yusuke1997/dblp-id-title huggingface dataset:
10 years for the Journal of Bioinformatics and Computational Biology (2003-2013) - A retrospective
Tutorial on de novo peptide sequencing using MS/MS Mass spectrometry
Methods for cell-type annotation on scRNA-seq data: A recent overview
Large-Scale Structural Modeling of protein complexes at Low Resolution
Denoising Protein-Protein interaction network via variational graph auto-encoder for protein complex detection
Reconstructing protein and gene phylogenies using reconciliation and soft-clustering
Ranking differential Hubs in gene Co-Expression Networks
Prenet: Predictive network from ATAC-SEQ data
Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter
Discovery of novel antimicrobial peptides: A transcriptomic study of the sea anemone Cnidopus japonicus
Genetic algorithm applied to simultaneous parameter estimation in bacterial growth
Ruleminer: a Knowledge System for Supporting High-throughput Protein Function Annotations
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes
A general heuristic for genome rearrangement problems
Iterative Non-Sequential protein Structural Alignment
Modelling and optimizing combination therapeutic strategies for KRAS- and EGFR-mutant lung cancer
The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families
Cell cycle and protein complex dynamics in discovering signaling pathways
Introduction to selected papers from MCCMB 2015
Feature Selection in Validating Mass Spectrometry Database Search Results
The apparent enhancement of CpG transversions in primate lineage is a consequence of multiple replacements
A Recursive Method for Solving Haplotype Frequencies with Application to Genetics
An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra
Body plan evolvability: The role of variability in gene regulatory networks
Analysis of clonal evolution in cancer: A computational perspective
PLMABFW: A deep learning framework for predicting Antibody-Antigen interactions using protein language model
Alternative splicing can lead to chaos
Graph Wavelet Alignment Kernels for Drug Virtual Screening
Gtie-Rt: A comprehensive graph learning model for predicting drugs targeting metabolic pathways in human
Assessment of optimized Markov models in protein fold classification
Detection and Decomposition: Treatment-induced Cyclic gene Expression Disruption in High-Throughput Time-Series Datasets
Vire2-Dependent Pores for ssDNA Transfer across Artificial and Cell Membranes
Fuzzyart Neural Network for protein Classification
Identification of Essential proteins from Weighted protein-protein Interaction Networks
Prediction of the Exposure Status of transmembrane beta Barrel residues from protein Sequence
A deep attention network for predicting amino acid signals in the formation of α-helices
Promoter islands as a platform for interaction with nucleoid proteins and transcription factors
Introduction: Advances in Computational Systems Bioinformatics
Extraction of drug-drug interaction using neural embedding
Integrated Statistical Analysis of Cdna Microarray and Nir Spectroscopic Data Applied to a Hemp Dataset
Foreword: Special Issue for the 2019 International Conference on Bioinformatics and Computational Biology (BICOB-2019)
Modeling yeast Osmoadaptation at Different Levels of Resolution
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data
Computational study on transfer of L-ascorbic acid by UlaA through Escherichia coli membrane
Comparison of different approaches for identifying subnetworks in metabolic networks
ReSAPP: Predicting overlapping protein complexes by merging multiple-sampled partitions of proteins
Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric
Neural Models for Predicting Viral Vaccine Targets
Prophage loci predictor for bacterial genomes
How much can ChatGPT really help computational biologists in programming?
WDNfinder: A method for minimum driver node set detection and analysis in directed and weighted biological network
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes
Inferring disease and pathway associations of long non-coding RNAs using heterogeneous information network model
Counting of oligomers in Sequences Generated by Markov Chains for DNA Motif Discovery
A comment on two-locus epistatic interaction models for genome-wide association studies
Dynamically Searching for a Domain for protein Function Prediction
Dimensionality reduction for protein secondary structure and solvent accesibility prediction
Protein Structure-structure Alignment with Discrete FrÉchet Distance
3D U-Net: A voxel-based method in binding site prediction of protein structure
IPED2X: A robust pedigree reconstruction algorithm for complicated pedigrees
In Search of the protein Native State with a Probabilistic Sampling Approach
Selected Papers from the International Workshop on Cancer Bioinformatics and Intelligent Medicine (CBIM2018)
Inference of gene networks from gene expression time series using recurrent neural networks and sparse MAP estimation
Some Comments on False Discovery Rate
Admixture mapping of growth related traits in F 2 mice dataset using ancestry informative markers
Exploring Alternative Transcript Structure in the Humangenome Using Blocks and Interpro
Computational design and experimental confirmation of conformationally constrained peptides to compete with coactivators for pediatric PPARα by minimizing indirect readout effect
Inferring the Regulatory Interaction Models of transcription Factors in transcriptional Regulatory Networks
Population-specific adaptation in malaria-endemic regions of asia
Robustness versus evolvability analysis for regulatory feed-forward loops
A Tutorial of Techniques for Improving Standard Hidden Markov Model Algorithms
Transcriptional processes: Models and inference
Dimension Reduction of microarray Gene Expression Data: the Accelerated Failure Time Model
ASSA: Fast identification of statistically significant interactions between long RNAs
Lex-SVM: Exploring the Potential of exon Expression Profiling for Disease Classification
Progressive Multiple Alignment Using Sequence Triplet Optimizations and Three-residue Exchange Costs
Discovery of Highly Differentiative Gene Groups from Microarray Gene Expression Data Using the Gene Club Approach
ACES: A co-evolution simulator generates co-varying protein and nucleic acid sequences
Computation and analysis of stationary and periodic solutions of the COVID-19 infection dynamics model
Cnctdiscriminator: Coding and noncoding transcript Discriminator - an Excursion through Hypothesis Learning and Ensemble Learning Approaches
A Flexible nonparametric Approach to Find Candidate genes associated with disease in microarray Experiments
Embedding assisted prediction architecture for event trigger identification
Extended Backus-Systems for the Representation and Specification of the genome
Generation of a Large Gene/protein Lexicon by Morphological Pattern Analysis
Protein Structure and Fold Prediction Using Tree-augmented Naïve Bayesian Classifier
Investigation of non-hydroxamate scaffolds against HDAC6 inhibition: A pharmacophore modeling, molecular docking, and molecular dynamics simulation approach
Predicting Local Quality of a Sequence-Structure Alignment
Sparse Markov chain-based semi-supervised multi-instance multi-label method for protein function prediction
Systematic Variation Normalization in Microarray Data to Get Gene Expression Comparison Unbiased
Optimal Spectral Coordination of Subantennae in Natural Antennae as an Efficient Strategy for Light Harvesting in Photosynthesis
Metagenome sequence clustering with hash-based canopies
Comparison of gene regulatory networks to identify pathogenic genes for lymphoma
A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps
A systematic exploration of ΔΔG cutoff ranges in machine learning models for protein mutation stability prediction
Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets
Pairwise Protein Structure Alignment Based on an Orientation-independent Backbone Representation
Clustering Gene Expression Data with Kernel Principal Components
RMI-DBG algorithm: A more agile iterative de Bruijn graph algorithm in short read genome assembly
Using Formal Concept Analysis for microarray Data Comparison
An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks
The Purity Measure for genomic Regions leads to Horizontally Transferred genes
Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks (supplementary Material)
Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints
Testing and improving the performance of protein thermostability predictors for the engineering of cellulases
New multilocus linkage disequilibrium measure for tag SNP selection
Modeling Cancer: Integration of "omics" Information in Dynamic Systems
Molecular docking and molecular dynamics simulations of fumarate hydratase and its mutant H235N complexed with pyromellitic acid and citrate
Is It Possible to Predict Amyloidogenic Regions from Sequence Alone?
