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RNA methylation and diseases : experimental results, databases, Web servers and computational models
Privacy-preserving techniques of genomic data—a survey
A survey of software tools for microRNA discovery and characterization using RNA-seq
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data
Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems
Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets : 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma
An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies
Editorial
Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk
Proteomics and phosphoproteomics in precision medicine : applications and challenges
Precision medicine needs pioneering clinical bioinformaticians
Computational tools for plant small RNA detection and categorization
MicroRNAs and complex diseases : from experimental results to computational models
Evaluation of variable selection methods for random forests and omics data sets
Machine learning approaches to decipher hormone and HER2 receptor status phenotypes in breast cancer
Translational medicine in the Age of Big Data
Towards dynamic genome-scale models
A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies
A rank-based algorithm of differential expression analysis for small cell line data with statistical control
Toward completion of the Earth’s proteome : an update a decade later
Elucidating the editome : bioinformatics approaches for RNA editing detection
Prediction of protein–protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.)
Principal component analysis of binary genomics data
A comprehensive review and comparison of existing computational methods for intrinsically disordered protein and region prediction
Advanced bioinformatics methods for practical applications in proteomics
Comparative analysis of differential gene expression tools for RNA sequencing time course data
Web-based drug repurposing tools : a survey
Systematic bias of correlation coefficient may explain negative accuracy of genomic prediction
Critical assessment and performance improvement of plant–pathogen protein–protein interaction prediction methods
PHAST, PHASTER and PHASTEST : Tools for finding prophage in bacterial genomes
MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis
A new pan-European Train-the-Trainer programme for bioinformatics : pilot results on feasibility, utility and sustainability of learning
A review of methods and databases for metagenomic classification and assembly
Systematic comparative study of computational methods for T-cell receptor sequencing data analysis
Bioinformatics in the Netherlands : the value of a nationwide community
Microbial genome analysis : the COG approach
Next-generation sequencing data analysis
MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data
MAFFT online service : multiple sequence alignment, interactive sequence choice and visualization
Association score testing for rare variants and binary traits in family data with shared controls
Identifying mutual exclusivity across cancer genomes : computational approaches to discover genetic interaction and reveal tumor vulnerability
Understanding the disease genome : gene essentiality and the interplay of selection, recombination and mutation
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures
A global perspective on evolving bioinformatics and data science training needs
Federation in genomics pipelines : techniques and challenges
A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications
MetSigDis : a manually curated resource for the metabolic signatures of diseases
A broken promise : microbiome differential abundance methods do not control the false discovery rate
Accounting for differential variability in detecting differentially methylated regions
Facilitating prediction of adverse drug reactions by using knowledge graphs and multi-label learning models
The BioCyc collection of microbial genomes and metabolic pathways
Pathway enrichment analysis approach based on topological structure and updated annotation of pathway
Integrating regulatory features data for prediction of functional disease-associated SNPs
Systematic review regulatory principles of non-coding RNAs in cardiovascular diseases
Computational resources for ribosome profiling : from database to Web server and software
Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing
Big data management challenges in health research—a literature review
Discovering cooperative biomarkers for heterogeneous complex disease diagnoses
‘Multi-omic’ data analysis using O-miner
Metagenomic assembly through the lens of validation : recent advances in assessing and improving the quality of genomes assembled from metagenomes
On the dynamical incompleteness of the Protein Data Bank
VirGenA : a reference-based assembler for variable viral genomes
Computational approaches for discovery of mutational signatures in cancer
PATRIC as a unique resource for studying antimicrobial resistance
DOOR : a prokaryotic operon database for genome analyses and functional inference
Visualizing and comparing circular genomes using the CGView family of tools
AtCircDB : a tissue-specific database for Arabidopsis circular RNAs
Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species
An account of in silico identification tools of secreted effector proteins in bacteria and future challenges
OPATs : Omnibus P-value association tests
SEGtool : a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data
Proper joint analysis of summary association statistics requires the adjustment of heterogeneity in SNP coverage pattern
Bioinformatics on a national scale : an example from Switzerland
A strategy for multimodal data integration : application to biomarkers identification in spinocerebellar ataxia
CircView : a visualization and exploration tool for circular RNAs
Alignment-free inference of hierarchical and reticulate phylogenomic relationships
Network approaches to systems biology analysis of complex disease : integrative methods for multi-omics data
Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures
Mathematical modeling and computational prediction of cancer drug resistance
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity
The genetic architecture of heterochrony as a quantitative trait : lessons from a computational model
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity
Nanopore sequencing data analysis : state of the art, applications and challenges
Power and sample size calculations for high-throughput sequencing-based experiments
Recent computational developments on CLIP-seq data analysis and microRNA targeting implications
Biomedical text mining for research rigor and integrity : tasks, challenges, directions
Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants : a bioinformatics workflow
Dynamic-BM : multispecies Dynamic BodyMap database from temporal RNA-seq data
A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation
Seeing the wood for the trees : a forest of methods for optimization and omic-network integration in metabolic modelling
The genetic architecture of heterochrony as a quantitative trait : lessons from a computational model
ceRNAs in plants : computational approaches and associated challenges for target mimic research
Optimizing drug development in oncology by clinical trial simulation : Why and how?
Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments
Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes
Large-scale data-driven integrative framework for extracting essential targets and processes from disease-associated gene data sets
Subcellular locations of potential cell wall proteins in plants : predictors, databases and cross-referencing
Mutational signatures and mutable motifs in cancer genomes
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes
Deep learning for healthcare : review, opportunities and challenges
Advances in computational approaches in identifying synergistic drug combinations
In silico polypharmacology of natural products
Pioneering topological methods for network-based drug–target prediction by exploiting a brain-network self-organization theory
A review of connectivity map and computational approaches in pharmacogenomics
Long noncoding RNA : a crosslink in biological regulatory network
Improving data workflow systems with cloud services and use of open data for bioinformatics research
Bioinformatics in Germany : toward a national-level infrastructure
Dynamic modeling and network approaches for omics time course data : overview of computational approaches and applications
Comparative analysis of de novo assemblers for variation discovery in personal genomes
Experimental design and data analysis of Ago-RIP-Seq experiments for the identification of microRNA targets
Next-generation sequencing data analysis Xinkun Wan
CASH : a constructing comprehensive splice site method for detecting alternative splicing events
The anatomy of phenotype ontologies : principles, properties and applications
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites
Row versus column correlations : avoiding the ecological fallacy in RNA/protein expression studies
Context-based retrieval of functional modules in protein–protein interaction networks