yusuke1997/dblp-id-title huggingface dataset:
Integrating Heterogeneous Datasets in Genomic Mapping: Radiation Hybrids, YACs, Genes and STS Markers over the Entire Human Chromosome X
On the limits of computational functional genomics for bacterial lifestyle prediction
RNALfoldz: Efficient Prediction of Thermodynamically Stable, Local Secondary Structures
KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences
From Composite Patters to Pathways - Prediction of Key Regulators of Gene Expression
Genetic Algorithm for Selection of Oligonucleotides for Identification by Hybridisation of Genomic DNA Fragments Possessing Gene Potential
Combining diverse evidence for gene recognition in completely sequenced bacterial genomes
Similarity Search in 3D Protein Databases
Detecting relationships between amino acid residue sequences and 3D protein structures based on a new class of rotamer libraries
Genome Analysis in Barley: Consttuction of EST Databases
Conformational preferences of SH2 domains in free and ligand-bound states studied by molecular dynamics simulations
QVADIS - a Package to Compute Proton Transfer Pathways in Proteins
Sequence Periodicities in Complete Genomes Reflect Supercoiling
Simulating the Interplay of Structure, Kinetics, and Dynarnics in Complex Biochemical Networks
Automatic clustering of large sequence databases
Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotation
Theatre: A Novel Tool For The Comparative Investigation and Display of Evolutionary Diversity of Functional and Structural Features in DNA Sequences
Invited Talk: Pushing Details into Interaction Networks
A promoter model based on different combinations of binding sites
Specific LTR Model Detected Transcriptionally Active Match in Sequence Database
Model Reduction Approaches for Biochemical Reaction Systems
Towards accurate transcription start site prediction: a modelling approach
Comparative Analysis of the Secondary Structure of mRNA Encoded by High- and Low-Expression Eukaryotic Genes
Overexpression of Yeast Fructose-l, 6-Bisphosphatase in Escherichia Coli : A Comprehensive Model of the Anaerobic Glucose Metabolism
3D modeling of macromolecular structures and reactions in the context of genomes
Redundancy in the yeast genome: Paralogous gene sets and chromosome organization
Mining Combinations of Structural Motif from SSU 16 S Ribosomal RNA Secondary Structures
ModeScore: A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles
A Statistical Analysis of the success of exon prediction algorithms on the Arabidopsis genome
Integrative Analysis of Transcriptome and Metabolome Data
Perspectives on analysis and annotation of bacterial, archeal, and eukaryotic genomes
A Genetic Algorithm for Multiple Sequence Alignment
W2H: a WWW Interface to Applications in Bioinformatics
Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localizations
Fast and efficient computation of domain-domaininteractions from known protein structures in the PDB
Modeling of Gene Regulatory Network of Cell Cycle Control. Role of E2F Feedback Loops
An individual cell-based model of the growth regulation of epithelial cell-populations in-vitro
What can bioinformatics contribute to explain the origin of life?
Pathway Analysis of Bacillus subtillis Metabolic Network Based on Genomic Information
A Simulation Model for In-Vitro Cell Growth under Treatment
Modeling of Branching Plant Forms and Simulation of their Development using L-Systems
Structural Constraints and Neutrality in RNA
Docking experiences, AutoDock - a Case Study
Three Variations on Word Counting
Abstract Resource Language and an Example for its Application in Molecular Biology
Understanding the classification of tumors with a support-vector-machine: A case-based explanation scheme
Modeling of the Human Lipoprotein Metabolism - metabolic fluxes and genetic variations involved in exchange and transfer processes
Zinc Finger and zinc binding motifs in the yeast genome
Density functional study of guanine quartet structures
Automatic classification of Loop-Structures in Proteins by an Unsupervised Neural Network
Integration and Visualisation of Multimodal Biological Data
Using residue propensities and tightness of fit to improve rigid-body protein-docking
Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments
SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world
German Conference on Bioinformatics 2013, GCB 2013, Göttingen, Germany, September 10-13, 2013
Kohonen maps are suitable for a biologically meaningful classification of transcription factor binding site matrices
The predictive Power of short strucfural motifs for Protein stability engineering
Towards a New Curation Environment for the TrEMBL Database
Fractual Patters formed during Diffusion controlled Growth of Bacterial Colonies
Essential Motions in Lipases and their Relationship to the Biological Function
The Identification of Locally Ordered Features an Completely unaligned Genomic Sequences by using an Unsupervised Neural Classifier
Forecasting Blood Glucose Concentrations from the Time Course of Counterregulatory Hormones Using a Neural Network Approach
Carbohydrates: -Second-Class Citizens in Biomedicine and Bioinformatics?
