Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models
Predicting drug–target interactions from chemical and genomic kernels using Bayesian matrix factorization
Integrating literature-constrained and data-driven inference of signalling networks
Efficient sampling for Bayesian inference of conjunctive Bayesian networks
Context-specific transcriptional regulatory network inference from global gene expression maps using double two-way t -tests
Metabolite identification and molecular fingerprint prediction through machine learning
Network inference using steady-state data and Goldbeter–koshland kinetics
Targeted retrieval of gene expression measurements using regulatory models
A regression model for estimating DNA copy number applied to capture sequencing data
Fast and accurate read alignment for resequencing
A bioimage informatics approach to automatically extract complex fungal networks
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
ANGES: reconstructing ANcestral GEnomeS maps
RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
Cell-Dock: high-performance protein–protein docking
GAPIT: genome association and prediction integrated tool
CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data
CySBML: a Cytoscape plugin for SBML
DanteR: an extensible R-based tool for quantitative analysis of -omics data
ECCB 2012: The 11th European Conference on Computational Biology
ECCB 2012 Organization
Telescoper: de novo assembly of highly repetitive regions
Long read alignment based on maximal exact match seeds
Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd -trees
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Decoding properties of tRNA leave a detectable signal in codon usage bias
Accurate estimation of short read mapping quality for next-generation genome sequencing
MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis
Nonlinear dimension reduction with Wright–Fisher kernel for genotype aggregation and association mapping
Evolution of gene neighborhoods within reconciled phylogenies
Uncovering the co-evolutionary network among prokaryotic genes
Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements
Fractionation, rearrangement and subgenome dominance
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
Multiple instance learning of Calmodulin binding sites
Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding
A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
Protein domain recurrence and order can enhance prediction of protein functions
EnrichNet: network-based gene set enrichment analysis
LocTree2 predicts localization for all domains of life
Techniques to cope with missing data in host–pathogen protein interaction prediction
Identifying functional modules in interaction networks through overlapping Markov clustering
Graphlet-based edge clustering reveals pathogen-interacting proteins
Identification of chemogenomic features from drug–target interaction networks using interpretable classifiers
Boolean approach to signalling pathway modelling in HGF-induced keratinocyte migration
Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks
The architecture of the gene regulatory networks of different tissues
Random sampling of elementary flux modes in large-scale metabolic networks
Relating drug–protein interaction network with drug side effects
Comprehensive estimation of input signals and dynamics in biochemical reaction networks
Trajectory-oriented Bayesian experiment design versus Fisher A-optimal design: an in depth comparison study
Reveal—visual eQTL analytics
Hybrid spatial Gillespie and particle tracking simulation
Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions
An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB
ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings
Event extraction across multiple levels of biological organization
Gene–gene interaction analysis for the survival phenotype based on the Cox model
Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
An accurate paired sample test for count data
Bayesian assignment of gene ontology terms to gene expression experiments
Drug target prediction using adverse event report systems: a pharmacogenomic approach
From phenotype to genotype: an association study of longitudinal phenotypic markers to Alzheimer's disease relevant SNPs
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis