Genome Informatics Meeting at CSHL #GI2013
The meeting is taking place currently. Please follow #GI2013 at twitter for running commentary. A list of talks and posters are given below from this page.
Presenting Author
Abstract Title
Talk/Poster
Abolude, O.
Human Microbiome Project data
analysis and coordination center resources for
user-friendly, automated metagenomic analysis
poster
Adhikari, B.
Genomic analysis of atoxigenic
isolates of Aspergillus flavus
poster
Aganezov, S.
Varying-resolution synteny blocks
construction for large-scale phylogenomics
poster
Ainsley, J.A.
Genome wide characterization of
ribosome-bound mRNA from activated dendrites
talk
Aitken, S.
Kinetic signaturesA novel
approach to time series expression data analysis
poster
Akatsuka, S.
Informatics for analyzing
distribution of oxidative DNA damages across the entire
genome in mammalian cells
poster
Alameer, R.S.
Modeling complex genetic and
environmental influences on ALS and FTD
poster
Alekseyev, M.
Reconstruction of ancestral
genomes in presence of gene loss
talk
Argimon, S.
In silico
__ genome subtraction
to simplify the discovery of accessory sequences in
microbial genomes
poster
Ballouz, S.
Characterizing RNA-seq through the
meta-analysis of co-expression networks
poster
Barrell, D.
Ensembl Gene Annotation 2013
poster
Beier, S.
Assembling barley chromosome 3H by
multiplexed Illumina sequencing
poster
Benoukraf, T.
Visualizing the DNA/DNA
interactome using ChromoLens
poster
Berthelot, C.
Benchmarking ChIP-seq pipelines
for non-model species data
poster
Blankenberg, D.
Wrangling Galaxys reference data
poster
Bouvier, E.
Improving reproducibility using
automated testing frameworks
poster
Boyle, A.P.
The real effect of SNPs on
transcription factor binding
poster
Brody, T.
Tools for analysis and comparison
of enhancer structure
talk
Canzar, S.
CutterheadRecovering
low-expressed transcripts from RNA-seq
poster
Carmel, L.
Paleo-epigeneticsReconstructing
the DNA methylation maps of archaic hominins
talk
Chan, P.P.
RNA-seq analysis workflow
comparison on Ion Torrent data
poster
Chin, J.
String graph assembly for diploid
genomes with long reads
talk
Coffman, A.
DGIdbMining the druggable genome
poster
Colak, R.
ELASPICCombining ensemble
learning and structure-based modeling to accurately predict
effects on affinity and stability of protein mutations
talk
Colak, R.
Novel machine learning approach
identifies 30-40% of alternative splicing isoforms as novel
functional proteins
poster
Coraor, N.
Galaxy’s long-term
sustainabilityDeployment to the XSEDE system
talk
Criscione, S.W.
RepEnrichA new method to estimate
repetitive element enrichment reveals age-associated changes
in retrotransposon expression
poster
Daugherty, S.C.
The IGS analysis engine
poster
Davila, J.
Analysis and characterization of
immunoglobulin light chain SMRT sequencing data in normal
and amyloid samples
poster
Day, D.S.
Responsive histone modifications
at regulatory elements activated upon VEGFA stimulation of
human endothelial cells
talk
De Pons, J.L.
Search, visualization, comparison,
and annotation of next-gen rat strain sequence at the Rat
Genome Database
poster
DeBoever, C.M.
Transcriptome sequencing reveals
aberrant 3 splicing and alternative 3 UTR usage in _
SF3B1_-mutated cancers
poster
Denas, O.
Deep modeling of gene expression
regulation during erythropoiesis
poster
Dobin, A.
Circular RNA detection and
classification using RNA-seq data
poster
Dror, I.
Widespread evidence for DNA shape
dependent transcription-factor binding preferences
talk
Erickson, D.T.
ENCODE Project data access via
REST API and JSON
poster
Erlich, Y.
Genetic media
talk
Ferretti, V.
The new ICGC data portal and its
underlying scalable software architecture
poster
Fiume, M.
MedSavantGraphical search engine
for genetic variants
talk
Fortini, E.
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
poster
Fourrage, C.
Identification and visualization
of alternative splicing events in Uveal Melanoma RNA-seq
samples using EASANA
poster
Frankish, A.
Identifying functional nonsense
across the human genome
poster
Friedberg, I.