Predicting transcription factor binding sites by constructing context specific matrices
Protein family analysis at the domain-level
EST Clustering at GENIUSnet, the German EMBnet node
Characterization of The Compact Model Genome of The Japanese Puffer Fish (Fugu rubripes) Using A Cosmid Sequence Scanning Approach
Extended Sunflower Hidden Markov Models for the recognition of homotypic cis-regulatory modules}
Neutral Evolutionary Dynamics
Kernel Method for Estimation of Functional Site Local Consensi: Classification of Transcription Initiation Sites in Eukaryotic Genes
Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database
Algorithmic approach to quantifying the hydrophobic force contribution in protein folding
A Conceptual Object Model of Gene Mutation Data
A structural approach to the analysis of metabolic networks illustrated with erythrocyte metabolism
glycosciences.de: An Internet Portal for Glyco-related Data from Open Access Resources
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs
Data and knowlage based experimental design for bioprocess optimization
Reliability of Microarray Data and Clustering
GENIO/scan - EST Guided Identification of Genes in Human Genomic DNA
FRANz: Fast Reconstruction of Wild Pedigrees
RigFit: a new approach to superimposing ligand molecules
Modelling the Organization of Flower Morphogenesis by Transcription Factor Networks Using Lindenmayer Systems
Modeling the Architecture of Regulatory Networks
Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation
[Invited Lecture] Fold Recognition: Techniques, Applications, and Pitfalls
Detectability of Sequence Homology by DNA Hybridization
Automated Hypothesis Formation of Molecular Structures and Interactions using Physics-based Modeling and Simulation
Invited Talk: Docking Protein Domains Using a Contact Map Representation
Computing Elementary Flux Modes in Genome-scale Metabolic Networks
Shape-based Barrier Estimation for RNAs
Bioinformatics, German Conference on Bioinformatics, Leipzig, Germany, September 30 - October 2, 1996, Selected Papers
Unrestrained molecular dynamics simulation of the FMN-RNA Aptamer complex
Invited Talk: Information Flux Through Proteins
CUDA-based Multi-core Implementation of MDS-based Bioinformatics Algorithms
IntEnz - The Enzyme Database in Oracle
Microarray Layout as Quadratic Assignment Problem
Genome annotation with PSI-BLAST: Benchmark and application
Modelling interacting cell systems in biology and medicine with cellular automata
Mutual Information Analysis of Surrogate Gene Expression Data
Using constraint programming for lattice protein folding
Irreversible Metabolic Transitions in Bistable Dynamic Systems: The Fructose 6-Phosphat/Fructose 1, 6-Bisphosphate Cycle in Liver
Associative Data Base of Biomolecuiar Sequences
On the estimation of metabolic profiles in metagenomics
Biomathematical and in vitro analysis of destabilized regions in the interferon gene cluster
A structural motif of three disulfide bridges and three beta strands in peptides
Expected Gene Order Distances and Model Selection in Bacteria
New Developments in the Linking of Biological Databases and Computer-Generation of Annotation
Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs
Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics
CYTOMER® : A database on gene expression sources
Improvement of sequence-structure alignment quality by an empirical energy function
Predicting miRNA targets utilizing an Extended Profile HMM
Reconstruction of metabolic and regulatory networks of Klebsiella pneumoniae from genome data
Knowledge-Based Loop Prediction
Genome duplication and the evolution of gene Order and chromosome number in yeast
Computational approaches to identify Leucine Zippers
Studies on the evolution of short-chain and medium-chain dehydrogenases/reductases
Drug Design Using an Iterative Computer Aided Process
Adequacy of Evolutionary Models with Correlations and Rate Heterogeneity
PALMA: Perfect Alignments using Large Margin Algorithms
Comparative Generalized Logic Modeling Reveals Differential Gene Interactions during Cell Cycle Exit in Drosophila Wing Development
From sequence to function: a quantitative model of lipase enantioselectivity
The IMB Jena Image Library of Biological Macromolecules - New Features
Blockclust: efficient clustering and classification of non-coding rnas from short Read RNA-seq profiles
Interactive and dynamic web-based visual exploration of high dimensional bioimages with real time clustering
Proceedings of the German Conference on Bioinformatics (GCB 2000), Heidelberg, October 5-7, 2000
Biolmage, the database of biological microscopy data
A Propagation-based Algorithm for Inferring Gene-Disease Assocations
A Tool for Automatic Genome Annotation
Exploiting scale-free information from expression data for cancer classification
