yusuke1997/dblp-id-title huggingface dataset:
Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction
PASS-based approach to predict HIV-1 reverse transcriptase resistance
Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM
Samira-VP: A simple protein alignment method with rechecking the alphabet vector positions
Transmembrane Structure Predictions with Hydropathy Index/charge Two-Dimensional Trajectories of Stochastic Dynamical Systems
An Optimization Method for the Identification of Minimal Sets of Discriminating Gene Markers: Application to Cultivar Identification in Wheat
Tuning the Precision of Predictors to Reduce overestimation of protein Disorder over Large Datasets
Histone modifications influence skipped exons inclusion
An Introduction to some New Results in Bioinformatics and Computational Biology
High Torsional Energy Disulfides: Relationship between Cross-strand Disulfides and Right-handed Staples
DNA sequence, physics, and promoter function: Analysis of high-throughput data On T7 promoter variants activity
TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network
Aligning Multiple Protein Structures by Deterministic Annealing
Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins
Graph kernels combined with the neural network on protein classification
Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence
Prima: Peptide Robust Identification from Ms/ms Spectra
Metagenomic Taxonomic Classification Using Extreme Learning Machines
State Space Modeling of yeast gene Expression Dynamics
Conformational Dynamics of HIV-1 protease: a Comparative molecular Dynamics Simulation Study with Multiple AMBER Force Fields
Glycine-induced formation and druggability score prediction of protein surface pockets
Mathematical model of LsrR-binding and derepression in Escherichia coli K12
Analysis of Conserved Hydrophobic Cores in Proteins and Supramolecular Complexes
HemoNet: Predicting hemolytic activity of peptides with integrated feature learning
Protein Secondary Structure Prediction Using NMR Chemical Shift Data
Reverse engineering of gene regulatory network using restricted gene expression programming
Min3: Predict microRNA target gene using an improved binding-site representation method and support vector machine
COLDLNA: Enhancing long-range node features extraction to improve robust generalization ability of drug-target binding affinity prediction in cold-start scenarios
Prediction of protein-protein interaction network using a multi-objective optimization approach
CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea
The novel design of a multi-epitope vaccine candidate against the dengue virus using advanced immunoinformatics and structural analysis
Identification of phenotype-relevant differentially expressed genes in breast cancer demonstrates enhanced quantile discretization protocol's utility in multi-platform microarray data integration
Potential HIV-1 fusion inhibitors mimicking gp41-specific broadly neutralizing antibody 10E8: In silico discovery and prediction of antiviral potency
Mango: Multiple Alignment with n Gapped Oligos
Sequence-Based enzyme catalytic Domain Prediction Using Clustering and Aggregated Mutual Information Content
Improving the Inter-Corpora Compatibility for protein Annotations
Compactness Determines protein Folding Type
Comparative Genomic Analysis of Transcription Regulation Elements Involved in Human Map Kinase G-protein Coupling Pathway
PCA-constrained multi-core matrix fusion network: A novel approach for cancer subtype identification
Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets
Direct Prediction of T-cell Epitopes Using Support Vector Machines with Novel Sequence Encoding Schemes
Event Extraction with Complex Event Classification Using Rich Features
Overlapping group screening for binary cancer classification with TCGA high-dimensional genomic data
A Simple Shortcut to Unsupervised Alignment-Free phylogenetic genome Groupings, even from Unassembled sequencing reads
Relative von Neumann Entropy for Evaluating amino acid conservation
Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons
Transcript Annotation Prioritization and Screening System (TRApss) for Mutation Screening
Computational identification of physicochemical signatures for host tropism of influenza A virus
Protein Folding on the Hexagonal Lattice in the Hp Model
An Amino Acid Substitution Matrix for Protein Conformation Identification
A hybrid model of cell cycle in mammals
Prediction of cis -Regulatory Elements: from High-Information Content Analysis to Motif Identification
Introduction to the JBCB special issue on CBC 2019
RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy
Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method
A protein succinylation sites prediction method based on the hybrid architecture of LSTM network and CNN
MAMMOTh: A new database for curated mathematical models of biomolecular systems
Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network
Centrality and the shortest path approach in the human interactome
Editorial - Bioinformatics development at the BGRS\SB conference series: 10th anniversary
Multiclass Molecular Cancer Classification by Kernel Subspace Methods with Effective Kernel Parameter Selection
Automated analysis of karyotype images
Repertoire of protein kinases Encoded in the genome of zebrafish shows remarkably Large Population of PIM kinases
An alignment-independent three-dimensional quantitative structure-activity relationship study on ron receptor tyrosine kinase inhibitors
A Novel Coherence Measure for Discovering Scaling Biclusters from Gene Expression Data
Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction
An Overview of the Algorithmic Session of MCCMB'05
An Empirical Study of the Universal Chemical Key Algorithm for Assigning Unique Keys to Chemical Compounds
Local RNA folding revisited
Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes
Support vector machine-based prediction of pore-forming toxins (PFT) using distributed representation of reduced alphabets
Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach
Identification of Functional Modules in a PPI Network by Bounded Diameter Clustering
Is Lgi2 the Candidate Gene for Partial Epilepsy with Pericentral Spikes?