A network-based dynamic criterion for identifying prediction and early diagnosis biomarkers of complex diseases
Identifying Uniformly Mutated Segments within Repeats
Adjusted Geometric-mean: a Novel Performance Measure for Imbalanced Bioinformatics Datasets Learning
An empirical Bayes method for robust variance estimation in detecting DEGs using microarray data
Quantificational evaluation of the resolving power of qualitative biomarkers with different cardinal numbers based on a magnitude-standardized index
Recursive protein Modeling: a Divide and Conquer Strategy for protein Structure Prediction and its Case Study in CASP9
Exploring relationship between hypercholesterolemia and instability of atherosclerotic plaque - An approach based on a matrix population model
Antibody Cdr H3 Modeling Rules: Extension for the Case of Absence of Arg H94 and Asp H101
Gene Loss under Neighborhood Selection Following Whole genome Duplication and the Reconstruction of the Ancestral Populus genome
Contribution of bacterial promoter elements to transcription start site detection accuracy
An improved method for predicting interactions between virus and human proteins
Automatic Modeling of Signaling Pathways by Network Flow Model
Intragenic PROMOTOR-Like Sites in the genome of Escherichia coli Discovery and Functional Implication
Integrating temporal and spatial variabilities for identifying ion binding proteins in phage
Consensus properties and their large-scale applications for the gene duplication problem
Electrostatic Properties of Promoter Recognized by e. Coli Rna Polymerase Esigma 70
FCDECOMP: Decomposition of metabolic networks based on flux coupling relations
Disease named entity recognition using long-short dependencies
Matalign: Precise Protein Structure Comparison by Matrix Alignment
A Wavelet Approach for the Analysis of Folding Trajectory of Protein Trp-cage
Quartets and Unrooted phylogenetic Networks
Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms
Analyzing omics data by feature combinations based on kernel functions
Homologous synteny Block Detection Based on Suffix Tree Algorithms
Prediction of Dna-binding Residues from Sequence Features
Spider: Software for Protein Identification from Sequence Tags with de Novo Sequencing Error
Bioinformatics Meets Proteomics - Bridging the Gap between Massspectrometry Data Analysis and Cell Biology
Predicting ncRNA-Protein interactions with a graph attention model exploiting personalized subgraphs
Alignment of Minisatellite Maps Based on Run-Length Encoding Scheme
Erratum: " In Silico Phenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples"
Constrained Multiple Sequence Alignment Tool Development Andits Application to Rnase Family Alignment
Supervised learning method for predicting chromatin boundary associated insulator elements
Unix interfaces, Kleisli, bucandin structure, etc. - The heroic beginning of bioinformatics in Singapore
An Effective Data Mining Technique for Reconstructing gene Regulatory Networks from Time Series Expression Data
A Peak Alignment Algorithm with Novel Improvements in Application to Electropherogram Analysis
A Hybrid-System Model of the coagulation Cascade: Simulation, sensitivity, and Validation
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model
A Compressed Sensing Based Approach for Subtyping of Leukemia from gene Expression Data
Cubic: Identification of Regulatory Binding Sites through Data Clustering
Impacts of reference selection on the assembly of suspicious coronavirus genome
Recognition of cis-Regulatory Elements with Vombat
Neural System Modeling and Simulation Using Hybrid Functional Petri Net
Ubiquitous Reassortments in influenza a viruses
Metabolic Pathway Analysis of S. Pneumoniae : an in silico Approach towards Drug-Design
A Chemical Group Graph Representation for Efficient High-Throughput Analysis of atomistic protein Simulations
A tripartite Clustering Analysis on microRNA, gene and Disease Model
Complexity and Approximability of Double Digest
MicroTarget: MicroRNA target gene prediction approach with application to breast cancer
INTRODUCTION - The First IEEE Conference on Healthcare Informatics, Imaging, and Systems biology HISB'11
Prediction of Protein Subcellular Locations Using a New Measure of Information Discrepancy
Angle: a Sequencing Errors Resistant Program for Predicting Protein Coding Regions in Unfinished Cdna
Is the average shortest path length of gene set a reflection of their biological relatedness?
