A distance-based approach for testing the mediation effect of the human microbiome
BAUM : Improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach
VIPER : a web application for rapid expert review of variant calls
Optimal water networks in protein cavities with GAsol and 3D-RISM
MAGNAMWAR : An R package for genome-wide association studies of bacterial orthologs
Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer
Enhanced Functionalities for Annotating and Indexing Clinical Text with the NCBO Annotator+
PEATH : Single Individual Haplotyping by a Probabilistic Evolutionary Algorithm with Toggling
iPat : Intelligent Prediction and Association Tool for Genomic Research
QuantumClone : Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction
A Rapid Epistatic Mixed-model Association Analysis by Linear Retransformations of Genomic Estimated Values
Informational and Linguistic Analysis of Large Genomic Sequence Collections via Efficient Hadoop Cluster Algorithms
A benchmark study of scoring methods for non-coding mutations
PyChimera : Use UCSF Chimera modules in any Python 2.7 project
Protein classification using modified n-grams and skip-grams
Mustguseal : a server for multiple structure-guided sequence alignment of protein families
myTAI : evolutionary transcriptomics with R
DiffGraph : an R package for identifying gene network rewiring using differential graphical models
SimulaTE : simulating complex landscapes of transposable elements of populations
pyHVis3D : Visualising Molecular Simulation deduced H-bond networks in 3D
LeNup : Learning Nucleosome positioning from DNA sequences with improved convolutional neural networks
A network approach to exploring the functional basis of gene-gene epistatic interactions in disease susceptibility
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy
Enrichment analysis with EpiAnnotator
Toppar : An interactive browser for viewing association study results
Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors
Tumor purity quantification by clonal DNA methylation signatures
CGManalyzer : an R package for analyzing continuous glucose monitoring studies
PGA : post-GWAS analysis for disease gene identification
SV2 : Accurate Structural Variation Genotyping and De Novo Mutation Detection from Whole Genomes
ChopStitch : exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data
MIIC online : a web server to reconstruct causal or non-causal networks from non-perturbative data
Aligning dynamic networks with DynaWAVE
ChronQC : a quality control monitoring system for clinical next generation sequencing
CHROMIXS : automatic and interactive analysis of chromatography-coupled small angle X-ray scattering data
DyNetViewer : a Cytoscape app for dynamic network construction, analysis and visualization
Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification
polyPK : an R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach
A Benchmark for Comparing Precision Medicine Methods in Thyroid Cancer Diagnosis using Tissue Microarrays
Towards Self-Learning Based Hypotheses Generation in Biomedical Text Domain
PINE-SPARKY.2 for automated NMR-based protein structure research
A high-resolution map of the human small non-coding transcriptome
DeepSig : deep learning improves signal peptide detection in proteins
Multiple hot-deck imputation for network inference from RNA sequencing data
An automated benchmarking platform for MHC class II binding prediction methods
Computational identification of binding energy hot spots in protein–RNA complexes using an ensemble approach
DPMIND : degradome-based plant miRNA–target interaction and network database
R2DGC : threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R
CRNET : an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data
mTM-align : an algorithm for fast and accurate multiple protein structure alignment
Genome U-Plot : A Whole Genome Visualization
PRAPI : post-transcriptional regulation analysis pipeline for Iso-Seq
GenSSI 2.0 : multi-experiment structural identifiability analysis of SBML models
TCGA-assembler 2 : software pipeline for retrieval and processing of TCGA/CPTAC data
GRAM-CNN : a deep learning approach with local context for named entity recognition in biomedical text
Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations
Personal Cancer Genome Reporter : variant interpretation report for precision oncology
JASPAR RESTful API : accessing JASPAR data from any programming language
Delta : a new web-based 3D genome visualization and analysis platform
DeepSynergy : predicting anti-cancer drug synergy with Deep Learning
Analyzing large scale genomic data on the cloud with Sparkhit
K 2 and K * 2 : Efficient alignment-free sequence similarity measurement based on Kendall statistics
fMLC : fast multi-level clustering and visualization of large molecular datasets
GIGI-Quick : a fast approach to impute missing genotypes in genome-wide association family data
Sequential Feature Selection and Inference using Multivariate Random Forests
Rcupcake : an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API
