S. |
ADAGE—A method for the unsupervised integration of gene expression experiments applied to Pseudomonas aeruginosa |
poster |
|
Gurtowski, J. |
The genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano |
poster |
|
Gymrek, M.A. |
Characterization of the microsatellite mutation process at every locus in the genome |
talk |
|
Ha, K. |
Systematic analysis of alternative polyadenylation during neurogenesis of murine embryonic stem cells |
poster |
|
Habegger, L. |
CLAMMS—A scalable pipeline for CNV calling and quality control, applied to over 40,000 exomes |
poster |
|
Hackl, T. |
proovread-3.0—PacBio hybrid error correction for di-/polyploid genomes, metagenomes and transcriptomes |
poster |
|
Hansen, N.F. |
Utilization of very large read depth sequencing data for the detection of variation in a father-mother-son trio |
poster |
|
Hao, Y. |
TEpeaks—A tool for including repetitive sequences in ChIP-seq and Clip-seq analyses |
poster |
|
Harris, J. |
CNVThresher—Combining multiple lines of evidence to construct high-quality CNV call sets |
poster |
|
Hartley, S.W. |
JunctionSeq—Detecting differential splice junction usage via RNA-Seq |
talk |
|
Hause, R.J. |
The landscape of microsatellite instability in cancer exomes |
poster |
|
Hauser, F.E. |
On the relativity of time and space of tumors—Clinical segmentation is the key to eradicate breast cancer |
poster |
|
Havrilla, J. |
Using the landscape of genetic variation in protein domains to improve functional consequence predictions |
poster |
|
He, M. |
Encore—A comprehensive framework for cancer sequencing analysis |
poster |
|
HEBRARD, M. |
MetaTreeMap—Visual representation of taxonomic assignment |
poster |
|
Helaers, R. |
Highlander—Variant filtering made easier |
poster |
|
Hicks, S.C. |
On the widespread and critical impact of batch effects and systematic bias in single-cell RNA-Seq data |
poster |
|
Hide, W.A. |
PCxN, the pathway co-activity map—A new approach for the unification of functional biology |
talk |
|
Hitz, B. |
The ENCODE Uniform Analysis Pipelines—
Case studies in cloud-based data analysis and distribution |
poster |
|
Hoffman, M. |
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet |
talk |
|
Hong, C. |
Integrated approach to identify clinically relevant CNVs in ClinSeq� cohort |
poster |
|
Hwang, B. |
De novo assembly and next-generation sequencing to analyze full-length gene variants from codon-barcoded libraries |
poster |
|
Itan, Y. |
Discovery of genetic heterogeneity in a context of physiological homogeneity by biological distance clustering |
talk |
|
Itan, Y. |
The human gene damage index—A novel gene-level approach to prioritize exome variations |
poster |
|
Itan, Y. |
The mutation significance cutoff (MSC)—A gene-specific approach to predicting the impact of human gene variants |
poster |
|
Jacques, P. |
Large scale correlation of epigenomics data |
poster |
|
Jaffe, A.E. |
Interrogating the mechanisms of schizophrenia genetic risk in the fully characterized human brain transcriptome |
poster |
|
Jaiswal, P. |
Plant Reactome—A reference resource for analyzing plant metabolic and regulatory pathways |
poster |
|
Jex, A.R. |
Genomic assembly and analysis of highly heterzygotic polyploidal parasitic protists |
talk |
|
Jin, Y. |
BAMQC—A quality control tool for mapped next generation sequencing datasets |
poster |
|
Jongeneel, V. |
Benchmarking ultrafast workflows for human genome variant calling |
poster |
|
Joshi, J. |
Utilization of high-throughput sequencing to detect candidate genes associated with mouse reproductive longevity |
poster |
|
Kadarmideen, H.N. |
Construction of transcription factor networks for obesity using RNAseq transcriptomics |
poster |
|
Kadarmideen, H.N. |
Genetic network method based analysis of antidepressant treatment |
poster |
|
Kahles, A. |
Building a meta-metagenome graph |
poster |
|
Karro, J.E. |
A dynamic programming approach to the reconstruction of prokaryote gene block evolution history |
poster |
|
Kelley, D.R. |
Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks |
talk |
|
Khan, H. |
Chop-Stitch—Targeted assembly of genes using transcriptome assembly and Bloom filter-based de Bruijn graphs |
poster |
|
Khan, M.M. |
Role of lincRNA in T helper cell differentiation |
poster |
|
Kim, D. |
