Issue navigation
Volume 22, Issue 3, May 2021
Articles
Letter to the Editor: Methods for mapping quantitative trait loci in autotetraploid species
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbz148, https://doi.org/10.1093/bib/bbz148
In silico prediction of host–pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbz162, https://doi.org/10.1093/bib/bbz162
Distance-based phylogenetic inference from typing data: a unifying view
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa147, https://doi.org/10.1093/bib/bbaa147
CeRNASeek: an R package for identification and analysis of ceRNA regulation
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa048, https://doi.org/10.1093/bib/bbaa048
Detection of somatic structural variants from short-read next-generation sequencing data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa056, https://doi.org/10.1093/bib/bbaa056
RSVdb: a comprehensive database of transcriptome RNA structure
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa071, https://doi.org/10.1093/bib/bbaa071
Computational recognition of lncRNA signature of tumor-infiltrating B lymphocytes with potential implications in prognosis and immunotherapy of bladder cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa047, https://doi.org/10.1093/bib/bbaa047
mUSP: a high-accuracy map of the in situ crosstalk of ubiquitylation and SUMOylation proteome predicted via the feature enhancement approach
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa050, https://doi.org/10.1093/bib/bbaa050
Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa081, https://doi.org/10.1093/bib/bbaa081
iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa058, https://doi.org/10.1093/bib/bbaa058
Drug-pathway association prediction: from experimental results to computational models
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa061, https://doi.org/10.1093/bib/bbaa061
A statistical framework for predicting critical regions of p53-dependent enhancers
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa053, https://doi.org/10.1093/bib/bbaa053
PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa077, https://doi.org/10.1093/bib/bbaa077
Therapeutic targets and signaling mechanisms of vitamin C activity against sepsis: a bioinformatics study
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa079, https://doi.org/10.1093/bib/bbaa079
M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa055, https://doi.org/10.1093/bib/bbaa055
A novel deep learning method for predictive modeling of microbiome data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa073, https://doi.org/10.1093/bib/bbaa073
Disease characterization using a partial correlation-based sample-specific network
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa062, https://doi.org/10.1093/bib/bbaa062
Recent advances in biomedical literature mining
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa057, https://doi.org/10.1093/bib/bbaa057
Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow?
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa059, https://doi.org/10.1093/bib/bbaa059
PL-search: a profile-link-based search method for protein remote homology detection
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa051, https://doi.org/10.1093/bib/bbaa051
Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa060, https://doi.org/10.1093/bib/bbaa060
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa076, https://doi.org/10.1093/bib/bbaa076
miRactDB characterizes miRNA–gene relation switch between normal and cancer tissues across pan-cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa089, https://doi.org/10.1093/bib/bbaa089
Significance miRactDB, the first resource for comprehensive annotation of miRNA–gene relation, provides expression profiles, prognostic landscapes and potential mechanisms of action across multiple cancer and healthy tissue types.
iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa065, https://doi.org/10.1093/bib/bbaa065
Mechanistically derived patient-level framework for precision medicine identifies a personalized immune prognostic signature in high-grade serous ovarian cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa069, https://doi.org/10.1093/bib/bbaa069
CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa063, https://doi.org/10.1093/bib/bbaa063
Attentional multi-level representation encoding based on convolutional and variance autoencoders for lncRNA–disease association prediction
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa067, https://doi.org/10.1093/bib/bbaa067
SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa162, https://doi.org/10.1093/bib/bbaa162
CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa045, https://doi.org/10.1093/bib/bbaa045
Systematic evaluation of machine learning methods for identifying human–pathogen protein–protein interactions
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa068, https://doi.org/10.1093/bib/bbaa068
Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa066, https://doi.org/10.1093/bib/bbaa066
Beware of the generic machine learning-based scoring functions in structure-based virtual screening
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa070, https://doi.org/10.1093/bib/bbaa070
Scoring functions for drug-effect similarity
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa072, https://doi.org/10.1093/bib/bbaa072
Predicting the stability of mutant proteins by computational approaches: an overview
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa074, https://doi.org/10.1093/bib/bbaa074
Computational principles and practice for decoding immune contexture in the tumor microenvironment
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa075, https://doi.org/10.1093/bib/bbaa075
gutMEGA: a database of the human gut MEtaGenome Atlas
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa082, https://doi.org/10.1093/bib/bbaa082
Improving structure-based virtual screening performance via learning from scoring function components