ProbAnnoWeb and ProbAnnoPy : probabilistic annotation and gap-filling of metabolic reconstructions
Computational identification of micro-structural variations and their proteogenomic consequences in cancer
A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases
MOSAIC : a chemical-genetic interaction data repository and web resource for exploring chemical modes of action
Curatr : a web application for creating, curating and sharing a mass spectral library
CscoreTool : fast Hi-C compartment analysis at high resolution
GeoBoost : accelerating research involving the geospatial metadata of virus GenBank records
Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
NGLview–interactive molecular graphics for Jupyter notebooks
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
DaMiRseq—an R/Bioconductor package for data mining of RNA-Seq data : normalization, feature selection and classification
TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants
IndeCut evaluates performance of network motif discovery algorithms
gene2drug : a computational tool for pathway-based rational drug repositioning
SANA NetGO : a combinatorial approach to using Gene Ontology (GO) terms to score network alignments
PEITH(Θ) : perfecting experiments with information theory in Python with GPU support
FROGS : Find, Rapidly, OTUs with Galaxy Solution
SPRING : a kinetic interface for visualizing high dimensional single-cell expression data
Gene Graphics : a genomic neighborhood data visualization web application
Matrix factorization-based data fusion for the prediction of lncRNA–disease associations
Accurate mapping of tRNA reads
LitPathExplorer : a confidence-based visual text analytics tool for exploring literature-enriched pathway models
DeepSF : deep convolutional neural network for mapping protein sequences to folds
DNCON2 : improved protein contact prediction using two-level deep convolutional neural networks
Aether : leveraging linear programming for optimal cloud computing in genomics
Model-based design of bistable cell factories for metabolic engineering
Integrating 5hmC and gene expression data to infer regulatory mechanisms
ASAR : visual analysis of metagenomes in R
Bicycle : a bioinformatics pipeline to analyze bisulfite sequencing data
Identifying functionally informative evolutionary sequence profiles
ThetaMater : Bayesian estimation of population size parameter θ from genomic data
Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies
RecoverY : k-mer-based read classification for Y-chromosome-specific sequencing and assembly
iDINGO—integrative differential network analysis in genomics with Shiny application
bioBakery : a meta’omic analysis environment
Genome Context Viewer : visual exploration of multiple annotated genomes using microsynteny
CALQ : compression of quality values of aligned sequencing data
SATORI : a system for ontology-guided visual exploration of biomedical data repositories
Reproducible and flexible simulation experiments with ML-Rules and SESSL
Myriads : P-value-based multiple testing correction
scHiCNorm : A Software Package to Eliminate Systematic Biases in Single-Cell Hi-C Data
Reactome diagram viewer : data structures and strategies to boost performance
PipelineDog : a simple and flexible graphic pipeline construction and maintenance tool
ASElux : an ultra-fast and accurate allelic reads counter
CytoCtrlAnalyser : a Cytoscape app for biomolecular network controllability analysis
Meta-analytic principal component analysis in integrative omics application
SAPP : functional genome annotation and analysis through a semantic framework using FAIR principles
DDR : efficient computational method to predict drug–target interactions using graph mining and machine learning approaches
bioalcidae, samjs and vcffilterjs : object-oriented formatters and filters for bioinformatics files
Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network
PlanNET : Homology-based predicted interactome for multiple planarian transcriptomes
SPECTRE : a suite of phylogenetic tools for reticulate evolution
The OncoPPi Portal : an integrative resource to explore and prioritize protein–protein interactions for cancer target discovery
GDSCTools for mining pharmacogenomic interactions in cancer
Mapping-free variant calling using haplotype reconstruction from k-mer frequencies
MOCASSIN-prot : a multi-objective clustering approach for protein similarity networks
Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations
FUn : a framework for interactive visualizations of large, high-dimensional datasets on the web
An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition
shinyCircos : an R/Shiny application for interactive creation of Circos plot
Cpf1-Database : web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1
Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing
3dRPC : a web server for 3D RNA–protein structure prediction
Semi-supervised network inference using simulated gene expression dynamics
glactools : a command-line toolset for the management of genotype likelihoods and allele counts