Conditional estimation of local pooled dispersion parameter in small-sample RNA-Seq data improves differential expression test
A Note on the Calculation of n-Statistics
Accurate Discrimination of outer membrane proteins using secondary Structure Element Alignment and Support Vector Machine
Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions
Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L.
Recognition of protein Function Using the Local Similarity
Large-scale parallel genome assembler over cloud computing environment
Numerical study of chronic hepatitis B infection using Marchuk-Petrov model
Boosted neural networks scoring functions for accurate ligand docking and ranking
Classifying Temporal microarray Data by Selecting Informative genes
Computational methodology for predicting the landscape of the human-microbial interactome region level influence
Deriving Pathway Maps from Automated Text Analysis Using a Grammar-based Approach
Exploring the potential microRNA sponge interactions of breast cancer based on some known interactions
Protein-protein interaction site prediction using random forest proximity distance
Bone marrow cavity segmentation using graph-cuts with wavelet-based texture feature
Disease-Related Concept Mining by Knowledge-Based Two-Dimensional gene Mapping
Gene Function Prediction by a Combined Analysis of Gene Expression Data and Protein-protein Interaction Data
Construction of a multi-tissue compound-target interaction network of Qingfei Paidu decoction in COVID-19 treatment based on deep learning and transcriptomic analysis
Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes
Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular Design
A Regionalizable Statistical Model of Intersecting Regions in protein-ligand binding Cavities
Molecular dynamics simulations of ribosome-binding sites in theophylline-responsive riboswitch associated with improving the gene expression regulation in chloroplasts
Three-dimensional Definition of Leaf Morphological Traits of arabidopsis in Silico Phenotypic Analysis
Short prokaryotic DNA Fragment Binning Using a Hierarchical Classifier Based on Linear Discriminant Analysis and Principal Component Analysis
Accounting for treatment during the development or validation of prediction models
Quality assessment of modeled protein structure using physicochemical properties
Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions
Residue Conservation Information for Generating near-native Structures in Protein-protein Docking
A method to predict different mechanisms for blood-brain barrier permeability of CNS activity compounds in Chinese herbs using support vector machine
Inference of genetic networks using random forests: Assigning different weights for gene expression data
Erratum: Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics
Involving repetitive regions in scaffolding improvement
Gene Expression Data Analysis in Subtypes of Ovarian Cancer Using Covariance Analysis
Quantitative structure-activity relationship modeling reveals the minimal sequence requirement and amino acid preference of sirtuin-1's deacetylation substrates in diabetes mellitus
Mendelian randomization and AlphaFold3 analysis suggest putative causal plasma proteins in graves' disease
A Multi-Strategy Approach to Informative Gene Identification from Gene Expression Data
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)
A Universal operon Predictor for prokaryotic genomes
Building maps of protein structure spaces in template-free protein structure prediction
Detecting Copy Number Variations from Array CGH Data Based on a Conditional Random Field Model
Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics
An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis
Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches
Mining Time-dependent Gene Features
Optimized leaf ordering with class labels for hierarchical clustering
Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction
On Cooperative Quasi-Equilibrium Models of transcriptional Regulation
P.R.E.S.S. - an R-package for Exploring Residual-Level protein Structural Statistics
On the Inference of Parsimonious Indel Evolutionary Scenarios
An Automated Procedure for the Extraction of Metabolic Network Information from Time Series Data
Mathematical Model for Suppression of Subgenomic Hepatitis C Virus RNA Replication in Cell Culture
DSRIG: Incorporating graphical structure in the regularized modeling of SNP data
The Probability Distribution for a Random Match between an Experimental-theoretical Spectral Pair in Tandem Mass Spectrometry
Computational prediction of antifungal peptides via Chou's PseAAC and SVM