Evaluating Mixture Models for Building RNA Knowledge-Based Potentials
On the Asymmetry of the Residue Compositions of the Binding Sites on protein Surfaces
A Quantitative Analysis of Interfacial Amino Acid Conservation in Protein-protein Hetero Complexes
Testing Differential Expression in Nonoverlapping gene Pairs: a New Perspective for the Empirical Bayes Method
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene
Haplotype Inference and Block Partitioning in Mixed Population Samples
Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins
Exploring disease comorbidity in a module-module interaction network
In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression
Multi-Classification of Drug-Drug interaction based on a complete graph convolutional neural network and explainable artificial intelligence
Direct interaction network inference for compositional data via codaloss
Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm
in Silico Search for Natural Antisense Transcripts Reveals their Differential Expression in Human Tumors
A Novel Approach to DNA Copy Number Data Segmentation
Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
Metatox - Web application for generation of metabolic pathways and toxicity estimation
A Practical Question Based on Cross-Platform microarray Data Normalization: are Boec More Like Large Vessel or microvascular Endothelial Cells or Neither of Them?
Comparative metagenome analysis of an Alaskan glacier
A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis
Improving drug-target interaction prediction through dual-modality fusion with InteractNet
Motif Discovery with Data Mining in 3D protein Structure Databases: Discovery, Validation and Prediction of the U-Shape zinc binding ("Huf-zinc") Motif
ExAtlas: An interactive online tool for meta-analysis of gene expression data
De novo sequencing with Limited Number of Post-Translational Modifications per peptide
A transfer learning approach via procrustes analysis and mean shift for cancer drug sensitivity prediction
Introductory note for JBCB special issue
Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features
Identifying differentially expressed genes in Time-Course microarray Experiment without Replicate
A Probabilistic Framework to Improve microRNA Target Prediction by Incorporating Proteomics Data
Deriving Topology and Sequence Alignment for the Helix Skeleton in Low-Resolution protein Density Maps
On Comparing Two Structured RNA Multiple alignments
Mathematical modeling of bacterial cell cycle: The problem of coordinating genome replication with cell growth
M 3 -20M: A large-scale multi-modal molecule dataset for AI-driven drug design and discovery
Systematic analysis and integrative discovery of active-site subpocket-specific dehydroquinate synthase inhibitors combating antibiotic-resistant Staphylococcus aureus infection
Integration of multi-omics data to mine cancer-related gene modules
Knowledge-based generalization of metabolic networks: A practical study
Constant Time Clash Detection in protein Folding
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks
IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction
Generalized Hill Function Method for Modeling Molecular Processes
Choosing Snps Using Feature Selection
Fractal dimensionality of a coiled helical coil
A Theoretical Analysis of the Selection of Differentially Expressed Genes
Explore the hidden treasure in protein-protein interaction networks - An iterative model for predicting protein functions
DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder
Optimal Pairwise Alignment of Fixed protein Structures in Subquadratic Time
Probabilistic Non-Negative Matrix Factorization: Theory and Application to microarray Data Analysis
The Importance of inhibitors for the Simulation of metabolic Processes: in silico Zn 2+ Inhibition of M-Aconitase from Analysis of glycolysis and Krebs Cycle Kinetic Models
Index-based Similarity Search for Protein Structure Databases
Development of Image Processing Program for Yeast Cell Morphology
DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost
MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment
Approximate Matching of Structured Motifs in Dna Sequences
Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources
Prediction of Cell Wall Sorting Signals in Gram-Positive bacteria with a Hidden Markov Model: Application to Complete genomes
A Comprehensive Whole Genome Bacterial Phylogeny Using Correlated Peptide Motifs Defined in a High Dimensional Vector Space
Comparing Virus Classification using genomic Materials According to Different Taxonomic Levels
Bteval: a Server for Evaluation of beta-turn Prediction Methods
Rearrangement distance with reversals, indels, and moves in intergenic regions on signed and unsigned permutations
Optimizing taxon addition order and branch lengths in the construction of phylogenetic trees using maximum likelihood
Formal modeling of a system of chemical reactions under uncertainty
A model study of the morphogenesis of D. melanogaster mechanoreceptors: The central regulatory circuit
Stably expressed genes in single-cell RNA sequencing
The Janus-Faced E-Values of Hmmer2: Extreme Value Distribution or logistic Function?