Global proteomics profiling improves drug sensitivity prediction : results from a multi-omics, pan-cancer modeling approach
Classifying next-generation sequencing data using a zero-inflated Poisson model
SimulaTE : simulating complex landscapes of transposable elements of populations
Extreme learning machines for reverse engineering of gene regulatory networks from expression time series
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks
Predicting loop conformational ensembles
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction
Identification of topological features in renal tumor microenvironment associated with patient survival
microRPM : a microRNA prediction model based only on plant small RNA sequencing data
Deep learning for tumor classification in imaging mass spectrometry
PREFMD : a web server for protein structure refinement via molecular dynamics simulations
Cost-effective and accurate method of measuring fetal fraction using SNP imputation
Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability
Bringing numerous methods for expression and promoter analysis to a public cloud computing service
LIBRA-WA : a web application for ligand binding site detection and protein function recognition
RepLong : de novo repeat identification using long read sequencing data
AIRVF : a filtering toolbox for precise variant calling in Ion Torrent sequencing
Membranome 2.0 : database for proteome-wide profiling of bitopic proteins and their dimers
MOAT : efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool
PERF : an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences
CommWalker : correctly evaluating modules in molecular networks in light of annotation bias
NanoStringNormCNV : pre-processing of NanoString CNV data
TabPath : interactive tables for metabolic pathway analysis
ViraPipe : scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads
Estimation of QTL heritability based on pooled sequencing data
orchid : a novel management, annotation, and machine learning framework for analyzing cancer mutations
FunImageJ : a Lisp framework for scientific image processing
pLoc-mHum : predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information
DFAST : a flexible prokaryotic genome annotation pipeline for faster genome publication
Mosdepth : quick coverage calculation for genomes and exomes
BEAM web server : a tool for structural RNA motif discovery
pedigreejs : a web-based graphical pedigree editor
Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra
MetaCherchant : analyzing genomic context of antibiotic resistance genes in gut microbiota
Machine learning annotation of human branchpoints
Simulating the dynamics of targeted capture sequencing with CapSim
GRASS : semi-automated NMR-based structure elucidation of saccharides
pStab : prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration
Predicting protein–DNA binding free energy change upon missense mutations using modified MM/PBSA approach : SAMPDI webserver
Visualization portal for genetic variation (VizGVar) : a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains
Efficient comparative phylogenetics on large trees
TMEM132 : an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules
DIEGO : detection of differential alternative splicing using Aitchison’s geometry
An exact test for comparing a fixed quantitative property between gene sets
ViewBS : a powerful toolkit for visualization of high-throughput bisulfite sequencing data
Dynamic assessment of microbial ecology (DAME) : a web app for interactive analysis and visualization of microbial sequencing data
MutaNET : a tool for automated analysis of genomic mutations in gene regulatory networks
ndexr—an R package to interface with the network data exchange
ChIPWig : a random access-enabling lossless and lossy compression method for ChIP-seq data
Drug–drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths
netReg : network-regularized linear models for biological association studies
Unsupervised multiple kernel learning for heterogeneous data integration
Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information
iSmaRT : a toolkit for a comprehensive analysis of small RNA-Seq data
A fast fiducial marker tracking model for fully automatic alignment in electron tomography
Bartender : a fast and accurate clustering algorithm to count barcode reads
xMWAS : a data-driven integration and differential network analysis tool
heatmaply : an R package for creating interactive cluster heatmaps for online publishing
ArachnoServer 3.0 : an online resource for automated discovery, analysis and annotation of spider toxins
Evaluation of tools for long read RNA-seq splice-aware alignment
VecScreen_plus_taxonomy : imposing a tax(onomy) increase on vector contamination screening
PROSPERous : high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy
CLIFinder : identification of LINE-1 chimeric transcripts in RNA-seq data
SeqBox : RNAseq/ChIPseq reproducible analysis on a consumer game computer
ROSC-Pred : web-service for rodent organ-specific carcinogenicity prediction