Identifying cancer type specific oncogenes and tumor suppressors using limited size data
Efficiently Finding Regulatory Elements Using Correlation with Gene Expression
Hierarchical Classification of Gene Ontology Terms Using the Gostruct Method
Neanderthal and Denisovan ancestry in Papuans: A functional study
Application of Automatic Mutation-gene Pair Extraction to Diseases
Modeling and simulation of spatial-temporal calcium distribution in T lymphocyte cell by using a reaction-diffusion equation
Introduction to the JBCB Special Issue on Selected Papers from BICOB-2020
Biomarker Discovery and Visualization in gene Expression Data with Efficient Generalized Matrix Approximations
Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics
Application of Bioinformatics Resources for Genosensor Design
Patterns of Hydrophobicity Found in the First and Second transmembrane Domains of solute Transporters Suggest a Possible Role in Nascent protein Anchoring and Organization
A variational Bayes beta Mixture Model for Feature Selection in DNA methylation Studies
Multi-layer composite mechanical modeling for the inhomogeneous biofilm mechanical behavior
Protein tertiary structure prediction using hidden Markov model based on lattice
Predicting GHS toxicity using RTCA and discrete-time Fourier transform
Reverse engineering of gene regulatory networks based on S-systems and Bat algorithm
Search for Folding Initiation Sites from amino acid Sequence
Reconstructing Tumor phylogenies from Heterogeneous Single-Cell Data
Optimal Spaced Seeds for Homologous Coding Regions
RPPAware: A software suite to preprocess, analyze and visualize reverse phase protein array data
A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments
Quantification of the presence of enzymes in gelatin zymography using the Gini index
Reversals and transpositions distance with proportion restriction
The study of unfoldable self-avoiding walks - Application to protein structure prediction software
Binding Matrix: a Novel Approach for Binding Site Recognition
Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data
From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models
A drug similarity network for understanding drug mechanism of action
PSSP: Protein splice site prediction algorithm using Bayesian approach
MIMPFC: Identifying miRNA-mRNA regulatory modules by combining phase-only correlation and improved rough-fuzzy clustering
From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales
Increasing Power by using Haplotype Similarity in a Multimarker Transmission/disequilibrium Test
Robustness, Stability and Efficiency of Phage lambda Genetic Switch: Dynamical Structure Analysis
Accurate refinement of docked protein complexes using evolutionary information and deep learning
Comparing Multiple Chip-Sequencing Experiments
Alignment of time-resolved data from high throughput experiments
Unsupervised multi-instance learning for protein structure determination
Mirror2.0: a Platform for Assessing the Joint Action of microRNAs in Cell regulation
On correlated reaction sets and coupled reaction sets in metabolic networks
Relative sensitivity analysis of the predictive properties of sloppy models
Flexibility and Mobility in Mesophilic and Thermophilic homologous proteins from Molecular Dynamics and Foldunfold Method
Knowledge-based reasoning to annotate noncoding RNA using multi-agent system
Analyzing microarray Data with Transitive Directed Acyclic Graphs
Early lifespan prediction in Caenorhabditis elegans via contrastive learning and channel attention
The 24th International Conference on genome Informatics, Giw2013, in Singapore
Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly
Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry
CBDT-Oglyc: Prediction of O-glycosylation sites using ChiMIC-based balanced decision table and feature selection
A Robust Biomarker Discovery Pipeline for High-Performance Mass Spectrometry Data
A Bayesian approach to analyzing phenotype microarray data enables estimation of microbial growth parameters
Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes
Small parsimony for natural genomes in the DCJ-indel model
A new signal characterization and signal-based Chou's PseAAC representation of protein sequences
Minimal Marker: an Algorithm and Computer Program for the Identification of Minimal Sets of Discriminating DNA Markers for Efficient Variety Identification
MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents
Target-based drug discovery for β-globin disorders: drug target prediction using quantitative modeling with hybrid functional Petri nets
Trend of Amino Acid Composition of Proteins of Different Taxa