Critical assessment of function
annotations 2Lessons learned and the road ahead
poster
Fu, F.
RNA-Seq based transcriptome
assembly, profiling, and polymorphism identification of two
alfalfa genotypes
poster
Fu, Y.
Conserved secondary structure
prediction for RNA homologs with domain insertionsDynalign
II
poster
Garber, M.
Evolutionary dynamics and tissue
specificity of human long noncoding RNAs in six mammals
talk
Gerstein, M.B.
Integrative annotation of variants
from 1,092 humansApplication to cancer genomics
talk
Ghosh, S.
Evaluation of methods to analyze
isoform expression from RNA-Seq data generated by the Ion
Torrent *Proton platform
poster
Ghosh, S.
Two-step alignment for optimal ION
*Proton RNA-Seq analysis
poster
Giardine, B.M.
Using workflows for consistent
analysis of ChIP-seq and RNA-seq data
poster
Goecks, J.
Understanding cancer genomes using
Galaxy
poster
Gonnella, G.
HarlekinEffective and scalable
homopolymer error correction for NGS data
poster
Gonzalez, J.M.
Increasing the GENCODE mouse
lncRNA gene repertoire using RNAseq data
poster
Gout, A.
Transcriptome analysis reveals
novel gene coding variants and fusion transcripts in infant
acute lymphoblastic leukemia
poster
Gupta, V.
GABoxA “white-box” genome
annotation pipeline
poster
Gurtowski, J.
An improved method for hybrid
correction of long-read, low-identity sequencing data
poster
Gymrek, M.A.
Short tandem repeat polymorphisms
create an abundant source of expression variability
talk
Haberman Ziv, Y.
Ileal transcriptome analysis in
treatment nave pediatric Crohns disease supports
age-related immune maturation that is associated with
induction and pathogenesis of disease in the ileum
poster
hajirasouliha, i.
A combinatorial approach for
constructing ancestral history of tumors, using inferred
mutational frequencies in deep sequenced genomes
poster
Halpern, A.
Use of known variants within the
iSAAC variant calling pipeline, with evaluation using the
Platinum Genomes resource
poster
Hansen, N.F.
BARDDetection of copy number
alterations in next-generation sequence from tumors and
matched normal samples
poster
Hara, Y.
Identification and
characterization of ultramicro inversions within local
alignments between closely related species
talk
Hayden, K.E.
Complete sequence representation
across human centromeric regions
talk
Hayes, R.D.
Transitioning phytozome genome
visualization to JBrowse
poster
Herrero, J.
Ancestry of single base pair
variants in the human genome
talk
Herrero, J.
Genome assembly assessment based
on single copy genes
poster
Hide, W.
Community development of validated
variant calling pipelines
talk
Hon, C.
Determinants for the localization
of short antisense transcripts at 3’end of protein-coding
genes in protozoan Entamoeba histolytica is encoded
in the genome
talk
Hong, S.
Draft genome sequence of three _
Pseudomonas _sp. strain H1, H5-1 and H5-2, analysis
revealing genes for caprolactam degradation
poster
Hou, M.
Detecting pico-inversions using
multi-species alignment
poster
Imai, T.
New genome assembly algorithm
using only PacBio continuous long reads for genomes larger
than bacterial genomes
poster
Isomoto, A.
Population based discovery of
tobacco-smoking-related differential DNA methylation
poster
Jacobsen, A.
Systematic analysis of microRNA
target interactions across diverse cancer types
poster
Jain, D.P.
SBRIA sampling based quantitative
index to evaluate ChIP-Seq reproducibility
poster
Janga, S.
Dissecting the expression
landscape of RNA-binding proteins implicated in human
cancers
poster
Janin, L.
Versatile cloud-based genomics
with compressed text indexes
poster
Janky, R.
Detecting master regulators and
cis-regulatory interactions in human cancer related gene
networks
poster
Jex, A.R.
The draft_ Trichuris suis_
genome
poster
Jiao, Y.
Maize Pan-genome construction by
short reads assembly
poster
Jose, A.
Functional annotation of
transcriptomes assembled de-novo from RNA-Seq data using
random walk with return
poster
JUNG, B.
Bacterial community structure and
yield of the red pepper, Capsicum annum L., under
different cropping systems via 454-pyrosequencing
poster
Kannan, S.
Optimal algorithms and fundamental
limits for de novo transcriptome assembly
talk
Kasowski, M.