Chromatin accessibility prediction via a hybrid deep convolutional neural network
PaRSnIP : sequence-based protein solubility prediction using gradient boosting machine
DISC : DISulfide linkage Characterization from tandem mass spectra
Constructing prediction models from expression profiles for large scale lncRNA–miRNA interaction profiling
ARCS : scaffolding genome drafts with linked reads
PESTO : Parameter EStimation TOolbox
DEEPre : sequence-based enzyme EC number prediction by deep learning
Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates
mORCA : sailing bioinformatics world with mobile devices
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease
SliceMap : an algorithm for automated brain region annotation
PyBEL : a computational framework for Biological Expression Language
Cancer progression models and fitness landscapes : a many-to-many relationship
Krait : an ultrafast tool for genome-wide survey of microsatellites and primer design
Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques
SAGE2 : parallel human genome assembly
Machine learning accelerates MD-based binding pose prediction between ligands and proteins
MATAM : reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes
SELANSI : a toolbox for simulation of stochastic gene regulatory networks
AEGS : identifying aberrantly expressed gene sets for differential variability analysis
Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data
Beyond similarity assessment : selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm
UC2 search : using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics
An omnibus test for differential distribution analysis of microbiome sequencing data
Generalized correlation measure using count statistics for gene expression data with ordered samples
Compound image segmentation of published biomedical figures
HiCapTools : a software suite for probe design and proximity detection for targeted chromosome conformation capture applications
ThreaDNA : predicting DNA mechanics’ contribution to sequence selectivity of proteins along whole genomes
Detecting hidden batch factors through data-adaptive adjustment for biological effects
Squeakr : an exact and approximate k-mer counting system
findGSE : estimating genome size variation within human and Arabidopsis using k-mer frequencies
Compression of genomic sequencing reads via hash-based reordering : algorithm and analysis
DIBS : a repository of disordered binding sites mediating interactions with ordered proteins
PyDREAM : high-dimensional parameter inference for biological models in python
MALDIrppa : quality control and robust analysis for mass spectrometry data
BetaSerpentine : a bioinformatics tool for reconstruction of amyloid structures
Towards unified quality verification of synthetic count data with countsimQC
diffuStats : an R package to compute diffusion-based scores on biological networks
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs
diffloop : a computational framework for identifying and analyzing differential DNA loops from sequencing data
OncomiR : an online resource for exploring pan-cancer microRNA dysregulation
Nephele : a cloud platform for simplified, standardized and reproducible microbiome data analysis
Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data
Tumor Origin Detection with Tissue-Specific miRNA and DNA methylation Markers
DeepGO : predicting protein functions from sequence and interactions using a deep ontology-aware classifier
On the mechanisms of protein interactions : predicting their affinity from unbound tertiary structures
Canvas SPW : calling de novo copy number variants in pedigrees
The systematic analysis of ultraconserved genomic regions in the budding yeast
DiversePathsJ : Diverse Shortest Paths for Bioimage Analysis
A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data
AQUa : An Adaptive Framework for Compression of Sequencing Quality Scores with Random Access Functionality
Genome-wide pre-miRNA discovery from few labeled examples
RRDB : A comprehensive and nonredundant benchmark for RNA-RNA docking and scoring
A collaborative filtering-based approach to biomedical knowledge discovery
Structure-based prediction of protein– peptide binding regions using Random Forest
Protein–protein interaction specificity is captured by contact preferences and interface composition
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data
QuASAR-MPRA : accurate allele-specific analysis for massively parallel reporter assays
Sipros Ensemble improves database searching and filtering for complex metaproteomics
graphkernels : R and Python packages for graph comparison
Segway 2.0 : Gaussian mixture models and minibatch training
Quality of biological images, reconstructed using localization microscopy data
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer’s disease
DeepLoc : prediction of protein subcellular localization using deep learning
GradDock : rapid simulation and tailored ranking functions for peptide-MHC Class I docking
