yusuke1997/dblp-id-title huggingface dataset:
Docking-MM-GB/SA and ADME Screening of HIV-1 NNRTI Inhibitor: Nevirapine and its Analogues
Evaluation of Codon Bias Perspectives in Phage Therapy of Mycobacterium tuberculosis by Multivariate Analysis
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption
A computational framework for finding parameter sets associated with chaotic dynamics
The CpG Island Searcher: A new WWW resource
MaXlab: A Novel Application for the Cross Comparison and Integration of Biological Signatures from Microarray Studies
Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae
M@IA: A Modular Open-Source Application for Microarray Workflow and Integrative Datamining
Modeling and characterization of inter-individual variability in CD8 T cell responses in mice
Bioinformatics classification and functional analysis of PhoH homologs
Distributions of exons and introns in the human genome
Gene Knockout Experiments to Quantify a G2/M Genetic Network Simulation for Mammary Cancer Susceptibility
IIUDB: An object-oriented system for modelling, integration and analysis of gene controlled metabolic networks
How well do we understand the clusters found in microarray data?
Homology model building of Hho1p supports its role as a yeast histone H1 protein
IMGT-ONTOLOGY for immunogenetics and immunoinformatics
Estimation of Membrane Proteins in the Human Proteome
Natural Antisense as Potential Regulator of Alternative Initiation, Splicing and Termination
Influence of C-H...π Hydrogen Bonds in Interleukins
Homology model building of prospero-type homeodomains
Analysis of Secondary Structure Predictions of Dengue Virus Type 2 NS2B/NS3 Against Crystal Structure to Evaluate the Predictive Power of theIn Silico Methods
Accessing Optimal Primer Distance from Insert
A simple model for Lutz and Bujard's controllable promoters and its application for analyzing a simple genetic oscillator
Revealing the set of mutually correlated positions for the protein families of immunoglobulin fold
A Simple Mathematical Model of Adaptation to High Osmolarity in Yeast
An in silico Mining for Simple Sequence Repeats from Expressed Sequence Tags of Zebrafish, Medaka, Fundulus, and Xiphophorus
Cell Interaction Knowledgebase: An Online Database for Innate Immune Cells, Cytokines and Chemokines
Motif detection in Arabidopsis: Correlation with gene expression data
Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology
Analysis of Codon Usage Patterns and Predicted Highly Expressed Genes for Six Phytopathogenic Xanthomonas Genomes Shows a High Degree of Conservation
MemO: A Consensus Approach to the Annotation of a Protein's Membrane Organization
Moonlighting proteins - an approach to systematize the concept
FREX: A query interface for biological processes with hierarchical and recursive structures
RNAmodel Web Server: Modeling Classic Attenuation in Bacteria
Transcriptional Regulatory Networks via Gene Ontology and Expression Data
Molecular Analysis of A 348 Base-Pair Segment of Open Reading Frame 2 of Human Astrovirus. A Characterization of Colombian Isolates
Primer Design for Whole Genome Amplification Using Genetic Algorithms
Bioinformatics Databases and Tools in Virology Research: An Overview
IMGT Standardization for Statistical Analyses of T Cell Receptor Junctions: The TRAV-TRAJ Example
Supporting genotype-phenotype correlation with the rare metabolic diseases database Ramedis
Global gene expression analysis by combinatorial optimization
Comparing bound and unbound protein structures using energy calculation and rotamer statistics
CoPreTHi: A Web tool which combines transmembrane protein segment prediction methods
SubCellProt: Predicting Protein Subcellular Localization Using Machine Learning Approaches
Molecular Modeling and Docking Studies of Glutamate Racemase in Vibrio vulnificus CMCP6
Clusters of proteins in archaeal and bacterial proteomes using compositional analysis
An Emergent Self-Organizing Map Based Analysis Pipeline for Comparative Metabolome Studies
Genetic Flows in a Structured One-Dimensional Population: Simulation and Real Data on Baikalian Polychaetes M. Godlewskii
Molecular and Structural Basis of Drift in the Functions of Closely-Related Homologous Enzyme Domains: Implications for Function Annotation Based on Homology Searches and Structural Genomics
Genome-wide Prediction and Annotation of Burkholderia Pseudomallei AraC/XylS Family Transcription Regulator
Specificity and Sensitivity of PROMIR, ERPIN and MIR-ABELA in Predicting Pre-MicroRNAs in the Chicken Genome
I-Superfamily Conotoxins: Sequence and Structure Analysis
Good Publication Practice As A Prerequisite for Comparable Enzyme Data?