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa094, https://doi.org/10.1093/bib/bbaa094
Different molecular enumeration influences in deep learning: an example using aqueous solubility
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa092, https://doi.org/10.1093/bib/bbaa092
MetaFS: Performance assessment of biomarker discovery in metaproteomics
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa105, https://doi.org/10.1093/bib/bbaa105
Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa083, https://doi.org/10.1093/bib/bbaa083
DenvInD: dengue virus inhibitors database for clinical and molecular research
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa098, https://doi.org/10.1093/bib/bbaa098
Landscape of drug-resistance mutations in kinase regulatory hotspots
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa108, https://doi.org/10.1093/bib/bbaa108
CCLA: an accurate method and web server for cancer cell line authentication using gene expression profiles
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa093, https://doi.org/10.1093/bib/bbaa093
RaacLogo: a new sequence logo generator by using reduced amino acid clusters
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa096, https://doi.org/10.1093/bib/bbaa096
MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa104, https://doi.org/10.1093/bib/bbaa104
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa109, https://doi.org/10.1093/bib/bbaa109
Proper imputation of missing values in proteomics datasets for differential expression analysis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa112, https://doi.org/10.1093/bib/bbaa112
Survey and comparative assessments of computational multi-omics integrative methods with multiple regulatory networks identifying distinct tumor compositions across pan-cancer data sets
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa102, https://doi.org/10.1093/bib/bbaa102
Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa084, https://doi.org/10.1093/bib/bbaa084
The impact of compound library size on the performance of scoring functions for structure-based virtual screening
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa095, https://doi.org/10.1093/bib/bbaa095
Dr AFC: drug repositioning through anti-fibrosis characteristic
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa115, https://doi.org/10.1093/bib/bbaa115
Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa099, https://doi.org/10.1093/bib/bbaa099
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa120, https://doi.org/10.1093/bib/bbaa120
RNCE: network integration with reciprocal neighbors contextual encoding for multi-modal drug community study on cancer targets
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa118, https://doi.org/10.1093/bib/bbaa118
Enriching contextualized language model from knowledge graph for biomedical information extraction
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa110, https://doi.org/10.1093/bib/bbaa110
Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa086, https://doi.org/10.1093/bib/bbaa086
SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa097, https://doi.org/10.1093/bib/bbaa097
A novel privacy-preserving federated genome-wide association study framework and its application in identifying potential risk variants in ankylosing spondylitis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa090, https://doi.org/10.1093/bib/bbaa090
Evaluation of gene–drug common module identification methods using pharmacogenomics data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa087, https://doi.org/10.1093/bib/bbaa087
PredCID: prediction of driver frameshift indels in human cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa119, https://doi.org/10.1093/bib/bbaa119
ExoBCD: a comprehensive database for exosomal biomarker discovery in breast cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa088, https://doi.org/10.1093/bib/bbaa088
Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa107, https://doi.org/10.1093/bib/bbaa107
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa125, https://doi.org/10.1093/bib/bbaa125
A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa126, https://doi.org/10.1093/bib/bbaa126
Gene-based mediation analysis in epigenetic studies
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa113, https://doi.org/10.1093/bib/bbaa113
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa124, https://doi.org/10.1093/bib/bbaa124
Prostate cancer early diagnosis: circulating microRNA pairs potentially beyond single microRNAs upon 1231 serum samples
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa111, https://doi.org/10.1093/bib/bbaa111
Using deep neural networks and biological subwords to detect protein S-sulfenylation sites
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa128, https://doi.org/10.1093/bib/bbaa128
scCancer: a package for automated processing of single-cell RNA-seq data in cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa127, https://doi.org/10.1093/bib/bbaa127
Boosting predictabilities of agronomic traits in rice using bivariate genomic selection
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa103, https://doi.org/10.1093/bib/bbaa103
Federated sharing and processing of genomic datasets for tertiary data analysis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa091, https://doi.org/10.1093/bib/bbaa091
MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa117, https://doi.org/10.1093/bib/bbaa117
Normal tissue content impact on the GBM molecular classification
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa129, https://doi.org/10.1093/bib/bbaa129
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa123, https://doi.org/10.1093/bib/bbaa123
Testing cell-type-specific mediation effects in genome-wide epigenetic studies
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa131, https://doi.org/10.1093/bib/bbaa131