HISAT2—Graph-based alignment of next-generation sequencing reads to a population of human genomes |
talk |
|
Kim, H. |
Comprehensive, flexible pipelines for alternative polyadenylation analysis |
poster |
|
Kim, J. |
Identification and filtration of false somatic variants caused by vector contamination |
poster |
|
Kim, S. |
Genomic-based 16S ribosomal RNA database web server and tools |
poster |
|
Kitts, P. |
Improving accessibility and usability of genome data at NCBI |
poster |
|
Knnight, J. |
JBAM quality score compression |
poster |
|
Koren, S. |
Canu—A new single-molecule sequence assembler for genomes large and small |
poster |
|
Kozaki, T. |
Phylogeny of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) from Japan reconstructed by their transcriptomes |
poster |
|
Krishnan, A. |
Bringing genomic data into focus for studying complex diseases in specific biological contexts |
poster |
|
Kucuk, M. |
Kollector—Transcript-guided targeted assembly of genes |
poster |
|
Kucukural, A. |
Dolphin—Large-scale sequencing analysis platform |
poster |
|
Kumar, N. |
Multimedia annotation using the iCLiKVAL browser extension |
poster |
|
Kumar, V. |
The DOE Systems Biology Knowledgebase—A system for collaborative and reproducible inference and modeling of biological function |
poster |
|
Lage, K. |
A comparative analysis of network mutation burdens across 21 tumor types predicts new candidate cancer genes in the tail of the mutation distribution of existing cancer genomes |
poster |
|
Lage, K. |
Large-scale prediction of pathways from GWAS and exome-sequencing projects by a systematic analysis of differential pathway architectures in diverse functional genomic networks |
poster |
|
Lamichhaney, S. |
Identification of the genetic basis underlying alternative reproductive strategies in the ruff (Philomachus pugnax) |
poster |
|
Lee, H. |
The resurgence of reference quality genome |
poster |
|
Lee, Y. |
Unified framework for genome-wide characterization of human diseases |
poster |
|
Legault, M. |
Forward—A bioinformatics tool to manage, execute and explore phenomic studies |
poster |
|
Lemieux Perreault, L. |
genipe —A Python module to perform genome-wide imputation analysis |
poster |
|
Lenz, F. |
FastqDemultiplex—A flexible demultiplexing tool for Illumina reads |
poster |
|
Li, Q. |
Improved methods for NGS-based conotoxin discovery |
talk |
|
Liang, S. |
Speeding up long-read assembly by reducing alignments overlap due to repeats |
poster |
|
Lim, E. |
Poseidon—A highly sensitive and efficient taxonomy classifier |
poster |
|
Liyakat Ali, T. |
Transcriptome and epigenome profiling of human olfactory mucosa stem cells as a model system for autism spectrum disorders |
poster |
|
Low, L.E. |
Genomsawit—A one-stop genome information portal for oil palm |
poster |
|
Lunter, G. |
Basecalling from raw Oxford Nanopore data |
talk |
|
Luo, Z. |
Genome-wide copy number variation analysis for Plasmodium vivax global isolates |
talk |
|
Macleon, S. |
Determining the hypoxic gene expression response of S. cerevisiae cells using RNA-seq and statistical analysis of time-course data |
poster |
|
MADOUI, A. |
Microbial genome assembly using synthetic error-free reads |
poster |
|
McLysaght, A. |
Dosage sensitive genes in evolution and disease |
talk |
|
Melsted, P. |
Kallisto—Near-optimal RNA-Seq quantification |
talk |
|
Meltz Steinberg, K.N. |
Identifying low frequency and rare coding variation influencing cardiometabolic traits through whole exome sequencing of 20,000 Finns—The FinMetSeq Study |
talk |
|
Meynert, A.M. |
Targeted sequencing of FFPE ovarian cancer tumour samples on the Ion PGM platform |
poster |
|
Miller, C. |
Assessing tumor heterogeneity and tracking clonal clearance in response to therapy |
talk |
|
Molik, D. |
Automated transfer of workflows from Galaxy to Yabi and command line tools |
poster |
|
Mulvaney, J.D. |
Searching and exploring Gramene’s comparative genomics datasets on the web |
poster |
|
Nakato, R. |
Comparative analysis of chromatin states and gene expression profiles for various endothelium cells |
poster |
|
Nattestad, M. |
Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing |
talk |
|
Nellore, A. |
An analysis of splicing variation across the sequence read archive with Rail-RNA |
talk |
|
Neretti, N. |