Classification of short kinetics by shape
Simulation of Coevolution in Community by Using the "Evolutionary Constructor" Program
In silico Analysis of Genes Nucleoprotein, Neuraminidase and Hemagglutinin: A Comparative Study on Different Strains of Influenza A (Bird Flu) Virus Sub-Type H5N1
ChemModLab: A Web-Based Cheminformatics Modeling Laboratory
Prediction of 3-Dimensional Structure of Salivary Odorant-Binding Protein-2 of the Mosquito Culex Quinquefasciatus, the Vector of Human Lymphatic Filariasis
Effects of Misdiagnosis in Input Data on the Identification of Differential Expression Genes in Incipient Alzheimer Patients
Web-based visualisation of the transcriptional control network of Escherichia coli
waveTM: Wavelet-based transmembrane segment prediction
Efficient Shape Descriptors for Feature Extraction in 3D Protein Structures
Molecular modeling of insect ferritins
Translation of Both Complementary Strands Might Govern Early Evolution of the Genetic Code
In Silico Identification and Characterization of mRNA-Like Noncoding Transcripts in Medicago truncatula
Comparative analysis of the Arabidopsis and rice Expressed Sequence Tag (EST) sets
Preface: The Second Workshop on Ontology and Genome
ROSY - A Flexible and Universal Database and Bioinformatics Tool Platform for Roseobacter Related Species
Quantitative Petri net model of gene regulated metabolic networks in the cell
Mixture model analysis reflecting dynamics of the population diversity of 2009 pandemic H1N1 influenza virus
Expression of matrix metalloproteinase 9 (MMP-9/gelatinase B) in adenocarcinomas strongly correlated with expression of immune response genes
New assessment of a structural alphabet
A Machine Learning Based Method for the Prediction of Secretory Proteins Using Amino Acid Composition, Their Order and Similarity-Search
GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools
Ontologies for molecular biology and bioinformatics
In silico Comparison of Real-Time PCR Probes for Detection of Pathogens
Prediction of C α -H·O and C α -H·π Interactions in Proteins Using Recurrent Neural Network
MEGU: Pathway Mapping Web-Service Based on KEGG and SVG
NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression
Microsatellite Motifs with Moderate GC Content Are Clustered Around Genes on Arabidopsis thaliana Chromosome 2
In Silico Analysis of the Lateral Organ Junction (LOJ) Gene and Promoter of Arabidopsis Thaliana
Development of a Database and Ontology for Pathogenic Pathways in Periodontitis
A Calcium Dependent De-Adhesion Mechanism Regulates the Direction and Rate of Cell Migration: A Mathematical Model
How well does charge reparametrisation account for solvent screening in molecular mechanics calculations? The example of myosin
Amino-Acid Residue Association Models for Large Scale Protein-Protein Interaction Prediction
Identification and Characterization of Polyadenylation Signal (PAS) Variants in Human Genomic Sequences Based on Modified EST Clustering
GUIMACS - A Java Based Front End for GROMACS
In silico Identification of Putative Drug Targets from Different Metabolic Pathways of Aeromonas hydrophila
Folded RNA from an Intron of One Gene Might Inhibit Expression of a Counteracting Gene
The Use of Multiple Hierarchically Independent Gene Ontology Terms in Gene Function Prediction and Genome Annotation
Identification and analysis of a new family of bacterial serine proteinases
Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature
Where Do CABs Exist? Verification of a specific region containing concave Actin Bundles (CABs) in a 3-Dimensional confocal image
Analysis of Insertional Sites of the SIRE1 Retroelement Family from Glycine Max Using GenBank BAC-end Sequences
Protein Subcellular Localization Prediction Using a Hybrid of Similarity Search and Error-Correcting Output Code Techniques That Produces Interpretable Results
In Silico Discrimination of Single Nucleotide Polymorphisms and Pathological Mutations in Human Gene Promoter Regions by Means of Local DNA Sequence Context and Regularity
SEView: a Java applet for browsing molecular sequence data
Indexing anatomical concepts to OMIM Clinical Synopsis using UMLS Metathesaurus
Mathematical Modeling of Regulation of Type III Secretion System in Salmonella enterica Serovar Typhimurium by SirA
Towards a virtual C. elegans: A framework for simulation and visualization of the neuromuscular system in a 3D physical environment
Multiscale modeling of tumor response to vascular endothelial growth factor (VEGF) inhibitor