Predicting microRNA–disease associations from lncRNA–microRNA interactions via Multiview Multitask Learning
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa133, https://doi.org/10.1093/bib/bbaa133
SCEBE: an efficient and scalable algorithm for genome-wide association studies on longitudinal outcomes with mixed-effects modeling
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa130, https://doi.org/10.1093/bib/bbaa130
Comparison of high-throughput single-cell RNA sequencing data processing pipelines
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa116, https://doi.org/10.1093/bib/bbaa116
State-of-the-art web services for de novo protein structure prediction
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa139, https://doi.org/10.1093/bib/bbaa139
Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa143, https://doi.org/10.1093/bib/bbaa143
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa136, https://doi.org/10.1093/bib/bbaa136
Bioinformatics toolbox for exploring protein phosphorylation network
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa134, https://doi.org/10.1093/bib/bbaa134
A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa138, https://doi.org/10.1093/bib/bbaa138
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa135, https://doi.org/10.1093/bib/bbaa135
Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa132, https://doi.org/10.1093/bib/bbaa132
FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa144, https://doi.org/10.1093/bib/bbaa144
Benchmarking variant callers in next-generation and third-generation sequencing analysis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa148, https://doi.org/10.1093/bib/bbaa148
Predicting human microbe–disease associations via graph attention networks with inductive matrix completion
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa146, https://doi.org/10.1093/bib/bbaa146
Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa140, https://doi.org/10.1093/bib/bbaa140
Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa137, https://doi.org/10.1093/bib/bbaa137
Recent advances in user-friendly computational tools to engineer protein function
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa150, https://doi.org/10.1093/bib/bbaa150
Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa149, https://doi.org/10.1093/bib/bbaa149
Computational methods for the integrative analysis of single-cell data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa042, https://doi.org/10.1093/bib/bbaa042
A survey on predicting microbe-disease associations: biological data and computational methods
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa157, https://doi.org/10.1093/bib/bbaa157
Spatial molecular profiling: platforms, applications and analysis tools
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa145, https://doi.org/10.1093/bib/bbaa145
AntiCP 2.0: an updated model for predicting anticancer peptides
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa153, https://doi.org/10.1093/bib/bbaa153
Integrative biomarker detection on high-dimensional gene expression data sets: a survey on prior knowledge approaches
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa151, https://doi.org/10.1093/bib/bbaa151
Current development of integrated web servers for preclinical safety and pharmacokinetics assessments in drug development
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa160, https://doi.org/10.1093/bib/bbaa160
Microbes and complex diseases: from experimental results to computational models
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa158, https://doi.org/10.1093/bib/bbaa158
Integrated omics analysis reveals the alteration of gut microbe–metabolites in obese adults
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa165, https://doi.org/10.1093/bib/bbaa165
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa142, https://doi.org/10.1093/bib/bbaa142
LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa178, https://doi.org/10.1093/bib/bbaa178
DeepATT: a hybrid category attention neural network for identifying functional effects of DNA sequences
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa159, https://doi.org/10.1093/bib/bbaa159
Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa156, https://doi.org/10.1093/bib/bbaa156
A powerful framework for an integrative study with heterogeneous omics data: from univariate statistics to multi-block analysis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa166, https://doi.org/10.1093/bib/bbaa166
MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa161, https://doi.org/10.1093/bib/bbaa161
An approach for normalization and quality control for NanoString RNA expression data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa163, https://doi.org/10.1093/bib/bbaa163
Prognosis and personalized treatment prediction in TP53-mutant hepatocellular carcinoma: an in silico strategy towards precision oncology
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa164, https://doi.org/10.1093/bib/bbaa164
The functional determinants in the organization of bacterial genomes
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa172, https://doi.org/10.1093/bib/bbaa172
An in silico approach to identification, categorization and prediction of nucleic acid binding proteins
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa171, https://doi.org/10.1093/bib/bbaa171
Publishing reproducible dynamic kinetic models
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa152, https://doi.org/10.1093/bib/bbaa152
Vertical integration methods for gene expression data analysis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa169, https://doi.org/10.1093/bib/bbaa169
RNA-binding protein recognition based on multi-view deep feature and multi-label learning
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa174, https://doi.org/10.1093/bib/bbaa174
Heritability jointly explained by host genotype and microbiome: will improve traits prediction?