Reorganization of chromosome architecture in cellular senescence |
talk |
|
Nevedomskaya, E. |
Probing transcriptional regulation in tumor specimens yields hallmarks of prostate cancer outcome |
poster |
|
Nie, K. |
Computational analysis of target specificity of double-stranded RNA binding protein Staufen |
poster |
|
Ning, Z. |
Genome scaffolding and structural variation detection from MinION Nanopore sequencing data |
talk |
|
Oguz, C. |
Predictive modeling of coronary artery calcification using decision trees |
talk |
|
Okagaki-Vraspir, L.H. |
Comparative genome analysis of members of the Magnaporthaceae family of fungi |
poster |
|
Olson, A. |
Integrated web services supporting search and interactive analysis tools at Gramene |
poster |
|
Park, M. |
The identification of the gene expression signatures of tissue-specific effects of pioglitazone treatments in a murine model of type 2 diabetes |
poster |
|
Park, Y. |
Using Mendelian randomization to investigate association between gene expression variation and complex traits |
talk |
|
Paropkari, A. |
Effects of hormonal changes and cigarette smoking on oral microbiome |
poster |
|
Pedersen, B.S. |
Enhancing the utility and usability of gemini for rare and common disease research |
poster |
|
Pembroke, W.G. |
Temporal transcriptomics reveals dysregulation of twin-peaking genes which reset the clock in a mouse model of psychiatric disease |
talk |
|
Pertea, M. |
Accurate and efficient transcript identification and quantification using RNA-Seq data |
poster |
|
Phan, L. |
NCBI’s Genetic Variation Resources |
poster |
|
Phillippy, A. |
How to compare and cluster every known genome in about an hour |
talk |
|
Piccolo, S.R. |
Mixture models that estimate gene-expression activation on a single-sample basis for any expression platform |
poster |
|
Pimentel, H. |
Transcript differential analysis of RNA-Seq data with sleuth |
poster |
|
Pinello, L. |
Genome-wide characterization of chromatin state plasticity |
poster |
|
Postma, A.V. |
New genetic approaches in patients with transposition of the great arteries |
poster |
|
Prasad, M. |
An automated data management system for hereditary cancer analysis in clinical diagnostics |
poster |
|
Pritt, M.J. |
Boiler—A compression tool for BAM files supporting fast, accurate queries |
poster |
|
Pruitt, K. |
Annotating, maintaining, and curating RefSeq prokaryotic genomes |
poster |
|
Pulman, J.A. |
Variation in tissue-specific codon usage across four members of the Poaceae |
poster |
|
Qi, R. |
Using ERCC spike-ins and erccdashboard R package to assess performance of differential gene expression detection by Ion AmpliSeqTM Transcriptome assays |
poster |
|
Quinlan, A.R. |
Why is “querying” the genome so difficult? |
talk |
|
Rabani, M. |
Unbiased discovery of cis-regulatory elements that determine mRNA post-transcriptional regulation during early development |
talk |
|
Ramani, A.K. |
The role of alternative splicing and gene expression in diffuse intrinsic pontine gliomas |
poster |
|
Rasmussen, S.H. |
microRNA target sites act as regulatory hotspots in 3’UTRs |
poster |
|
Ratan, A. |
Accurate prediction of breakpoints in sequences |
poster |
|
Razaviyayn, M. |
Iso-Seq bioinformatics analysis with PacBio long reads |
poster |
|
Rescheneder, P. |
Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis |
poster |
|
Ribeiro, D. |
Comparative genomics over 50 newly-sequenced species of parasitic worms |
talk |
|
Rowicka, M. |
Clarify and quantifying mechanisms of DSB formation using mathematical modelling and BLESS sequencing |
poster |
|
Rubanova, Y. |
Using a bump hunting approach for genome-wide identification of novel imprinted genes |
talk |
|
Saunders, G. |
Normalizing variation between open-access variation datasets |
poster |
|
Sauria, M. |
The Galaxy HiC browser—An interactive multi-dimensional genome topology browser and data repository |
poster |
|
Schlaffner, C. |
Quantitative proteogenomics application to personalised proteomics |
poster |
|
Schneider, V.A. |
Updating approaches to reference assembly curation |
poster |
|
Schones, D.E. |
Regulatory variation in mice with diverse responses to environmental stimuli is driven by transposable element variation and environmentally induced chromatin remodeling at tissue specific transcription factor binding sites |
