OOIR: Observatory of International Research

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 2020-11-01 to 2024-11-01.)

Article	Citations
DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning	25
3D U-Net: A voxel-based method in binding site prediction of protein structure	15
HemoNet: Predicting hemolytic activity of peptides with integrated feature learning	12
Comparing the topology of phylogenetic network generators	11
Incorporating intergenic regions into reversal and transposition distances with indels	9
Prediction of adverse drug reactions using drug convolutional neural networks	7
Unsupervised multi-instance learning for protein structure determination	6
An evaluation of combined strategies for improving the performance of molecular docking	6
A protein succinylation sites prediction method based on the hybrid architecture of LSTM network and CNN	6
Prediction of miRNA-disease associations based on Weighted K-Nearest known neighbors and network consistency projection	6
KFGRNI: A robust method to inference gene regulatory network from time-course gene data based on ensemble Kalman filter	6
iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method	5
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets	5
The potential of family-free rearrangements towards gene orthology inference	4
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures	4
Small parsimony for natural genomes in the DCJ-indel model	4
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric	4
DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost	4
Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases	4
SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks	4
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model	3
Evidence for exon shuffling is sensitive to model choice	3
Population-specific adaptation in malaria-endemic regions of asia	3
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
A symmetry-inclusive algebraic approach to genome rearrangement	3

DeepBtoD: Improved RNA-binding proteins prediction via integrated deep learning	3
Sparse robust graph-regularized non-negative matrix factorization based on correntropy	3
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases	3
RMI-DBG algorithm: A more agile iterative de Bruijn graph algorithm in short read genome assembly	3
RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures	3
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine	3
TemporalGSSA: A numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets	3
Protein–protein interaction site prediction using random forest proximity distance	3
A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA	2
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family	2
Antimicrobial peptides recognition using weighted physicochemical property encoding	2
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy	2
Scaling laws of graphs of 3D protein structures	2
In silico de novo drug design of a therapeutic peptide inhibitor against UBE2C in breast cancer	2
ReHiC: Enhancing Hi-C data resolution via residual convolutional network	2
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect	2
Prophage loci predictor for bacterial genomes	2
Overlapping group screening for binary cancer classification with TCGA high-dimensional genomic data	2
EdClust: A heuristic sequence clustering method with higher sensitivity	2
Identifying protein complexes from protein–protein interaction networks based on the gene expression profile and core-attachment approach	2
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images	2
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data	2
Integratedin silico–in vitrorational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes	2
Prediction of nucleosome dynamic interval based on long–short-term memory network (LSTM)	2
BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium	2
Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence	2
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm	2
Shared ancestry of core-histone subunits and non-histone plant proteins containing the Histone Fold Motif (HFM)	2
Identification of deregulation mechanisms specific to cancer subtypes	2
Clinical drug response prediction from preclinical cancer cell lines by logistic matrix factorization approach	2
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network	2
Numerical study of chronic hepatitis B infection using Marchuk–Petrov model	2
Genetic algorithm applied to simultaneous parameter estimation in bacterial growth	2
Detecting genetic associations with brain imaging phenotypes in Alzheimer’s disease via a novel structured KCCA approach	2
A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction	2
Denoising of scanning electron microscope images for biological ultrastructure enhancement	2
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides	2