Evaluating synteny for improved comparative studies
EPIQ—efficient detection of SNP–SNP epistatic interactions for quantitative traits
A statistical approach for inferring the 3D structure of the genome
Inferring gene ontologies from pairwise similarity data
Automated detection and tracking of many cells by using 4D live-cell imaging data
Using association rule mining to determine promising secondary phenotyping hypotheses
Inductive matrix completion for predicting gene–disease associations
Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data
Pareto-optimal phylogenetic tree reconciliation
Large scale analysis of signal reachability
Cross-study validation for the assessment of prediction algorithms
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Deep learning of the tissue-regulated splicing code
Functional association networks as priors for gene regulatory network inference
Graph-regularized dual Lasso for robust eQTL mapping
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics
Metabolite identification through multiple kernel learning on fragmentation trees
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach
MIRA: mutual information-based reporter algorithm for metabolic networks
GRASP: analysis of genotype–phenotype results from 1390 genome-wide association studies and corresponding open access database
Detecting independent and recurrent copy number aberrations using interval graphs
Privacy preserving protocol for detecting genetic relatives using rare variants
Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
DrugComboRanker: drug combination discovery based on target network analysis
Scale-space measures for graph topology link protein network architecture to function
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions
An efficient parallel algorithm for accelerating computational protein design
Tertiary structure-based prediction of conformational B-cell epitopes through B factors
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
ExSPAnder: a universal repeat resolver for DNA fragment assembly
Ragout—a reference-assisted assembly tool for bacterial genomes
Stochastic EM-based TFBS motif discovery with MITSU
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
Accurate viral population assembly from ultra-deep sequencing data
Condition-specific target prediction from motifs and expression
TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
EXTREME: an online EM algorithm for motif discovery
Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures
Discrete mixture modeling to address genetic heterogeneity in time-to-event regression
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC)
Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals
iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array
Dynamic networks reveal key players in aging
Deciphering kinase–substrate relationships by analysis of domain-specific phosphorylation network
An APN model for Arrhythmic beat classification
Automated analysis of giant unilamellar vesicles using circular Hough transformation
MRHMMs: Multivariate Regression Hidden Markov Models and the variantS
jHeatmap: an interactive heatmap viewer for the web
ADaCGH2: parallelized analysis of (big) CNA data
CanSNPer: a hierarchical genotype classifier of clonal pathogens
SBARS: fast creation of dotplots for DNA sequences on different scales using GA-,GC-content
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing
SKINK: a web server for string kernel based kink prediction in α-helices
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing
MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes
BioPlat: a software for human cancer biomarker discovery
BicOverlapper 2.0: visual analysis for gene expression
Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis
GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms
Canto: an online tool for community literature curation