Talks and Posters at the Genome Informatics Conference
This poorly arranged conference by CSHL requires you to pay to even see the abstracts. Talk about rise of sharing and open-access in science !! Most talks are uninteresting and the political connection (read NHGRI) appears to be the selection criterion rather than quality of science. A number of good scientists I know are dropping out of CSHL-arranged conferences.
talks
Aboukhalil, R. - GinkgoInteractive analysis and quality assessment of single- cell CNV data
BAE, S. - A genetic analysis of a complex trait in a genetically intractable gut microbe
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
Chiang, C. - Detection and interpretation of genome structural variation in GTEx samples
Chin, J. - Diploid genome assembly and comprehensive haplotype sequence reconstruction
Church, D.M. - The Rumsfeldian challenges of developing clinical sequencing tests
Cooke, D. - Haplotype-based somatic mutation calling in heterogeneous cancer samples
Dabdoub, S. - Computational analysis of disease-associated functional shifts in the periodontal microbiome
Vera, D. - Differential nuclease sensitivity profiling of human chromatin reveals cell-type specific nucleosome positions, nucleosome sensitivity, open chromatin, and transcription factor binding
De, S. - SASE-hunterA computational method to detect signatures of accelerated somatic evolution in non-coding regions of cancer genomes
Fang, H. - Scikit-riboAccurate A-site prediction and robust modeling of translation control from Riboseq and RNAseq data
Friedberg, I. - A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins
Gymrek, M.A. - Characterization of the microsatellite mutation process at every locus in the genome
Lunter, G. - Basecalling from raw Oxford Nanopore data
Luo, Z. - Genome-wide copy number variation analysis for Plasmodium vivax global isolates
McLysaght, A. - Dosage sensitive genes in evolution and disease
Melsted, P. - KallistoNear-optimal RNA-Seq quantification
Meltz Steinberg, K.N. - Identifying low frequency and rare coding variation influencing cardiometabolic traits through whole exome sequencing of 20,000 FinnsThe FinMetSeq Study
Miller, C. - Assessing tumor heterogeneity and tracking clonal clearance in response to therapy
Nattestad, M. - Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing
Nellore, A. - An analysis of splicing variation across the sequence read archive with Rail-RNA
Neretti, N. - Reorganization of chromosome architecture in cellular senescence
Ning, Z. - Genome scaffolding and structural variation detection from MinION Nanopore sequencing data
Oguz, C. - Predictive modeling of coronary artery calcification using decision trees
Park, Y. - Using Mendelian randomization to investigate association between gene expression variation and complex traits
Pembroke, W.G. - Temporal transcriptomics reveals dysregulation of twin- peaking genes which reset the clock in a mouse model of psychiatric disease
Phillippy, A. - How to compare and cluster every known genome in about an hour
Quinlan, A.R. - Why is querying the genome so difficult?
Rabani, M. - Unbiased discovery of cis-regulatory elements that determine mRNA post-transcriptional regulation during early development
Ribeiro, D. - Comparative genomics over 50 newly-sequenced species of parasitic worms
Rubanova, Y. - Using a bump hunting approach for genome-wide identification of novel imprinted genes
Siepel, A.C. - Genome-wide inference of natural selection on regulatory sequences in the human genome
Singer, M. - Identifying novel drivers of CD8 T cell exhaustion in tumor
Siska, C.J. - Evaluating the application of sequencing data to differential coexpression using the discordant method
Stokowy, T. - RareVariantVisA new tool for identification of causative variants in rare monogenic disorders from whole genome sequencing data
TANG, Y. - Hidden RNA codes revealed from the plant in vivo RNA structurome
Trapnell, C. - Differential analysis of bifurcating single-cell gene expression trajectories
Hartley, S.W. - JunctionSeqDetecting differential splice junction usage via RNA-Seq
Hide, W.A. - PCxN, the pathway co-activity mapA new approach for the unification of functional biology
Hoffman, M. - Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Itan, Y. - Discovery of genetic heterogeneity in a context of physiological homogeneity by biological distance clustering
Kelley, D.R. - Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks
Kim, D. - HISAT2Graph-based alignment of next-generation sequencing reads to a population of human genomes
Li, Q. - Improved methods for NGS-based conotoxin discovery
Jex, A.R. - Genomic assembly and analysis of highly heterzygotic polyploidal parasitic protists
posters
Abyzov, A. - Comprehensive profiling of somatic mosaicism in human brain
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
Balasubramanian, G.
Detection of pathogen integration sites in cancer
poster
Ballouz, S.
