yusuke1997/dblp-id-title huggingface dataset:
Prediction of miRNA-disease associations based on Weighted K-Nearest known neighbors and network consistency projection
Putracer: a Novel Method for Identification of continuous-Domains in Multi-Domain proteins
Computational Approaches for Drug Repositioning and Combination Therapy Design
Identifying and Reconstructing Lateral Transfers from Distance Matrices by Combining the Minimum Contradiction Method and Neighbor-Net
Discovery of synergistic genetic network: A minimum spanning tree-based approach
RepeatsPlus - program for finding motifs and repeats in data sequences
A novel model-based on FCM-LM algorithm for prediction of protein folding rate
A new algorithm for DNA motif discovery using multiple sample sequence sets
Identification of a seven autophagy-related gene pairs signature for the diagnosis of colorectal cancer using the RankComp algorithm
Prediction of Protein Coarse Contact Maps
Expansin gene family database: A comprehensive bioinformatics resource for plant expansin multigene family
Finding Alternative Splicing Patterns with Strong Support from expressed Sequences on Individual exons/introns
DEEPSMP: A deep learning model for predicting the ectodomain shedding events of membrane proteins
Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues
Conserved features of complexes of TATA-box binding proteins with DNA
Parallel Stochastic Simulation of Macroscopic calcium currents
Support Vector Machines for Prediction and Analysis of Beta and Gamma-turns in Proteins
Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring
Detection of homologous recombination in closely related strains
Deeper investigation into the utility of functional class scoring in missing protein prediction from proteomics data
Exact solutions for species Tree Inference from discordant gene Trees
Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback
Validation of signalling pathways: Case study of the p16-mediated pathway
Towards a Systematic Evaluation of protein Mutation Extraction Systems
Sequence-based prediction of transcription upregulation by auxin in plants
A Graph-Based Semantic Similarity Measure for the gene Ontology
NEAT-FLEX: Predicting the conformational flexibility of amino acids using neuroevolution of augmenting topologies
Covariance thresholding to detect differentially co-expressed genes from microarray gene expression data
A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment
Joint Learning of Gene Functions - a Bayesian Network Model Approach
Integrating network topology, gene expression data and GO annotation information for protein complex prediction
A pharmacokinetic model based on the SSA-1DCNN-Attention method
PESM: A novel approach of tumor purity estimation based on sample specific methylation sites
A New Regulatory Interaction Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals
Comparative analysis of false discovery rate methods in constructing metabolic association networks
Evolution of the Nadr Regulon in Enterobacteriaceae
A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle
Guiding protein docking with Geometric and Evolutionary Information
A probabilistic version of Sankoff's maximum parsimony algorithm
An O(n3) algorithm for sorting signed genomes by reversals, transpositions, transreversals and block-interchanges
Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments
Dna Structural Features and Architecture of promoter Regions Play a Role in gene Responsiveness of S. Cerevisiae
Numerical constructions of optimal feedback in models of chemotherapy of a malignant tumor
A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model
Root locus-based stability analysis for biological systems
Querying metabolism under Different Physiological Constraints
Identification of inflammatory bowel disease-related proteins using a reverse k-nearest neighbor search
Suite of Tools for Statistical n-Gram Language Modeling for Pattern Mining in whole genome Sequences
Iterative Two-Pass Algorithm for Missing Data Imputation in SNP Arrays
A Tutorial on Markov Models Based on Mendel's Classical Experiments
A Fast and Sensitive Algorithm for Aligning Ests to the Human Genome
Dynamic Model-based Clustering for Time-course Gene Expression Data
Network motif-based analysis of regulatory patterns in paralogous gene pairs
Aligned genomic data compression via improved modeling
An evaluation of combined strategies for improving the performance of molecular docking
Reconn: a Cytoscape Plug-in for Exploring and Visualizing Reactome
Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides
Fitting protein Chains to cubic Lattice is NP-Complete
Principal component analysis in protein tertiary structure prediction
Calculation of immune cell proportion from batch tumor gene expression profile based on support vector regression
Trade-offs among transcription elongation rate, number, and duration of ubiquitous pauses on highly transcribed bacterial genes
Measuring consistency among gene set analysis methods: A systematic study
ThermalProGAN: A sequence-based thermally stable protein generator trained using unpaired data
Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins
A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction
Approaches for the identification of driver mutations in cancer: A tutorial from a computational perspective
FQC: A novel approach for efficient compression, archival, and dissemination of fastq datasets
KDSNP: A kernel-based approach to detecting high-order SNP interactions
Symbolic Modeling of Genetic Regulatory Networks
Decision Tree Based Information Integration for Automated Protein Classification