Extensive variation in chromatin
states across humans
talk
Katayama, K.
Histogram Clustering approach for
ChIP-seq data across multiple samples
poster
Khalfan, M.
DNA subwayGenomics, DNA
barcoding, and RNA-seq bringing cutting-edge biology into
the classroom
poster
Kim, D.
TopHat3Faster and more sensitive
spliced alignment
poster
Kucukural, A.
Flexible pipeline generation
platform for HPC systems
poster
Kumari, P.
EmergenceData-driven pipeline
discovery interface integrating multiple bioinformatics
platforms
poster
Kyriazopoulou Panagiotopoulou, S.
Integrating gene expression and
sequence data with existing biological knowledge to model
context-specific gene regulation
poster
Lam, E.
Mapping of a non-canonical
secondary structure, the G-quadruplex, in the mammalian
genome
poster
Lau, B.
Discovering more variants in a
human genomeNew algorithms applied to longer and less
biased reads
talk
Layer, R.M.
Efficient and accurate DNA
classification without sequence alignment
poster
Layer, R.M.
LUMPYA probabilistic framework
for structural variant discovery
poster
Lederman, R.
General purpose and customized
random-permutations-based mappers
poster
Lederman, R.
Using the long-range
“independence” property of DNA for read mapping
poster
Li, J.
OshellA comprehensive work
environment for NGS analysis
poster
Li, Q.
A regression model for assessing
factors that affect the reproducibility of high-throughput
experiments
poster
Liseron-Monfils, C.V.
The dynamic of regulatory network
based on transcription factors and miRNAs during plant
development and response to stresses
poster
Lister, R.
Global epigenomic reconfiguration
during mammalian brain development
talk
Liu, X.
Linear time de novo detection of
transposable elements with sequence variation
poster
Loraine, A.
Visualizing RNA-Seq data with
Integrated Genome Browser 7.0
poster
Ma, J.
Tracing the evolution of
lineage-specific transcription factor binding sites
talk
MacArthur, D.G.
Integrated analysis of
protein-coding variation in over 50,000 individuals
talk
Marques, A.
Chromatin status separates two
equally populated yet distinct classes of intergenic long
noncoding RNAs
talk
MARSHALL, J.
The future of the Samtools
software package
poster
Marshall, M.
Exome sequencing 1000 individuals
with extreme bone densityRare variant discovery and
Validation
poster
Martin, F.
Collared flycatcher genome
annotation
poster
Mascher, M.
Anchoring and ordering NGS contig
assemblies by population sequencing (POPSEQ)
talk
Middleton, S.A.
NoFoldRNA structure
characterization without folding or alignment
poster
Miller, J.R.
Scalable assembly of native
single-molecule reads
talk
Minot, S.
Evaluating novel metagenomic
classification algorithms for forensic microbial detection
poster
Mirmomeni, M.
Increasing genome assembly
quality using high performance computing
poster
Monaco, M.K.
GrameneA resource for comparative
plant genomics
poster
Moore, B.L.
The antecedents of higher-order
chromatinInsights from integrative modelling
poster
Morrissey, C.S.
Improving ChIP-seq peak
identification using subsampling
poster
Mortazavi, A.
A computational pipeline for the
validation of canonical RNA editing using ICE-seq
talk
Moxon, S.
A combined computational and
genetic approach to identify novel canonical and
non-canonical miRNAs in zebrafish
poster
Mukamel, E.A.
Genomic sequence determinants of
cell-type specific DNA methylation
poster
Naito, Y.
GGRNAA Google-like, ultrafast
search engine for genes and transcripts
poster
Nakaki, R.
CoLoA novel algorithm to
distinguish significant co-localizations through multiple
ChIP-seq data comparison
poster
Nakato, R.
Comparative ChIP-seq analysis of
cohesin and CTCF for multiple cells
poster
Narechania, A.
Finding clusters in the flockA
new method to explore incongruent gene partitions in
phylogenomic datasets
poster
Narzisi, G.
SCALPELMicro-assembly approach to
detect INDELs within exome-capture data
talk
Nekrutenko, A.
Finding missing analysis tools
with Galaxy ToolShedA case of mitochondrial RNA
modification
poster
Neretti, N.
Genome-wide transcriptional
landscape of repetitive elements in humans
talk
Ning, Z.