AuPairWiseBiologically 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 minutesBuilding 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
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 ProgressionHappier developers, happier users
poster
Chen, J.
slnckyA 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
Chilton, J.M.
Building more expressive Galaxy workflows
poster
Chougule, K.M.
Assessing new tools and best practices for RNA seq data analysis and visualization with iPlant cyberinfrastructure
poster
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
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
Derr, A.
ESATA new tool for analyzing end-sequencing RNA-Seq data
poster
Deshwar, A.G.
Reconstructing the evolutionary history of tumours
poster
Dobin, A.
Precision-STARUnbiased allele aware mapping of RNA-seq reads to personal genomes
poster
Dunn, N.A.
ApolloA 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.
TuneSimTunable variant set Simulator for NGS reads
poster
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
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.
DIDAA first digenic diseases database
poster
Gingeras, T.
PIPESA tool for classifying long RNA reads
poster
Girgis, H.Z.
RedAn 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.
MeTavGenA 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.
ADAGEA 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
Ha, K.
Systematic analysis of alternative polyadenylation during neurogenesis of murine embryonic stem cells
poster
Habegger, L.
CLAMMSA scalable pipeline for CNV calling and quality control, applied to over 40,000 exomes
poster
Hackl, T.
proovread-3.0PacBio 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.
TEpeaksA tool for including repetitive sequences in ChIP-seq and Clip-seq analyses
poster
Harris, J.
CNVThresherCombining multiple lines of evidence to construct high-quality CNV call sets
poster
Hause, R.J.
The landscape of microsatellite instability in cancer exomes
poster
Hauser, F.E.
On the relativity of time and space of tumorsClinical 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.
EncoreA comprehensive framework for cancer sequencing analysis
poster
HEBRARD, M.
MetaTreeMapVisual representation of taxonomic assignment
poster
Helaers, R.
HighlanderVariant 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
Hitz, B.
The ENCODE Uniform Analysis Pipelines
Case studies in cloud-based data analysis and distribution
poster
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.
The human gene damage indexA 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 ReactomeA reference resource for analyzing plant metabolic and regulatory pathways
poster
Jin, Y.
BAMQCA 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
Khan, H.
Chop-StitchTargeted 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, 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.
CanuA 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.
KollectorTranscript-guided targeted assembly of genes
poster
Kucukural, A.
DolphinLarge-scale sequencing analysis platform
poster
Kumar, N.
Multimedia annotation using the iCLiKVAL browser extension
poster
Kumar, V.
The DOE Systems Biology KnowledgebaseA 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.
ForwardA 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.
FastqDemultiplexA flexible demultiplexing tool for Illumina reads
poster
Liang, S.
Speeding up long-read assembly by reducing alignments overlap due to repeats
poster
Lim, E.
PoseidonA 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.
GenomsawitA one-stop genome information portal for oil palm
poster
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
Meynert, A.M.
Targeted sequencing of FFPE ovarian cancer tumour samples on the Ion PGM platform
poster
Molik, D.
Automated transfer of workflows from Galaxy to Yabi and command line tools
poster
Mulvaney, J.D.
Searching and exploring Gramenes comparative genomics datasets on the web
poster
Nakato, R.
Comparative analysis of chromatin states and gene expression profiles for various endothelium cells
poster
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
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
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
Pertea, M.
Accurate and efficient transcript identification and quantification using RNA- Seq data
poster
Phan, L.
NCBIs Genetic Variation Resources
poster
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.
BoilerA 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
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 3UTRs
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
Rowicka, M.
Clarify and quantifying mechanisms of DSB formation using mathematical modelling and BLESS sequencing
poster
Saunders, G.
Normalizing variation between open-access variation datasets
poster
Sauria, M.
The Galaxy HiC browserAn 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
Silverstein, K.A.
Highly dynamic expansions of antimicrobial loci among Medicago truncatula accessions are revealed by inclusion of SMRT sequencing
poster
Singh, A.P.
Duplex sequencing for low allele frequency detection
poster
Smith, K.S.
SomVarIUSSomatic variant identification from unpaired tissue samples
poster
Stein, J.C.
GrameneComparative plant genomics and pathway resources
poster
Sung, M.-H.
Profiling protein occupants of the genomeIs 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
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
Turaga, N.
Galaxy Methylation Toolkit as a galaxy flavor
poster
Turner-Maier, J.P.
200 MammalsSequence 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.
CRISPRscanDesigning highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
poster
Verleyen, W.
SAPLINGA 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 2Faster and more sensitive metagenomic classification
poster
Yang, C.
NanoSimNanopore 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
