ISMB/ECCB 2013 Proceedings Papers Committee
A high-throughput framework to detect synapses in electron microscopy images
Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans
Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields
FuncISH: learning a functional representation of neural ISH images
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
Information-theoretic evaluation of predicted ontological annotations
Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM
Design of shortest double-stranded DNA sequences covering all k -mers with applications to protein-binding microarrays and synthetic enhancers
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation
A framework for scalable parameter estimation of gene circuit models using structural information
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
Stability selection for regression-based models of transcription factor–DNA binding specificity
Predicting drug-target interactions using restricted Boltzmann machines
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets
CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways
Simple topological properties predict functional misannotations in a metabolic network
IBD-Groupon: an efficient method for detecting group-wise identity-by-descent regions simultaneously in multiple individuals based on pairwise IBD relationships
Efficient network-guided multi-locus association mapping with graph cuts
Inference of historical migration rates via haplotype sharing
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations
Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks
Multitask learning for host–pathogen protein interactions
Identifying proteins controlling key disease signaling pathways
Predicting protein interactions via parsimonious network history inference
ThreaDom: extracting protein domain boundary information from multiple threading alignments
Protein threading using context-specific alignment potential
Predicting protein contact map using evolutionary and physical constraints by integer programming
Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms
Compressive genomics for protein databases
GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment
The RNA Newton polytope and learnability of energy parameters
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution
Poly(A) motif prediction using spectral latent features from human DNA sequences
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
A graph kernel approach for alignment-free domain–peptide interaction prediction with an application to human SH3 domains
Using state machines to model the Ion Torrent sequencing process and to improve read error rates
Haplotype assembly in polyploid genomes and identical by descent shared tracts
Short read alignment with populations of genomes
Relation between sequence and structure in membrane proteins
Evidence for the dissemination of cryptic non-coding RNAs transcribed from intronic and intergenic segments by retroposition
Janus—a comprehensive tool investigating the two faces of transcription
Structural RNA alignment by multi-objective optimization
Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites
Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins
Updating RNA-Seq analyses after re-annotation
miMsg: a target enrichment algorithm for predicted miR–mRNA interactions based on relative ranking of matched expression data
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
NETAL: a new graph-based method for global alignment of protein–protein interaction networks
Sharing and executing linked data queries in a collaborative environment
FYPO: the fission yeast phenotype ontology
RSVSim: an R/Bioconductor package for the simulation of structural variations
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
BioBlend: automating pipeline analyses within Galaxy and CloudMan
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses
Twine: display and analysis of cis -regulatory modules
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites
MEME-LaB: motif analysis in clusters
pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring
iFUSE: integrated fusion gene explorer
NetworkTrail—a web service for identifying and visualizing deregulated subnetworks
pyGenClean: efficient tool for genetic data clean up before association testing
Automated annotation and quantification of glycans using liquid chromatography–mass spectrometry
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli
A universal open-source Electronic Laboratory Notebook