Self-taught Learning for Classification of Mass Spectrometry Data: A Case Study of Colorectal Cancer
Proceedings of the German Conference on Bioinformatics, GCB 1999, October 4-6, 1999, Hannover, Germany
Aspects of the Mechanism of Glucose Oxidase
Cytomer: A database on gene expression sources
Approximate Bayesian Discrimination between Alternative DNA Mosaic Structures
Computer Modeling of Organ Numbers in Plants
Interactive Biochemical Pathways
GENIO/frame - Frame Shift Analysis and Sequencing Error Detection of Eukaryotic CDS
[Invited Lecture] Structural motifs in the interior and on the surfaces of protein monomers and at protein-protein interfaces
GeneWays: A System for Mining Text and for Integrating Data on Molecular Pathways
Data Mining and Visualisation in Molecular Biology Databases
Invited Talk: Landscapes in RNA folding and evolution
Highly Immersive Molecular Modeling (HIMM): An Architecture for the Integration of Molecular Modeling and Virtual Reality
Annotation-based Distance Measures for Patient Subgroup Discovery in Clinical Microarray Studies
Conserved secondary structures in hepatitis B virus DNA
Molecular modelling and macromolecular visualisation with WHAT IF
A Dynamic Model of Spatial Cell Arrangement in Proliferative Epithelia using Locally Controlled Tesselation
E2F composite units in promoters of cell cycle genes
A CORBA server for the Radiation Hybrid Database
Finding transcription factor binding site combinations in the yeast genome
EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation
Invited Talk: Encoding Evolvability: The Hierarchical Language of Polyketide Synthase Protein Interactions
Non-linear conversion between genetic and physical chromosomal distances
The Semantic Metadatabase (SEMEDA): Ontology Based Integration of Federated Molecular Biological Data Sources
Exploiting gene interaction information from microarray expression data for cancer classification
Expression Profiles of Metabolic Models to Predict Compartmentation of Enzymes in Multicompartmental Systems
A Look at the Visual Modeling of Plants Using L-Systems
An efficient potential for protein sequence design
A New Tool for the in Silico Prediction of Matrix Attachment Regions in Large Genomic Sequences
Classifying Permanent and Transient Protein Interactions
TRANSPATH - a database on signal transduction networks
Converting DNA to Music: ComposAlign
Independent components analysis of starch deficient pgm mutants
Explaining gene responses by linear modeling
Looking at functional genomics from inside the Drosophila blastoderm
A Novel, Comprehensive Method to Detect and Predict Proteinprotein Interactions Applied to the Study of Vesicular Trafficking
Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region
Uncovering the Structure of Heterogenous Biological Data: Fuzzy Graph Partitioning in the k-partite Setting
Engineering Support Vector Machine Kerneis That Recognize Translation Initialion Sites
Integrating Heterogeneous Datasets in Genomic Mapping: Radiation Hybrids, YACS, Genes and STS Markers over the Entire Human Chromosom X
Combinatorial identification of promoters induced upon immune cell activation
DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignment
Repeat-aware Comparative Genome Assembly
An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases
Fast Retrieval of DNA and Protein Sequences
Computer Data Fitting in the Equilibrium Protein Folding Process Involving Multiple Intermediates
[Invited Lecture] The Evolution of Information storage and heredity
Time-Efficient Flexible Superposition of Medium-Sized Molecules and Molecular Fragments
Generation of 3D templates of active sites of proteins with rigid prosthetic groups
Quantitative microarray spot profile optimization: A systematic evaluation of buffer/slide combinations
Reconstructing Consensus Bayesian Network Structures with Application to Learning Molecular Interaction Networks
New Developments in Linking of Biological Databases and Computer-Generation of Annotations: SWISS-PROT and Its Computer-Annotated Supplement TREMBL
BRENDA, Enzyme Data for Metabolic pathways
Detecting Sporadic Recombination in DNA Alignments with Hidden Markov Models
Invited Talk: Macromolecular Simulations Using Continuum Solvent Models
IMGT/Collier de Perles, a LIGM-DB tool for Immunoglobulin and T-Cell Receptor 2D representations
Methods for Predicting Target Sites of Transcription Factors
Property Codes in Sets of Protein Sequences
Peptide Binding Landscapes
Predicting gene regulatory elements from their expression data in the complete yeast genome
Recognition of multiple patterns in unaligned sets of sequences. Comparison of kernel clustering method with other methods
Custom Megabase Sequencing of a Small Eucaryotic Genome in Germany
Transcription regulation regions revealed by Signal detection and fuzzy clusterfng
Building and Documenting Workflows with Python-Based Snakemake