Systematic Analysis of Disease-Related Regulatory Mutation Classes Reveals Distinct Effects on Transcription Factor Binding
A Steady State Model for the Transcriptional Regulation of Filamentous Growth in Saccharomyces cerevisiae
A DNA motif lexicon: cataloguing, annotating sequences
Deriving an ontology for human gene expression sources from the CYTOMER? database on human organs and cell types
An in silico Analysis of Cytochrome c from Phanerochaete chrysosporium: Its Amino Acid Sequence and Characterization of Gene Structural Elements
PlasmoID: A P. falciparum Information Discovery Tool
A Combination of Evolutionary Trace Method, Molecular Surface Accessibility and Hydrophobicity Analysis to Design a High Hydrophobicity Laccase
DoD: Database of Databases - Updated Molecular Biology Databases
Elementary Mode Analysis to Study the Preculturing Effect on the Metabolic State of Lactobacillus rhamnosus During Growth on Mixed Substrates
Role of mRNA Gestation and Senescence in Noise Reduction during the Cell Cycle
miRNA-mRNA network detects hub mRNAs and cancer specific miRNAs in lung cancer
Dynamical modeling of pro- and anti-inflammatory cytokines in the early stage of septic shock
A life-like virtual cell membrane using discrete automata
Identification of Novel Genomic Islands Associated with Small RNAs
PredictBias: A Server for the Identification of Genomic and Pathogenicity Islands in Prokaryotes
Classification of Information Fusion Methods in Systems Biology
Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations
DNA Motifs and Sequence Periodicities
GASCO: Genetic Algorithm Simulation for Codon Optimization
Structure and Mechanism of a Transmission Blocking Vaccine Candidate Protein Pfs25 from P. falciparum: A Molecular Modeling and Docking Study
BLASTing proteomes, yielding phylogenies
Remote Homology Detection Using a Kernel Method that Combines Sequence and Secondary-Structure Similarity Scores
Prediction of protein polypeptide fragments exposed to the solvent
CMDWave: Conserved Motifs Detection Using Wavelets
Computer system "Gene Discovery" for promoter structure analysis
The Evolution of the Hh-Signaling Pathway Genes: A Computer-Assisted Study
COPid: Composition Based Protein Identification
Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction
Structural Analysis of Catalase from Two Musa Accessions, FHIA18 and Williams, and from Ravenala madagascariensis
Empowering Spot Detection in 2DE Images by Wavelet Denoising
Numerical Characterization of Protein Sequences and Application to Voltage-Gated Sodium Channel α Subunit Phylogeny
Coordinated evolution among hepatitis C virus genomic sites is coupled to host factors and resistance to interferon
On Multiple Regulatory Mechanisms in the Tryptophan Operon System in Escherichia coli: In silico Study of Perturbation Dynamics
In Silico Detection of Binding Mode of J-Superfamily Conotoxin pl14a with Kv1.6 Channel
DomainDraw: A Macromolecular Feature Drawing Program
A Comparison of Database Systems for XML-Type Data
Selecting SNPs for association studies based on population frequencies: a novel interactive tool and its application to polygenic diseases
Automated Molecular Library Generation of Proteic Fragments by Virtual Proteolysis for Molecular Modelling Studies
The Integr8 project - a resource for genomic and proteomic data
Challenges for the identification of biological systems from in vivo time series data
Cell Illustrator 4.0: A Computational Platform for Systems Biology
Bioinformatics service, education and research: the EMBnet and CBI
The GP problem: Quantifying gene-to-phenotype relationships
Integrating Pathway Data for Systems Pathology
Sequence-Structure-Function Relation Characterized in silico
Computational Identification of Three-Way Junctions in Folded RNAs: A Case Study in Arabidopsis
A hypergraph-based method for unification of existing protein structure- and sequence-families
Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2
Modelling speciation: Problems and implications
A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ
SPI - Structure predictability index for protein sequences
MOLS - A Program to Explore the Potential Energy Surface of a Peptide and Locate Its Low Energy Conformations
On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules
CorrXpression - Identification of Significant Groups of Genes and Experiments by Means of Correspondence Analysis and Ratio Analysis
Self-Alignments to Detect Mutually Exclusive Exon Usage
The Wave Phenomena in Smooth Muscle Syncytia
Comparative Analysis of Methodologies for the Detection of Horizontally Transferred Genes: A Reassessment of First-Order Markov Models
A Data Integration Approach to Predict Host-Pathogen Protein-Protein Interactions: Application to Recognize Protein Interactions between Human and a Malarial Parasite
Improving the Performance of an SVM-Based Method for Predicting Protein-Protein Interactions
PGV - Prokaryotic Genome Viewer
In Silico Identification and Characterization of a Putative Phosphatidylinositol 4-Phosphate 5-Kinase (PIP5K) Gene in Eimeria Tenella
Basic Faced α-Helices are Widespread in the Peptide Extensions of the Eukaryotic Aminoacyl-tRNA Synthetases
MMT - A pathway modeling tool for data from rapid sampling experiments
Interface of Apoptotic Protein Complexes Has Distinct Properties
2D Gels and bioinformatics - An eye at the future
Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts
Distinct Patterns in the Regulation and Evolution of Human Cancer Genes
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways
Muscle actin genes: A first step towards computational classification of tissue specific promoters
Prediction of Neurotoxins Based on Their Function and Source
Evolved Cellular Automata for Protein Secondary Structure Prediction Imitate the Determinants for Folding Observed in Nature
A search tool for identification and analysis of conserved sequence patterns in Saccharomyces spp. orthologous promoters
Quantitative modeling of biochemical networks
Correlation Finder
AGenDA: Gene prediction by comparative sequence analysis
HIV1 V3 Loop Hypermutability is Enhanced by the Guanine Usage Bias in the Part of env Gene Coding for it
Clustering Gene Expression Data Using Graph Separators
SMS: Sequence, Motif and Structure - A Database on the Structural Rigidity of Peptide Fragments in Non-Redundant Proteins
Essential Amino Acids for the Stability of Human Butyrylcholinesterase as Predicted by CUPSAT Server
Noise Reduction from Genotyping Microarrays Using Probe Level Information
PRIME: automatically extracted PRotein Interactions and Molecular Information databas
Identification of Transcriptional Regulators Using Binding Site Enrichment Analysis
MACO: A Gapped-Alignment Scoring Tool for Comparing Transcription Factor Binding Sites
GeneNet database: description and modeling of gene networks
Rapid detection of conserved regions in protein sequences using wavelets
A system architecture for genomic data analysis
An overview on predicting the subcellular location of a protein
Comparison of protein structures reveals monophyletic origin of AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation
Workshop on "Storage and Annotation of Reaction Kinetics Data", Villa Bosch in Heidelberg, May 21-23, 2007
Genome-wide prediction and analysis of function-specific transcription factor binding sites
Modelling the Molecular Interactions in the Flower Developmental Network of Arabidopsis thaliana
Cellular automata model for human articular chondrocytes migration, proliferation and cell death: An in vitro validation
In silicoAnalysis of Microsatellites in Organellar Genomes of Major Cereals for Understanding Their Phylogenetic Relationships
Two genetic algorithms for identification of regulatory signals
In Silico Analysis of Voltage-gated Sodium Channel in Relation to DDT Resistance in Vector Mosquitoes
Consensus based validation of membrane porins
AMIGOS: A Method for the Inspection of Genomic Organisation or Structure and its Application to Characterise Conserved Gene Arrangements
Constraint-Based Knowledge Discovery from SAGE Data
scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data
Identification of Candidate Genes at Quantitative Trait Loci on Chicken Chromosome Z Using Orthologous Comparison of Chicken, Mouse, and Human Genomes
Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA
Differential transcriptional regulation by alternatively designed mechanisms: A mathematical modeling approach
GEN-SNiP: An Online Tool to Find Polymorphisms in a Genome
Constructing biological pathway models with hybrid functional Petri net
The system architecture of the BioPath system
Role of Wet Experiment Design in Data Generation: From in Vivo to in Silico and Back
PRIMe: A Web Site That Assembles Tools for Metabolomics and Transcriptomics
In silico determination of potential antisense targets for human beta-globin variants
A database on alternative splice forms on the Integrated Genetic Map Service (IGMS)
Illuminator: Increasing Synergies Between Medicinal And Computational Chemists
Molecular modeling and docking analysis of Beta-lactamases with inhibitors: A comparative study