A comprehensive assessment of long intrinsic protein disorder from the DisProt database
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data
FMtree : a fast locating algorithm of FM-indexes for genomic data
Phosphonormalizer : an R package for normalization of MS-based label-free phosphoproteomics
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants
Applying family analyses to electronic health records to facilitate genetic research
Identification and visualization of differential isoform expression in RNA-seq time series
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing
High Dimensional Classification with combined Adaptive Sparse PLS and Logistic Regression
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm
LDassoc : an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism
RUCS : rapid identification of PCR primers for unique core sequences
Kmer-SSR : a fast and exhaustive SSR search algorithm
Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim)
Dugong : a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses
FATHMM-XF : accurate prediction of pathogenic point mutations via extended features
Efficient inference for sparse latent variable models of transcriptional regulation
CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation
Enabling reproducible real-time quantitative PCR research : the RDML package
PhyloGeoTool : interactively exploring large phylogenies in an epidemiological context
An improved compound Poisson model for the number of motif hits in DNA sequences
HUGIn : Hi-C Unifying Genomic Interrogator
FIRE : functional inference of genetic variants that regulate gene expression
Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode
clustComp, a bioconductor package for the comparison of clustering results
Integrative structural and dynamical biology with PLUMED-ISDB
psygenet2r : a R/Bioconductor package for the analysis of psychiatric disease genes
MIRMMR : binary classification of microsatellite instability using methylation and mutations
MetaCache : context-aware classification of metagenomic reads using minhashing
Genome-wide association studies using a penalized moving-window regression
ncDR : a comprehensive resource of non-coding RNAs involved in drug resistance
Improving protein fold recognition by extracting fold-specific features from predicted residue–residue contacts
Prediction of Delayed Retention of Antibodies in Hydrophobic Interaction Chromatography from Sequence using Machine Learning
ALIGNSEC : viewing protein secondary structure predictions within large multiple sequence alignments
PyLasso : a PyMOL plugin to identify lassos
PiMP my metabolome : an integrated, web-based tool for LC-MS metabolomics data
Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment
HaploForge : a comprehensive pedigree drawing and haplotype visualization web application
Conditional asymptotic inference for the kernel association test
LLR : a latent low-rank approach to colocalizing genetic risk variants in multiple GWAS
ChAMP : updated methylation analysis pipeline for Illumina BeadChips
MAPseq : highly efficient k-mer search with confidence estimates, for rRNA sequence analysis
CRISPR-DAV : CRISPR NGS data analysis and visualization pipeline
Holmes : a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems
EMHP : an accurate automated hole masking algorithm for single-particle cryo-EM image processing
HiDi : an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation
Metagene projection characterizes GEN2.2 and CAL-1 as relevant human plasmacytoid dendritic cell models
Lep-MAP3 : robust linkage mapping even for low-coverage whole genome sequencing data
MusiteDeep : a deep-learning framework for general and kinase-specific phosphorylation site prediction
RealityConvert : a tool for preparing 3D models of biochemical structures for augmented and virtual reality
Predicting novel metabolic pathways through subgraph mining
Cloud-based interactive analytics for terabytes of genomic variants data
MWASTools : an R/bioconductor package for metabolome-wide association studies
wft4galaxy : a workflow testing tool for galaxy
Using uncertainty to link and rank evidence from biomedical literature for model curation
PLACNETw : a web-based tool for plasmid reconstruction from bacterial genomes
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies
FOLD : a method to optimize power in meta-analysis of genetic association studies with overlapping subjects
Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data
Cancer Hallmarks Analytics Tool (CHAT) : a text mining approach to organize and evaluate scientific literature on cancer
proFIA : a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry
GLASS : assisted and standardized assessment of gene variations from Sanger sequence trace data
cgHeliParm : analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations
AlloSigMA : allosteric signaling and mutation analysis server
SVM-dependent pairwise HMM : an application to protein pairwise alignments
Spresso : An ultrafast compound pre-screening method based on compound decomposition