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Volume 37, Issue 18, September 2021
ORIGINAL PAPERS
GENOME ANALYSIS
CoCoNet: an efficient deep learning tool for viral metagenome binning
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2803–2810, https://doi.org/10.1093/bioinformatics/btab213
SEQUENCE ANALYSIS
Mutalyzer 2: next generation HGVS nomenclature checker
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2811–2817, https://doi.org/10.1093/bioinformatics/btab051
Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2818–2824, https://doi.org/10.1093/bioinformatics/btab181
TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2825–2833, https://doi.org/10.1093/bioinformatics/btab198
STREME: accurate and versatile sequence motif discovery
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2834–2840, https://doi.org/10.1093/bioinformatics/btab203
A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2841–2847, https://doi.org/10.1093/bioinformatics/btab204
A critical assessment of gene catalogs for metagenomic analysis
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2848–2857, https://doi.org/10.1093/bioinformatics/btab216
BLight: efficient exact associative structure for k-mers
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2858–2865, https://doi.org/10.1093/bioinformatics/btab217
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866–2873, https://doi.org/10.1093/bioinformatics/btab219
STRUCTURAL BIOINFORMATICS
ZEAL: protein structure alignment based on shape similarity
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2874–2881, https://doi.org/10.1093/bioinformatics/btab205
GENE EXPRESSION
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2882–2888, https://doi.org/10.1093/bioinformatics/btab178
Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2889–2895, https://doi.org/10.1093/bioinformatics/btab192
GENETICS AND POPULATION ANALYSIS
L2,1-norm regularized multivariate regression model with applications to genomic prediction
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2896–2904, https://doi.org/10.1093/bioinformatics/btab212
SYSTEMS BIOLOGY
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2905–2911, https://doi.org/10.1093/bioinformatics/btab175
Queueing theory model of Krebs cycle
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2912–2919, https://doi.org/10.1093/bioinformatics/btab177
Multiscale part mutual information for quantifying nonlinear direct associations in networks
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2920–2929, https://doi.org/10.1093/bioinformatics/btab182
Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug–drug links based on graph neural network
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2930–2937, https://doi.org/10.1093/bioinformatics/btab191
Probabilistic thermodynamic analysis of metabolic networks
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2938–2945, https://doi.org/10.1093/bioinformatics/btab194
Quantification of cell behaviors and computational modeling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2946–2954, https://doi.org/10.1093/bioinformatics/btab201
DATA AND TEXT MINING
Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2955–2962, https://doi.org/10.1093/bioinformatics/btab174
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2963–2970, https://doi.org/10.1093/bioinformatics/btab185
HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2971–2980, https://doi.org/10.1093/bioinformatics/btab193
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2981–2987, https://doi.org/10.1093/bioinformatics/btab195
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2988–2995, https://doi.org/10.1093/bioinformatics/btab207
APPLICATIONS NOTES
GENOME ANALYSIS
HiCRep.py: fast comparison of Hi-C contact matrices in Python
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2996–2997, https://doi.org/10.1093/bioinformatics/btab097
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2998–3000, https://doi.org/10.1093/bioinformatics/btab107
MitoFlex: an efficient, high-performance toolkit for animal mitogenome assembly, annotation and visualization
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3001–3003, https://doi.org/10.1093/bioinformatics/btab111
PICS2: next-generation fine mapping via probabilistic identification of causal SNPs
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3004–3007, https://doi.org/10.1093/bioinformatics/btab122
ASimulatoR: splice-aware RNA-Seq data simulation
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3008–3010, https://doi.org/10.1093/bioinformatics/btab142
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3011–3013, https://doi.org/10.1093/bioinformatics/btab148
Megadepth: efficient coverage quantification for BigWigs and BAMs
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3014–3016, https://doi.org/10.1093/bioinformatics/btab152
LocusZoom.js: interactive and embeddable visualization of genetic association study results
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3017–3018, https://doi.org/10.1093/bioinformatics/btab186
SEQUENCE ANALYSIS
orfipy: a fast and flexible tool for extracting ORFs
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3019–3020, https://doi.org/10.1093/bioinformatics/btab090
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3021–3022, https://doi.org/10.1093/bioinformatics/btab101
Tumor IsomiR Encyclopedia (TIE): a pan-cancer database of miRNA isoforms
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3023–3025, https://doi.org/10.1093/bioinformatics/btab172
HCMMCNVs: hierarchical clustering mixture model of copy number variants detection using whole exome sequencing technology
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3026–3028, https://doi.org/10.1093/bioinformatics/btab183
Fast and sensitive taxonomic assignment to metagenomic contigs
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3029–3031, https://doi.org/10.1093/bioinformatics/btab184
PHYLOGENETICS
BAli-Phy version 3: model-based co-estimation of alignment and phylogeny
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3032–3034, https://doi.org/10.1093/bioinformatics/btab129
STRUCTURAL BIOINFORMATICS
Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3035–3037, https://doi.org/10.1093/bioinformatics/btab149
FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3038–3040, https://doi.org/10.1093/bioinformatics/btab176
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3041–3042, https://doi.org/10.1093/bioinformatics/btab180
GENE EXPRESSION
multiclassPairs: an R package to train multiclass pair-based classifier
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3043–3044, https://doi.org/10.1093/bioinformatics/btab088
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3045–3047, https://doi.org/10.1093/bioinformatics/btab108
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3048–3050, https://doi.org/10.1093/bioinformatics/btab135
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3051–3052, https://doi.org/10.1093/bioinformatics/btab159
LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3053–3055, https://doi.org/10.1093/bioinformatics/btab168
Integrative transcription start site identification with iTiSS
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3056–3057, https://doi.org/10.1093/bioinformatics/btab170
ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3058–3060, https://doi.org/10.1093/bioinformatics/btab179
GENETICS AND POPULATION ANALYSIS
pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3061–3063, https://doi.org/10.1093/bioinformatics/btab150
SYSTEMS BIOLOGY
multiTFA: a Python package for multi-variate thermodynamics-based flux analysis
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3064–3066, https://doi.org/10.1093/bioinformatics/btab151
DCI: learning causal differences between gene regulatory networks
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3067–3069, https://doi.org/10.1093/bioinformatics/btab167
DATA AND TEXT MINING
IsoTV: processing and visualizing functional features of translated transcript isoforms
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3070–3072, https://doi.org/10.1093/bioinformatics/btab103
HeteroGGM: an R package for Gaussian graphical model-based heterogeneity analysis
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3073–3074, https://doi.org/10.1093/bioinformatics/btab134
BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3075–3078, https://doi.org/10.1093/bioinformatics/btab173
BIOIMAGE INFORMATICS
BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3079–3081, https://doi.org/10.1093/bioinformatics/btab106
QuArray: an application for tissue array whole slide image export and signal analysis
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3082–3083, https://doi.org/10.1093/bioinformatics/btab119
An enhanced loss function simplifies the deep learning model for characterizing the 3D organoid models
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3084–3085, https://doi.org/10.1093/bioinformatics/btab120
DeepS: a web server for image optical sectioning and super resolution microscopy based on a deep learning framework
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3086–3087, https://doi.org/10.1093/bioinformatics/btab144
FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids
Bioinformatics, Volume 37, Issue 18, September 2021, Pages 3088–3090, https://doi.org/10.1093/bioinformatics/btab160