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa175, https://doi.org/10.1093/bib/bbaa175
Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa184, https://doi.org/10.1093/bib/bbaa184
Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa176, https://doi.org/10.1093/bib/bbaa176
Interpretation of deep learning in genomics and epigenomics
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa177, https://doi.org/10.1093/bib/bbaa177
LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa179, https://doi.org/10.1093/bib/bbaa179
Microsatellite instability status differentially associates with intratumoral immune microenvironment in human cancers
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa180, https://doi.org/10.1093/bib/bbaa180
Large-scale benchmark study of survival prediction methods using multi-omics data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa167, https://doi.org/10.1093/bib/bbaa167
The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa181, https://doi.org/10.1093/bib/bbaa181
Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa188, https://doi.org/10.1093/bib/bbaa188
DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa183, https://doi.org/10.1093/bib/bbaa183
The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa191, https://doi.org/10.1093/bib/bbaa191
Depiction of tumor stemlike features and underlying relationships with hazard immune infiltrations based on large prostate cancer cohorts
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa211, https://doi.org/10.1093/bib/bbaa211
Deep-belief network for predicting potential miRNA-disease associations
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa186, https://doi.org/10.1093/bib/bbaa186
Proteome-scale analysis of phase-separated proteins in immunofluorescence images
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa187, https://doi.org/10.1093/bib/bbaa187
Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa182, https://doi.org/10.1093/bib/bbaa182
FS–GBDT: identification multicancer-risk module via a feature selection algorithm by integrating Fisher score and GBDT
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa189, https://doi.org/10.1093/bib/bbaa189
Challenges in gene-oriented approaches for pangenome content discovery
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa198, https://doi.org/10.1093/bib/bbaa198
ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa192, https://doi.org/10.1093/bib/bbaa192
Scopy: an integrated negative design python library for desirable HTS/VS database design
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa194, https://doi.org/10.1093/bib/bbaa194
TERL: classification of transposable elements by convolutional neural networks
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa185, https://doi.org/10.1093/bib/bbaa185
How bioinformatics resources work with G4 RNAs
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa201, https://doi.org/10.1093/bib/bbaa201
Extended application of genomic selection to screen multiomics data for prognostic signatures of prostate cancer
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa197, https://doi.org/10.1093/bib/bbaa197
Discerning novel drug targets for treating Mycobacterium avium ss. paratuberculosis-associated autoimmune disorders: an in silico approach
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa195, https://doi.org/10.1093/bib/bbaa195
Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa202, https://doi.org/10.1093/bib/bbaa202
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa190, https://doi.org/10.1093/bib/bbaa190
NAMS webserver: coding potential assessment and functional annotation of plant transcripts
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa200, https://doi.org/10.1093/bib/bbaa200
Topoly: Python package to analyze topology of polymers
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa196, https://doi.org/10.1093/bib/bbaa196
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa206, https://doi.org/10.1093/bib/bbaa206
In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa223, https://doi.org/10.1093/bib/bbaa223
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa203, https://doi.org/10.1093/bib/bbaa203
AlzRiskMR database: an online database for the impact of exposure factors on Alzheimer’s disease
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa213, https://doi.org/10.1093/bib/bbaa213
Analysis, identification and visualization of subgroups in genomics
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa217, https://doi.org/10.1093/bib/bbaa217
TEnGExA: an R package based tool for tissue enrichment and gene expression analysis
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa221, https://doi.org/10.1093/bib/bbaa221
DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa205, https://doi.org/10.1093/bib/bbaa205
Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa210, https://doi.org/10.1093/bib/bbaa210
Modular arrangements of sequence motifs determine the functional diversity of KDM proteins
Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa215, https://doi.org/10.1093/bib/bbaa215