Model of the reception of Hedgehog morphogen concentration Gradient: Comparison with an Extended Range of Experimental Data
Clustering of Amino Acids for Protein Secondary Structure Prediction
Analysis of 4C-seq data: A comparison of methods
When Cloud Computing Meets Bioinformatics: a Review
Research on Parameterized Algorithms of the Individual Haplotyping Problem
GEREDB: Gene expression regulation database curated by mining abstracts from literature
Identifying human microRNA-disease associations by a new diffusion-based method
An efficient algorithm for pairwise local alignment of protein interaction networks
Rotational dynamics of bases in the gene coding interferon alpha 17 (IFNA17)
Discovering novel protein-protein interactions by measuring the protein semantic similarity from the biomedical literature
Genetic Network Analysis by Quasi-Bayesian Method
Complete assembly of circular and chloroplast genomes based on global optimization
Sensitivity Analysis for Studying the Relation between biochemical reactions and metabolic phenotypes
Computational Identification of Transcription Factors Involved in Early Cellular Response to a Stimulus
Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments
iAMY-RECMFF: Identifying amyloidgenic peptides by using residue pairwise energy content matrix and features fusion algorithm
Behavioral dynamics of bacteriophage gene regulatory networks
Structural bioinformatics survey on disease-inducing missense mutations
Optimized splitting of mixed-species RNA sequencing data
Function Prediction of uncharacterized proteins
Evaluation of Normalization and Pre-Clustering Issues in a Novel Clustering Approach: Global Optimum Search with Enhanced Positioning
Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations
Data Mining Tools for Biological Sequences
in Silico Phenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples
Exclusive Sequences of Different genomes
Predicting drug synergy for precision medicine using network biology and machine learning
Multiple Sequence Alignment Using an Exhaustive and Greedy Algorithm
Additive Risk Analysis of microarray Gene Expression Data via Correlation Principal Component Regression
Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers
Identification of best indicators of peptide-spectrum match using a permutation resampling approach
Using Weighted Permutation Scores to Detect Differential Gene Expression with Microarray Data
RNAknot: A new algorithm for RNA secondary structure prediction based on genetic algorithm and GRASP method
EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins
Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins
Modeling of Three Dimensional Structure of Human alpha-Fetoprotein complexed with Diethylstilbestrol: docking and molecular Dynamics Simulation Study
An approach to computer analysis of the ligand binding assay data on example of radioligand assay data
Uniqueness, Intractability and Exact Algorithms: Reflections on Level-k Phylogenetic Networks
The Comparison of Three Methods for Chromosomal Abnormality Detection
Modeling the heterogeneity of p53 dynamics in DNA damage response
Investigating noise tolerance in an efficient engine for inferring biological regulatory networks
On Preprocessing and Antisymmetry in de novo peptide Sequencing: Improving Efficiency and Accuracy
Path-based Systems to Guide Scientists in the Maze of Biological Data Sources
PR2S2Clust: Patched RNA-seq read segments' structure-oriented clustering
Drug Target prioritization in Plasmodium falciparum through metabolic Network Analysis, and inhibitor Designing using Virtual Screening and docking Approach
John Wooley and JBCB
Sorting permutations by fragmentation-weighted operations
Cancer classification and functional pathway discovery using TCGA transcriptomic profiles: A matched case-control framework
CLusFCM: an Algorithm for Predicting protein Functions Using homologies and protein Interactions
An investigation into eukaryotic pseudouridine synthases
Clarifying real receptor binding site between coronavirus HCoV-HKU1 and 9-O-Ac-Sia based on molecular docking
Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data
An effective differential expression analysis of deep-sequencing data based on the Poisson log-normal model
Pantograph: A template-based method for genome-scale metabolic model reconstruction
A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis
Functional Understanding of the Diverse exon-intron Structures of Human GPCR genes
A Method for Discovering Common Patterns from Two RNA Secondary Structures and its Application to Structural Repeat Detection
Introduction to selected papers from GIW/InCoB 2015
Transcription Binding Site Prediction Using Markov Models
Robustness of Metabolic Map Reconstruction
Protein Classification Using Comparative Molecular Interaction Profile Analysis System
Applying Robust Directional Similarity Based Clustering Approach Rdsc to Classification of Gene Expression Data
Search Similar protein Structures with Classification, Sequence and 3D alignments
Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information
Entropy-Based Cluster Validation and Estimation of the Number of Clusters in gene Expression Data
Application of a Generalized Mwc Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes
WBFQC: A new approach for compressing next-generation sequencing data splitting into homogeneous streams
Prediction of transcription Factor Binding Sites Using genetical genomics Methods
Progress in Computational Studies of Host-pathogen Interactions
Identification of biomarker genes for resistance to a pathogen by a novel method for meta-analysis of single-channel microarray datasets
A technique for preserving network structure in randomized Hi-C data
Judgment Algorithm for Periodicity of Time Series Data Based on Bayesian Information Criterion
Active Site Driven Ligand Design: an Evolutionary Approach
Prediction of antisense oligonucleotide Efficacy Using Aggregate motifs
Wrestling with Biomedical Research Results: Language Resources and Literature Analysis
Studying the Role of APOE in Alzheimer's disease Pathogenesis using a Systems Biology Model
A Cellular Automaton to Model the Development of Primary Shoot Meristems of Arabidopsis thaliana
Deppdb - DNA electrostatic Potential Properties Database: electrostatic Properties of genome DNA Elements
Integration of Bioinformatics and Computational Biology to Understand Protein-dna Recognition Mechanism
Modeling and Analysis of biopathways Dynamics
A New genotype calling Method for Affymetrix SNP Arrays
DeepRT: Predicting compounds presence in pathway modules and classifying into module classes using deep neural networks based on molecular properties
Prediction of gene-based drug indications using compendia of public gene expression data and PubMed abstracts
Snps in the HIV-1 TATA Box and the Aids pandemic
Multidimensional knowledge-based framework is an essential step in the categorization of gene sets in complex disorders
Analysis of Qpcr Data by Converting Exponentially Related CT Values into Linearly Related X 0 Values
AUSPP: A universal short-read pre-processing package
Identifying adverse drug reactions and drug-induced diseases using network-based drug mapping
A Dimensionless Fit Measure for Phylogenetic Distance Trees
Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function
Compression for population genetic data through finite-state entropy
Colorful orthology clustering in bounded-degree similarity graphs
Identification of Granger Causality between Gene Sets
Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach
Exhaustive Computation of Exact duplications via Super and Non-Nested Local Maximal repeats
An Integrated Feature Selection and Classification Method to Select Minimum Number of Variables on the Case Study of Gene Expression Data
Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles
Measurement of word frequencies in genomic DNA sequences based on partial alignment and fuzzy set
Unique Peptide Identification of Rnasea Superfamily Sequences Based on Reinforced Merging Algorithms
HisCoM-GGI: Hierarchical structural component analysis of gene-gene interactions
Using Directed Information to Build Biologically Relevant Influence Networks
ReHiC: Enhancing Hi-C data resolution via residual convolutional network
Representing a Set of Reconciliations in a Compact Way
Comparing Pearson, Spearman and Hoeffding's d Measure for Gene Expression Association Analysis
Effect of mutant NMDA receptors on the oscillations in a model of hippocampus
Combinatorial Reconstruction of Half-Sibling Groups from Microsatellite Data
Predicting Risk of Coronary Artery Disease from Dna Microarray-based Genotyping Using Neural Networks and Other Statistical Analysis Tool
Dynamic Integration of Gene Annotation and its Application to Microarray Analysis
Numerical algorithm for morphogen synthesis region identification with indirect image-type measurement data
Computationally predicting protein-RNA interactions using only positive and unlabeled examples
Training host-pathogen protein-protein interaction predictors
A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures
Analysis of multiple related phenotypes in genome-wide association studies
An Interactive Tool for Extracting Exons and Snp from Genomic Sequence: Isolation of Hcn1 and Hcn3 Ion Channel Genes
Heuristic Search in Constrained Bipartite Matching with Applications to Protein Nmr Backbone Resonance Assignment
PDB-2-PBv3.0: An updated protein block database
Identification of Shortened 3′ untranslated Regions from Expression Arrays
PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list
Hot spots localization in proteins by optimized short time Ramanujan Fourier transform
Retrieving Mutation-Specific Information for Human proteins in UniProt/Swiss-PROT knowledgebase
Antigen exposure leads to rigidification of germline antibody combining site
ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets
Coopps: a System for the Cooperative Prediction of Protein Structures
Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA
Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data
bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model
Breadth-First Search Approach to Enumeration of Tree-like Chemical Compounds
Prediction of nucleosome dynamic interval based on long-short-term memory network (LSTM)
An Almost Linear Time Algorithm for a General Haplotype Solution on Tree Pedigrees with no Recombination and its Extensions
A Case-Based Reasoning System for Genotypic Prediction of HIV-1 Co-receptor tropism
Translation Regulation of Intron-containing Genes in Chloroplasts