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures
Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis
Investigation of interaction between Pax5 isoforms and thioredoxin using de novo modelling methods
The application of abstract topology to RAS-related signal transduction pathways
GPAC: Benchmarking the Sensitivity of Genome Informatics Analysis to Genome Annotation Completeness
Analysis and Comparison of Benchmarks for Multiple Sequence Alignment
BRM-Parser: A Tool for Comprehensive Analysis of BLAST and RepeatMasker Results
An evolutionary classification of the metallo-beta-lactamase fold proteins
Petri Net Applications in Molecular Biology
Association of antigenic properties to structure of the hepatitis C virus NS3 protein
Thermo-search: lifestyle and thermostability analysis
A Pathway Finding System for the Cell Signaling Networks Database
SPLITS: A New Program for Predicting Split and Intron-Containing tRNA Genes at the Genome Level
Integrating data from biological experiments into metabolic networks with the DBE information system
Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing
Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topology
PREDICTOR: A Web-Based Tool for the Prediction of Atomic Structure from Sequence for Double Helical DNA with up to 150 Base Pairs
FASSM: Enhanced Function Association in Whole Genome Analysis Using Sequence and Structural Motifs
Frameshift Signals in Genes Associated with the Circular Code
Bioinformatic strategies for better understanding of immune function
POODLE-I: Disordered Region Prediction by Integrating POODLE Series and Structural Information Predictors Based on a Workflow Approach
Integration of CellDesigner and SABIO-RK
Conformational Dynamics and Thermal Stabilities of the αβ-Tubulin Dimer: A Molecular Dynamics Simulation Study
ExpertDiscovery and UGENE integrated system for intelligent analysis of regulatory regions of genes
Structural Considerations for Designing Adenosine Analogs as Selective Inhibitors of Trichomonas sp. Glyceraldehyde-3- Phosphate Dehydrogenase
GO for Integration of Expression Data
Positive Darwinian Selection on Crustacean Hyperglycemic Hormone (CHH) of the Green Shore Crab, Carcinus maenas
Evolutionary Origin of the Protozoan Parasites Histone-like Proteins (HU)
The channel in transporters is formed by residues that are rare in transmembrane helices
Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry
A novel genomics approach for the identification of drug targets in pathogens, with special reference to Pseudomonas aeruginosa
Correlation Between the Structural Stability and Aggregation Propensity of Proteins
YACOP: Enhanced gene prediction obtained by a combination of existing methods
STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes
Analyzing Stationary States of Gene Regulatory Network Using Petri Nets
A hybrid multiscale model for investigating tumor angiogenesis and its response to cell-based therapy
LyM: A Tool to Reach the Best Factor in Gene Expression Comparison
Hunting for Insect-Specific Protein Domains
Modeling of self-organized avascular tumor growth with cellular automata
Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases
BTXpred: Prediction of Bacterial Toxins
Impact of Delays and Noise on Dopamine Signal Transduction
Using amino acid patterns to accurately predict translation initiation sites
Computing TaqMan Probes for Multiplex PCR Detection of E. coli O157 Serotypes in Water
Cancer immunoediting: A game theoretical approach
A Database of Simple Sequence Repeats from Cereal and Legume Expressed Sequence Tags Mined in silico: Survey and Evaluation
Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response
First Exons and Introns - A Survey of GC Content and Gene Structure in the Human Genome
Sequence and Structural Analyses of Interleukin-8-Like Chemokine Superfamily
Analysis and Prediction of Helix Shift Errors in Homology Modeling
GeneInfoViz: Constructing and visualizing gene relation networks
Modeling cell population dynamics
The 3rd International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002) - Preface
Identification of Common Tumor Signatures Based on Gene Set Enrichment Analysis
PPD - Proteome Profile Database
A computational model of bidirectional axonal growth in micro-tissue engineered neuronal networks (micro-TENNs)
Enhanced Structure Prediction of Gene Products Containing Class III Adenylyl Cyclase Domains
Signal-Theoretical DNA Similarity Measure Revealing Unexpected Similarities of E. coli Promoters