Journal of Bioinformatics and Computational Biology

Papers
(The TQCC of Journal of Bioinformatics and Computational Biology is 2. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)
ArticleCitations
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning23
PROSPECT: A web server for predicting protein histidine phosphorylation sites22
Denoising Protein–Protein interaction network via variational graph auto-encoder for protein complex detection16
Single-cell RNA-seq data clustering: A survey with performance comparison study16
3D U-Net: A voxel-based method in binding site prediction of protein structure13
Comparing the topology of phylogenetic network generators11
EDeepSSP: Explainable deep neural networks for exact splice sites prediction10
HemoNet: Predicting hemolytic activity of peptides with integrated feature learning9
EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins8
Incorporating intergenic regions into reversal and transposition distances with indels8
Constructing gene regulatory networks from microarray data using non-Gaussian pair-copula Bayesian networks7
Unsupervised multi-instance learning for protein structure determination6
Prediction of adverse drug reactions using drug convolutional neural networks6
BENIN: Biologically enhanced network inference6
A protein succinylation sites prediction method based on the hybrid architecture of LSTM network and CNN6
An evaluation of combined strategies for improving the performance of molecular docking5
iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method5
Prediction of miRNA-disease associations based on Weighted K-Nearest known neighbors and network consistency projection5
KFGRNI: A robust method to inference gene regulatory network from time-course gene data based on ensemble Kalman filter5
Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases4
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets4
DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost4
Approaches for the identification of driver mutations in cancer: A tutorial from a computational perspective4
An integrated method for identifying essential proteins from multiplex network model of protein–protein interactions4
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric4
A symmetry-inclusive algebraic approach to genome rearrangement3
ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets3
Disease named entity recognition using long–short dependencies3
Population-specific adaptation in malaria-endemic regions of asia3
Protein–protein interaction site prediction using random forest proximity distance3
Identification of genes associated with cancer prognosis in glioma: In silico data analyses of Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA)3
Small parsimony for natural genomes in the DCJ-indel model3
Sparse robust graph-regularized non-negative matrix factorization based on correntropy3
The potential of family-free rearrangements towards gene orthology inference3
DEEPSMP: A deep learning model for predicting the ectodomain shedding events of membrane proteins3
Network motif-based analysis of regulatory patterns in paralogous gene pairs3
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine3
Cascading classifier application for topology prediction of transmembrane beta-barrel proteins3
Cell cycle period control through modulation of clock inputs3
PESM: A novel approach of tumor purity estimation based on sample specific methylation sites3
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures3
A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction2
ReHiC: Enhancing Hi-C data resolution via residual convolutional network2
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model2
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm2
Quantificational evaluation of the resolving power of qualitative biomarkers with different cardinal numbers based on a magnitude-standardized index2
Identification of deregulation mechanisms specific to cancer subtypes2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images2
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases2
A deep attention network for predicting amino acid signals in the formation of α-helices2
SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks2
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect2
Prophage loci predictor for bacterial genomes2
Shared ancestry of core-histone subunits and non-histone plant proteins containing the Histone Fold Motif (HFM)2
Identification of cancer-related module in protein–protein interaction network based on gene prioritization2
Impact of low-confidence interactions on computational identification of protein complexes2
Scaling laws of graphs of 3D protein structures2
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer2
Genetic algorithm applied to simultaneous parameter estimation in bacterial growth2
BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium2
Detecting genetic associations with brain imaging phenotypes in Alzheimer’s disease via a novel structured KCCA approach2
Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence2
DeepBtoD: Improved RNA-binding proteins prediction via integrated deep learning2
A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA2
Identifying protein complexes from protein–protein interaction networks based on the gene expression profile and core-attachment approach2
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network2
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data2
Integratedin silicoin vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes2
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