poster |
|
Sedlazeck, F.J. |
Detection of structural variants using third generation sequencing |
poster |
|
Sen, S.K. |
Reference-masked RNA-Seq assembly in human tissues relevant for cardiovascular disease and Type 2 diabetes reveals unannotated transcripts at the chr9p21 GWAS candidate locus |
poster |
|
Sheth, P. |
Optimizations of physical genome map contiguity by in silico ligation |
poster |
|
Siepel, A.C. |
Genome-wide inference of natural selection on regulatory sequences in the human genome |
talk |
|
Silverstein, K.A. |
Highly dynamic expansions of antimicrobial loci among Medicago truncatula accessions are revealed by inclusion of SMRT sequencing |
poster |
|
Singer, M. |
Identifying novel drivers of CD8 T cell exhaustion in tumor |
talk |
|
Singh, A.P. |
Duplex sequencing for low allele frequency detection |
poster |
|
Siska, C.J. |
Evaluating the application of sequencing data to differential coexpression using the discordant method |
talk |
|
Smith, K.S. |
SomVarIUS—Somatic variant identification from unpaired tissue samples |
poster |
|
Stein, J.C. |
Gramene—Comparative plant genomics and pathway resources |
poster |
|
Stokowy, T. |
RareVariantVis—A new tool for identification of causative variants in rare monogenic disorders from whole genome sequencing data |
talk |
|
Sung, M.-H. |
Profiling protein occupants of the genome—Is TF footprinting ready for prime time? |
poster |
|
Tanaka, H. |
De novo mutations induced by multiple DNA double strand breaks are revealed by whole-genome sequencing of Arabidopsis thaliana |
poster |
|
TANG, Y. |
Hidden RNA codes revealed from the plant in vivo RNA structurome |
talk |
|
Taylor, T.D. |
Increasing discoverability and connectivity of scientific media through annotation with iCLiKVAL |
poster |
|
Teer, J.K. |
Exploring database options for storage of diverse DNA sequence variation datasets |
poster |
|
Teo, Y. |
A comparative study of metagenomic analysis pipelines for accurate quantification of relative species abundance |
poster |
|
Trapnell, C. |
Differential analysis of bifurcating single-cell gene expression trajectories |
talk |
|
Turaga, N. |
Galaxy Methylation Toolkit as a galaxy flavor |
poster |
|
Turner-Maier, J.P. |
200 Mammals—Sequence conservation at the single basepair level |
poster |
|
Ullah, U. |
Identification of global regulators of T-helper cell lineages specification |
poster |
|
Vacca, A. |
An integrated analysis of the transcriptional response of human monocyte-derived macrophages to LPS |
poster |
|
Vejnar, C.E. |
CRISPRscan—Designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo |
poster |
|
Vera, D. |
Differential nuclease sensitivity profiling of human chromatin reveals cell-type specific nucleosome positions, nucleosome sensitivity, open chromatin, and transcription factor binding |
talk |
|
Verleyen, W. |
SAPLING—A tool for customized network analysis focusing on psychiatric genetics |
poster |
|
Wang, B. |
Unveiling the complexity of maize B73 transcriptome by single molecule long read sequencing |
poster |
|
Wang, L. |
Building a distributed system for sequence analysis |
poster |
|
Wang, Y. |
Rapid, dynamic, and interactive visualization framework for pathogen identification in complex respiratory specimens from unexplained respiratory disease outbreak responses |
poster |
|
Weber, M. |
A novel approach to determining null models and controls for co-expression networks |
poster |
|
Williams-DeVane, C.R. |
Decision tree-based method for integrating multi-domain data to identify childhood obesity disease endotypes |
poster |
|
Wintersinger, J.A. |
Scaling cancer subpopulation phylogeny reconstruction to thousands of tumors |
poster |
|
Wong, L. |
Genetic insights into juvenile idiopathic arthritis derived from deep whole genome sequencing |
poster |
|
Wood, D.E. |
Kraken 2—Faster and more sensitive metagenomic classification |
poster |
|
Yang, C. |
NanoSim—Nanopore sequencing read simulator based on statistical characterization |
poster |
|
Ye, K. |
Cloud-based variant discovery using GenomeVIP |
poster |
|
Ye, P. |
The role of PIWI-interacting RNAs in LINE-1 evolutionary dynamics |
poster |
|
Zhong, Y. |
Probabilistic model for detecting mRNA translation efficiency changes from ribosome profiling |
poster |