Cross_genomeAssembly Improvement
using cross species synteny
poster
Nip, K.
jhiveVisual network comparison
with differential hive plots
talk
Nissen, A.M.
Trio-based study of neuromuscular
dysfunction using whole exome sequencing
poster
Niu, B.
HOTSPOTA novel computational tool
for inferring functional importance of cancer mutations
through 3D proximity analyses
poster
Noutsos, C.
Atmosphere, iPlant Collaboratives
cloud computing for plant sciences
poster
Nutter, N.G.
Progress towards a turnkey system
for high-throughput variant discovery and interpretation
talk
O’Connor, B.D.
SeqWare on the multicloudEnabling
distributed analysis in disparate environments
poster
Oesper, L.
Analysis of complex genomic
rearrangements using high-throughput DNA sequencing data
talk
Olson, A.
Learning to tell the difference
between genes and junk
poster
Ono, H.
RefExReference expression dataset
for tissue transcriptome
poster
Onuki, R.
Development of a miRNAs prediction
pipeline for the wheat chromosome 6B genome sequence
poster
O’Rawe, J.A.
Integrating multiple sequencing
and informatics pipelines in the study of one large pedigree
poster
Ouellette, F.
Data availability and re-usability
in the transition from microarray to next-generation
sequencingCan we do better?
talk
Ouellette, F.
FGEDThe Functional Genomics Data
Society
poster
Ouellette, F.
Streamlining development and
maintenance of sequence analysis pipelines
poster
Park, G.
De novo
__ assembly and
insecticidal toxin gene mining of entomopathogenic bacteria,
Photorhabdus temperata M1021 genome
poster
Patro, R.
SailfishRNA-seq expression
estimates need not take longer than a cup of coffee
talk
Pendleton, M.R.
Detection and resolution of tandem
repeats from single molecule sequencing data
poster
Philip, G.
Bioinformatics tutorials using
Galaxy
poster
Piper, J.
WellingtonA novel method for the
accurate identification of digital genomic footprints from
DNase-seq data
poster
Prasad, A.
Genome sequence and initial
analysis of malaria model Plasmodium coatneyi
poster
Preece, J.S.
Plant ReactomeMetabolic and
regulatory networks for plants
poster
Price, T.S.
Benchmarking RNAseq algorithms to
detect differential expression of splice forms
poster
Quinlan, A.R.
Mining genetic variation with
GEMINI
talk
Raney, B.J.
Assembly data hubs support viewing
any sequence on the UCSC Genome Browser
poster
Rao, K.R.
Functional data-mining for protein
structure families without folding or homology modeling
poster
Ratsch, G.
Causes and consequences of cancer
transcriptome variability
talk
Ratsch, G.
PALMapperFast, accurate and
variation-aware RNA-Seq alignments
poster
Ream, D.
Towards a universal model of gene
block evolution in bacteria and archaeaThe case for
proteobacteria
poster
Rebolledo-Jaramillo, B.
Controlling for contamination in
re-sequencing studies with a reproducible phylogenetic
approach
poster
Regier, A.
Automatic interpretation of
non-protein coding somatic variants
poster
Rensch, T.
Modelling of complex tissue
ChIP-sequencing
poster
Rockowitz, S.
Comparison of REST cistromes
across human cell types reveals common and context-specific
functions
poster
Roest Crollius, H.
Ancestral reconstructions provide
insight in vertebrate molecular and structural genome
evolution
talk
Ronen, R.
Whole genome sequencing uncovers
the genetics of chronic mountain sickness in Andean
highlanders
talk
Rozowsky, J.
Comparison of 3 metazoan
transcriptomes
talk
Saha, S.
Composition of the maize
endophytic microbiome is correlated with maize genotype
poster
Sanchez-Vega, F.
Differential methylation in the _
ZNF154, _CASP8 and VHL promoters is
recurrent across a wide variety of cancer types
poster
Sankoff, D.
Genome aliquoting for ancient
polyploids grape, tomato and sacred lotus
poster
Sauria, M.
High-resolution HiC analysis
method reveals sub-TAD, functionally diverse chromatin
modules
poster
Sedlazeck, F.J.
Improving de novo genome and
transcriptome assemblies using a consensus assembly and
genetic linkage information
poster
Sese, J.
Statistical significance of
combinatorial regulations
poster
Shah, R.H.
Developing a framework for for
detection of low frequency somatic genetic alterations in
targeted sequencing data
poster
Shahid, S.