A non-parametric Bayesian joint model for latent individual molecular profiles and survival in oncology
Visualizing microarray Data for Biomarker Discovery by Matrix Reordering and Replicator Dynamics
Spectra-first feature analysis in clinical proteomics - A case study in renal cancer
Two Plus Two Does not Equal Three: Statistical Tests for Multiple genome Comparison
A Fast and Accurate Algorithm for Diploid Individual Haplotype Reconstruction
Evaluating feature-selection stability in next-generation proteomics
Molecular Networks in microarray Analysis
Identification of the PCA29 gene signature as a predictor in prostate cancer
iDNA6mA-Rice-DL: A local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method
Aliasing in Gene Feature Detection by Projective Methods
Exploring Protein's Optimal Hp Configurations by Self-organizing Mapping
Mathematical Modeling of Living Cell Metabolism Using the Method of Steady-state Stoichiometric Flux Balance
Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification
New variable selection strategy for analysis of high-dimensional DNA methylation data
Cwinnower Algorithm for Finding Fuzzy DNA Motifs
Single-cell RNA-seq data clustering: A survey with performance comparison study
A computational model of the effect of symplastic growth on cell mechanics in a linear leaf blade
a Priori Contact Preferences in Molecular Recognition
SS-DTI: A deep learning method integrating semantic and structural information for drug-target interaction prediction
A Workflow for Mutation Extraction and Structure Annotation
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm
A brief review and comparative analysis of RNA secondary structure prediction tools
Techniques for Optimization of Queries on Integrated Biological Resources
Clustering Algorithms for Detecting Functional Modules in protein Interaction Networks
Introduction to the 9th Young Scientists School on Systems Biology and Bioinformatics (SBB'2017)
Affygcqc: a Web-Based Interface to Detect Outlying GeneChips with Extreme studentized Deviate Tests
Identification of Biological Relationships from Text Documentsusing Efficient Computational Methods
Introductory note for BGRS\SB-2014 special issue
Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts
Representation of DNA sequences in genetic codon context with applications in exon and intron prediction
An innovative method for the selection of inhibitors of the viral spike-glycoprotein of the SARS-CoV
Dispom: a Discriminative de-novo Motif Discovery Tool Based on the Jstacs Library
SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks
Selection of Cryptic B-cell Epitopes Using Informational Analysis of Protein Sequenses
A novel graph kernel on chemical compound classification
ProgSIO-MSA: Progressive-based single iterative optimization framework for multiple sequence alignment using an effective scoring system
Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016)
Introduction to the selected papers from the 7th International Conference on Bioinformatics and Computational Biology (BICoB 2015)
Shared ancestry of core-histone subunits and non-histone plant proteins containing the Histone Fold Motif (HFM)
A New Method for Nonhomogeneous Time Course Expression Analysis
Modeling Classic Attenuation Regulation of gene Expression in bacteria
Identification of conserved Features of Laglidadg Homing endonucleases
In silico Screening of protein-protein Interactions with All-to-All Rigid docking and Clustering: an Application to Pathway Analysis
Sirius PSB: a Generic System for Analysis of Biological Sequences
A Survey on Haplotyping Algorithms for Tightly Linked Markers
Motif discovery in biological network using expansion tree
Noise-robust Soft Clustering of Gene Expression Time-course Data
An Ancova Approach to Normalize Microarray Data, and its Performance to Existing Methods
Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?
BENIN: Biologically enhanced network inference
Local Sequence-structure Motifs in Rna
Decomposition of Overlapping Patterns by Cumulative Local Cross-correlation
SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes
Computing the Breakpoint Distance between Partially Ordered genomes
EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes
An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type
Global metal-ion Binding protein Fingerprint: a Method to Identify Motif-Less metal-ion Binding proteins
Evaluating network-based missing protein prediction using p-values, Bayes Factors, and probabilities
Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery
SIN-KNO: A method of gene regulatory network inference using single-cell transcription and gene knockout data
Inference of Genetic Networks Using Lpms: Assessment of Confidence Values of Regulations
Minimizing the deep coalescence cost
PRIGSA: Protein repeat identification by graph spectral analysis
Protein-protein Interactions as New Targets for Drug Design: Virtual and Experimental Approaches
PSRna: Prediction of small RNA secondary structures based on reverse complementary folding method
An Integrated Comprehensive Workbench for Inferring Genetic Networks: voyagene
Likelihood of a Particular Order of Genetic Markers and the Construction of Genetic Maps
Algorithms for Challenging Motif Problems
Prediction of Loop Regions in protein Sequence
A novel network-based computational method to predict protein phosphorylation on tyrosine sites
Linear Independence of Pairwise Comparisons of Dna Microarray Data
EDeepSSP: Explainable deep neural networks for exact splice sites prediction
Peak Detection in Mass Spectrometry by Gabor Filters and Envelope Analysis