Identifying Hot Cancer and Novel Novel Cell-cycle Genes from Literature
A procedure for superposition of two arbitrary atomic arrangements
Improving Fold Recognition of Protein Threading by Experimental Distance Constraints
Hydroxynitrile lyase from Hevea brasiliensis . Molecular characterization and mechanism of enzyme catalysis
A Possible Origin of Power-Law Behavior in n -Tuple Zipf Analysis
Molecular Computing: From Conformational Pattern Recognition to Complex Processing Networks
Proteome Analysis: Application of InterPro and CluSTr for the Functional Classification of Proteins in Whole Genomes
An Algorithm for the Prediction of Proteasomal Cleavages
Challenges of Functional Genomic Data for Database Systems
A Context-Free Grammar of the DNA Functional Sites, based an Symmetrical Structures in the Genetic Text
Structure Motif Discovery and Mining the PDB
Visualization and analysis of gene expression data using freeware and GPL-Software
Classification of all putative permeases and other membrane multispanners of the Major Facilitator Superfamily encoded by the complete genome of Saccharomyces cerevisiae
Context-free method of pattern recognition in the genetic texts
The German EMBnet Node: GENIUSnet
Learning Pathway-based Decision Rules to Classify Microarray Cancer Samples
A Structural Perspective on Genome Evolution(Invited Talk)
A Program for the Construction of a Promoter Model From a Set of Upstream Sequences of Coregulated Genes
Flexible database-assisted graphical representation of metabolic networks for model comparison and the display of experimental data
Comparison of Centralities for Biological Networks
F-Workbench: a database-driven environment for the analysis of transcription factors
Evolutionary Grammars: A Granunatical Model for Genome Evolution
A hierarchy of databases for modeling gene regulatory mechanisms
[Invited Lecture] Genome sequence analysis and profile hidden Markov models
The German EMBNET node GENIUSnet
Efficient Similarity Retrieval of Protein Binding Sites based on Histogram Comparison
Phylogeny reconstruction from hydrophobicity profiles of Proteins: An Information-theoretic approach
Confidence Measures for Fold Recognition
Some Extensions of Schmidt's Partition Method for Sequence Comparison based an Binary Character Amino Acid Properties
Treatment of multifunctional enzymesin metabolic pathway analysis
E-CELL Project: Towards Whole Cell Simulation
Genome-wide Analysis of Functions Regulated by Sets of Transcription Factors
Bacterial Annotation Tools
BioPath Visualization of Biochemical Pathways
A general approach for discriminative de novo motif discovery from high-throughput data
Cutting/Recombination Systems as Generating Devices
Mining Putative Regulatory Elements in Gene Promoter Regions
Integrating public databases into an existing protein visualization and modeling program - BRAGI
Ensembl: Annotating metazoan genomes
Protein structure comparison based o n profiles of topological motifs: a feasible way to deal with information from negative examples
From DNA Recombination to DNA Computing, Via Formal Languages
The EMBL Nucleotide Sequence Database at the European Bioinformatics Institute (EBI): Sequence Similarity Searching & Database query/retrieval
BRENDA a resource for Enzyme data and metabolic pathway information
C-H...X Hydrogen Bonds in RNA Structures
Active analog modelling of novel siderophores
Identifying MicroRNAs and their Targets
W2H: WWW Interface to GCG/HUSAR
IXDB, an integrated database for genomic data of the Human X Chromosome
IMGT: Tools for the management, the annotation, the analysis and the display of immunogenetics data
Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD)
The Transpath Signal Transduction Database
Graph-Kernels for the Comparative Analysis of Protein Active Sites
TRRD and COMPEL Databases on Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences
Gene expression analysis on biochemical networks with the potts spin model
Water-Mediated Uracil-Cytosine Base Pairs in RNA - A Computational Study
Independent component analysis of gene expression data
Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, Germany, October 5-7, 2005
Glycosylation of Proteins: A Computer-Based Method for Rapid Exploration of Conformational Space of N-Glycans
FluxAnalyzer: A Graphical User Interface for Analyzing Structural Properties and Fluxes in Balanced Metabolic Networks
Utilizing Promoter Pair Orientations for HMM-based Analysis of ChIP-chip Data
Finding Characteristic Substructures for Metabolite Classes
A natural taxonomy of gene families from complete genomes
About the Validation of Homology Models: A Case Study on Factor D, a Serine Protease in the Human Complement System
The Third Ributtal of the Random Breakage Theory
What's new in the library? What's new in GenBank? Let PubCrawler tell you!