De novo
__ annotation of _
Amborella_ small RNAs using ShortStack reveals unique
prevalence of non-conserved 23-24-nt miRNAs
poster
Shimamura, T.
Hierarchical Bayes model-based
analysis of chromatin interaction maps
poster
Shu, S.
PERTRANPredict transcripts from
paired-end or single-end RNA-seq reads
poster
Sibbesen, J.A.
Probabilistic transcriptome
assembly
talk
Silverstein, K.A.
Detecting small plant peptides
using SPADA (Small Peptide Alignment Discovery Application)
poster
Singer, M.
Intragenic exon methylation
combined with a unique epigenetic signature is positively
correlated with exon expression
poster
Smith, S.
The Genome Modeling SystemAn
analysis engine for next generation genome sequencing
talk
Sompallae, R.
Clinical validation of targeted
cancer gene mutations using next-generation sequencing
poster
Song, G.
Comparative analysis of _
Saccharomyces cerevisiae_Integrating functional
annotation with genetic variation
poster
Song, L.
CLASSA program for accurate
reconstruction of genes and alternative splicing variations
from RNA-seq data
poster
Stadler, M.
Systematic exploration of coding
sequence determinants of heterologous protein yields in a
mammalian expression system
poster
Standage, D.S.
mRNAmarkupQuality control and
annotation of de novo transcriptome assemblies
poster
Stanke, M.
Simultaneous gene finding in
aligned genomes
talk
Syed, A.
Developing a data management
system for NGS clinical diagnostics
poster
Taghavi, Z.
Distilled single-cell genome
sequencing and de novo assembly for sparse microbial
communitiesComparison of different search techniques
poster
Tang, L.
Visualizing consequences of
genetic variation in biological networks
poster
Thiru, P.
Mining expression compendia to
identify differences in metabolism between cancer and normal
tissues
poster
Trinh, J.
Genome-wide linkage analysis and
rare variant association methods to identify LRRK2 p.G2019S
age of onset modifiers
poster
Verleyen, W.
Characterizing algorithmic and
data dependencies in the computational analysis of gene
function
poster
Wang, H.
Novel stress-induced smRNAs from
Brachypodium distachyon
poster
Wang, Q.
The core regulons orchestrating
the response of Clostridium acetobutylicum to butanol
and butyrate stress
poster
Wei, S.
Exploring rice phylogenomics with
GRAMENE
poster
Westholm, J.M.
Identification of thousands of
circular RNAs in three Drosophila species
poster
Whitley, P.
Effects of sequencing coverage
bias on NIPT aneuploidy detection
poster
Wong, E.
A metadata standard to improve
access to biological samples and diverse experimental data
sets
poster
Wong, E.
Allele-specific contributions to
transcription factor binding in mouse
poster
Wong, W.
Whole genome miRNA-mRNA-DNA
integrative analysis in family trios
poster
Wood, D.E.
Rapid phylogenetic sequence
classification through repeated k-mer comparisons
talk
Wu, T.
Hybrid strategies for aligning
high-throughput sequencing reads
poster
Xuan, Z.
Reveal significant association of
genomic loci from protein-protein interactions
poster
Yan, K.
OrthoClustAn orthology-based
network framework for expression clustering across multiple
species
talk
Yeung, J.
Whole transcriptome alternative
splicing pipeline for analysis of subtype-specific splicing
signature of prostate cancer
poster
Zad, N.
Coverage rate of ADME genes from
commercial genotyping and sequencing assays
poster
Zerbino, D.R.
Updating the Ensembl regulatory
features
poster
Zhang, J.
Classify breast cancer patients
based on somatic mutations and gene interacation networks
poster
Zhang, W.
Competition between Pol II and
positioned nucleosomes for access to core promoters during
Drosophila development
poster
Zhao, S.
TMM_RPKM for within- and
between-sample RNA-Seq data normalization
poster
Zhao, X.
A hybrid method of incorporating
functional consequences into set-based association test to
discover rare non-synonymous variants in complex disease
poster
Zhu, Y.
A framework to generate ortholog
annotation for cross-species comparative analysis
poster
Zhu, Y.
Comprehensive depiction of genomic
interactions in cancer based on TCGA data
poster
Zmasek, C.M.
Analysis of the evolution of the
repertoire of RNA recognition proteins hints at ancestrally
complex RNA regulation
poster