How to Choose a Normalization Strategy for miRNA Quantitative Real-Time (qPCR) Arrays
Preface to selected papers from the 6th International Conference on Computational Systems-Biology and Bioinformatics (CSBio2015)
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction
Automatic phylogenetic Classification of bacterial beta-Lactamase Sequences including Structural and Antibiotic substrate Preference Information
Introduction to the JBCB special issue on CSBio 2019
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
Fast and memory efficient approach for mapping NGS reads to a reference genome
ModFossa: A library for modeling ion channels using Python
Association of Feature Gene Expression with Structural Fingerprints of Chemical Compounds
Introduction to JBCB Special Issue on BICOB-2018
Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms
Mining Disease State converters for Medical Intervention of Diseases
Analytical workflow profiling gene expression in murine macrophages
Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas
Co-evolution analysis to predict protein-protein interactions within influenza virus envelope
Two Notes on Genome Rearrangement
Prediction of transcription Factor Binding Sites Using CHIP-Chip and Phylogenetic footprinting Data
Multimodal Phylogeny for Taxonomy: Integrating Information from nucleotide and amino acid Sequences
Evidence for exon shuffling is sensitive to model choice
Automated Identification of Single Nucleotide Polymorphismsfrom Sequencing Data
Toxicity prediction of small drug molecules of androgen receptor using multilevel ensemble model
Animal microRNA Target Prediction Using Diverse Sequence-Specific determinants
Antimicrobial peptides recognition using weighted physicochemical property encoding
Computational Challenges of Tumor Spheroid Modeling
Prediction of oxidoreductase subfamily classes based on RFE-SND-CC-PSSM and machine learning methods
Searching for Transcription Factor Binding Site Clusters: How True Are True Positives?
Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates
Transforming OMIC features for classification using siamese convolutional networks
Reduced Bio-basis Function Neural Networks for Protease Cleavage Site Prediction
Computational Gene knockout reveals Transdisease-Transgene Association Structure
Gene Regulatory Network Reconstruction by Bayesian Integration of Prior Knowledge and/or Different Experimental Conditions
Adjusted likelihood-ratio test for variants with unknown genotypes
Efficient Computation of Kinship and Identity Coefficients on Large Pedigrees
MethyMer: Design of combinations of specific primers for bisulfite sequencing of complete CpG islands
Resolving the multiple sequence alignment problem using biogeography-based optimization with multiple populations
Overlapping Alternative donor splice Sites in the Human genome
Clustering Biological Annotations and Gene Expression Data to Identify Putatively Co-regulated Biological Processes
Guiding Probabilistic Search of the protein conformational Space with Structural Profiles
Identification of potential drug targets for treatment of refractory epilepsy using network pharmacology
Is there codon usage bias for poly-Q stretches in the human proteome?
Modeling of glycerol-3-phosphate transporter suggests a Potential 'Tilt' Mechanism involved in its Function
Brief Introduction to Some New Results in Gene Expression Analysis, Systems Biology Modeling, Motif Identification, and (noncoding) RNA Analysis
Dissecting the Human Spliceosome through Bioinformatics and Proteomics Approaches
An integrated framework for identification of effective and synergistic anti-cancer drug combinations
Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm
Quantifying Slow Evolutionary Dynamics in RNA Fitness Landscapes
An ensemble approach for circular RNA-disease association prediction using variational autoencoder and genetic algorithm
Tensor decomposition based on the potential low-rank and p-shrinkage generalized threshold algorithm for analyzing cancer multiomics data
An accurate and fast alignment-free method for profiling microbial communities
Using Rigidity Analysis to Probe Mutation-induced Structural Changes in proteins
A Re-Evaluation of Biomedical Named Entity-Term Relations
Derived SNP Alleles are Used More Frequently than Ancestral Alleles as Risk-associated Variants in Common Human Diseases
A computational model for predicting transmembrane regions of retroviruses
A deep imputation and inference framework for estimating personalized and race-specific causal effects of genomic alterations on PSA
Observation Conflict Resolution in steady-State metabolic Network Dynamics Analysis
Structural profile matrices for predicting structural properties of proteins
Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History
Statistical method for estimation of the predictive power of a gene circuit model
A Gentle Introduction to SNP Analysis: Resources and Tools
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling
Permanent proteins in the urine of healthy humans during the Mars-500 experiment
A Graph-Based Algorithm for Mining Multi-Level Patterns in genomic Data
Disruption of protein complexes
Prediction of kinase-substrate relations based on heterogeneous networks
Detecting differentially expressed genes by smoothing effect of gene length on variance estimation
A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions
Comparative analysis of probiotic bacteria based on a new definition of core genome
Drug repurposing for non-small cell lung cancer by predicting drug response using pathway-level graph convolutional network