Quantitative Comparison of Genomic-Wide Protein Domain Distributions
Proceedings of the German Conference on Bioinformatics, GCB 1996, Leipzig, Germany, September 30 - October 2, 1996
Prediction of Protein Thermostability
Familz specific rates of protein evolution
From greedy to branch & bound and back: Assessing optimization strategies for incremental construction molecular docking tools
Functional Analysis of the Mammalian Genome by Large Scale Gene Trap Mutagenesis
Phylogeny meets sequence search
Towards an Objeet-Oriented Framework for the Modeling of Bacterial Metabolism
Recent Advances in Molecular Distance Geometry
Molecular Systematics in Three Dimensions
WWWTRRD: Hypertext Information System an Transcription Regulation
Yeast Genome Sequence Data on Display
German conference on bioinformatics 2014, September 28 - October 1, 2014, Bielefeld, Germany
ResqMi - a Versatile Algorithm and Software for Resequencing Microarrays
Simple Folding Model for HP Lattice Proteins
Docking of bile acids to [gamma][gamma]alcohol dehydrogenase
Molecular Graph Reaction Networks
Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores
Sites of Superhelical DNA Duplex Destabilization occour at Specific Regulatory Regions
Towards detection of sequence orthologs
A database framework for mapping expression patterns
Investigation of Complex Developmental and Phylogenetic Process using Computer Modeling Approaches
Gene Expression, Gene Clusters, and Genomic Regionality in Rates of Evolution
The Performance of Transversion Based Distance Estimates
MMT - A Metabolic Modeling Tool for Metabolic Engineering
Bioinformatics and Cheminformatics in the Drug Discovery Cycle
Proceedings of the German Conference on Bioinformatics, GCB 2007, September 26-28, 2007, Potsdam, Germany
Finding Transcription Factor Binding Sites in Coregulated Genes by Exhaustive Sequence Search
Computer science and biology: Proceedings of the German Conference on Bioinformatics, GCB 2001, October 7-10, 2001, Braunschweig, Germany
Bulge Induced Kinks in DNA Molecules - Validation of Experimental Results by Molecular Modeling Techniques
Fast Stochastic Simulation of Metabolic Networks
Polyglutamine and Polyalanine Tracts Are Enriched in Transcription Factors of Plants
Impact of integrating clinical and genetic information
Visualization and Analysis of the Complete Yeast Genome
Building Organelle Genome Databases using an Object-Oriented Approach
Whole genome camparisons: gene duplication and consenration in systematically sequenced organisms
Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation
On the Benefits of Multimodal Optimization for Metablic Network Modeling
Design of multi-stable nucleid acid sequences
Invited Talk: A large-scale application of comparative genomics for biodefense
Invited Talk: Genomic Variation and Incipient Speciation in Arabidopsis thaliana
Exploring the Enzyme Neighbourhood to Interpret Gene Expression Data
A Question Based Navigator for Exercising Distributed Bioinformatics Tasks
Statistics of large scale sequence searching
A Theoretical Model of Genome Redundancy
Gene Hunting without Sequencing Genomis Clones: the "Twenty Questions" game with genes
HOBACGEN: A database of homologous genes in bacteria
Implementing the Boyer-Moore Algorithm
Pattern discovery methods for protein topology diagrams
Efficient Implementation of Empirical Force Fields for Genetic Algorithm Molecular Structure Optimization
Small Molecules as Rotamers: Generation and Docking in RosettaLigand
Beyond Intra-Base-pair Hydrogen Bonds in DNA Structures: A Comprehensive Analysis
Proceedings of the German Conference on Bioinformatics, GCB 1998, University of Cologne, Germany, October 1998
A pipeline for insertion sequence detection and study for bacterial genome
GeneGenerator- a flexible algorfthm for gene prediction
Finding Relevant Biotransformation Routes in Weighted Metabolic Networks
Relative rates of evolutionary changes in ORF1 proteins of nonviral retroelements: groups of phylogenetical relationship
Supervised Posteriors for DNA-motif Classification