Beware of Moving targets: Reference proteome Content Fluctuates substantially over the Years
The origins and evolutionary history of human non-coding RNA regulatory networks
Bioinformatic identification of differentially expressed genes associated with prognosis of locally advanced lymph node-positive prostate cancer
Identification of jointly correlated gene sets
A Multivariate Extension of the gene Set Enrichment Analysis
Study of the mechanism of step-by-step interaction of viral proteins during replication and transcription
Quality assurance of the gene ontology using abstraction networks
Kernel-based Self-organized Maps Trained with Supervised Bias for Gene Expression Data Analysis
Evolving Connectivity between Genetic oscillators and Switches using Evolutionary Algorithms
Estimation of relative effectiveness of phylogenetic programs by machine learning
Predicting protein Folding Rate from amino acid Sequence
The Value of an in-Domain Lexicon in genomics QA
Universal informative CpG sites for inferring tumor purity from DNA methylation microarray data
Gene regulatory network inference based on modified adaptive lasso
Implementing a modeling software for animated protein-complex interactions using a physics simulation library
Knowledge-Based versus experimentally Acquired Distance and Angle Constraints for NMR Structure Refinement
Design and Analysis of an Efficient Recursive Linking Algorithm for Constructing Likelihood Based Genetic Maps for a Large Number of Markers
Exploiting Symmetry Properties of the Discretizable molecular Distance Geometry Problem
The mechanism accounting for DNA damage strength modulation of p53 dynamical properties
AAindex-PPII: Predicting polyproline type II helix structure based on amino acid indexes with an improved BiGRU-TextCNN model
Gene expression analysis reveals a pitfall in the molecular research of prostate tumors relevant to Gleason score
Simulation of Cell Movement and Interaction
An Evolutionary conservation-Based Method for Refining and Reranking protein Complex Structures
Effects of low dose ionizing radiation on DNA damage-caused pathways by reverse-phase protein array and Bayesian networks
Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks
Accurate prediction of human miRNA targets via graph modeling of the miRNA-target duplex
Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night
A 2-approximation algorithm for the contig-based genomic scaffold filling problem
Svm-Based Method for protein Structural Class Prediction Using Secondary Structural Content and Structural Information of amino acids
A hybrid solver for protein multiple sequence alignment problem
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML
Cross-cellular analysis of chromatin accessibility markers H3K4me3 and DNase in the context of detecting cell-identity genes: An "all-or-nothing" approach
Scaling laws of graphs of 3D protein structures
PROSPECT: A web server for predicting protein histidine phosphorylation sites
Noise model estimation with application to gene expression
Sheep: a Tool for Description of β-Sheets in protein 3D Structures
Improving the Performance of protein Threading Using Insertion/Deletion Frequency Arrays
Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation
Multi-Factorial Analysis of Class Prediction Error: Estimating Optimal Number of Biomarkers for Various Classification Rules
JBCB, the first decade
A Short Introduction to Some Recent Progress in phylogenetic Network Reconstruction, genome Mapping, gene Expression Analysis, molecular Dynamic Simulation, and Other Problems in Bioinformatics
Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017)
Efficient Computation of Minimum Recombination with genotypes (not Haplotypes)
Statistical Information Characterization of conserved Non-Coding Elements in vertebrates
Introduction to Selected Papers from InCoB 2021
Succinate aggravates NAFLD progression to liver cancer on the onset of obesity: An in silico model
Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1
Wave Packet Motions Coupled to electron Transfer in Reaction Centers of Chloroflexus Aurantiacus
Long-Range Information and Physicality Constraints Improve predicted protein Contact Maps
Co-Expression among Constituents of a Motif in the protein-protein Interaction Network
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny
Comparative Modeling of Coevolution in Communities of Unicellular Organisms: Adaptability and Biodiversity
A Hybrid Genetic Algorithm and Expectation Maximization Method for Global Gene Trajectory Clustering
Structure Prediction of Helical Transmembrane Proteins at Two Length Scales
Statistical Measures of the Structure of Genomic Sequences: Entropy, Complexity, and Position Information
Covariation Analysis of Local Amino Acid Sequences in Recurrent Protein Local Structures
Classification of the fragrant styles and evaluation of the aromatic quality of flue-cured tobacco leaves by machine-learning methods
Genome Wide Identification of Dna Binding Motifs of Nodd-factor in Sinorhizobium Meliloti and Mesorhizobium Loti
Prediction of Protein Secondary Structure Based on Residue Pairs
AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing
Using Attribute Behavior Diversity to Build Accurate Decision Tree Committees for microarray Data
Cluster Analysis of Dynamic Parameters of Gene Expression
Gene Ontology-Based Semantic Alignment of Biological Pathways by Evolutionary Search
Finding Non-Coding RNAs through genome-Scale Clustering
ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features
A Tabu Search Algorithm for Post-processing Multiple Sequence Alignment