yusuke1997/dblp-id-title huggingface dataset:
Inverse Design of Large Molecules using Linear Diophantine Equations
Prediction of Protein Function Using Protein-Protein Interaction Data
Volume Measurements in the Embryonic Zebrafish Heart using 4D Confocal Microscopy
An Adaptive Meta-Clustering Approach: Combining the Information from Different Clustering Results
Sequential Classification for Microarray and Clinical Data
Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis
Chemical Structure-Activity Relationship Visualization Using Structure Activity Maps
The SSAHA Trace Server
A Fast Shotgun Assembly Heuristic
Engineering a 1: 2 Bio-multiplexer for controlled stem cell differentiation
Haplotype Pattern Mining & Classification for detecting disease associated Site
Bacterial Whole Genome Phylogeny Using Proteome Comparison and Optimal Reversal Distance
Non-occurring and rare quads in PDB and translated introns from XPro with possible applications in nanostructure design
Fast and Accurate Probe Selection Algorithm for Large Genomes
Computational Inference of Regulatory Pathways in Microbes
Simultaneous Classification and Feature Clustering Using Discriminant Vector Quantization with Applications to Microarray Data Analysis
Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2005, Stanford, CA, USA, August 8-11, 2005
Experimental Studies of the Universal Chemical Key (UCK)Algorithm on the NCI Database of Chemical Compounds
Gene Ontology Friendly Biclustering of Expression Profiles
Alignment-Free Sequence Comparison with Vector Quantization and Hidden Markov Models
ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale
Efficient Sampling of Protein Folding Pathways using HMMSTR and Efficient Sampling of Protein Folding Pathways using HMMSTR and
Genome Annotation and Protein Structure
Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework
Embedded Computation of Maximum-Likelihood Phylogeny Inference Using Platform FPGA
Spaghetti Code, Soupy Logic, and the Expression of Genes
Gene Selection for Multi-Class Prediction of Microarray Data
Disease Gene Explorer: Display Disease Gene Dependency by Combining Bayesian Networks with Clustering
Using Easel for Modeling and Simulating the Interactions of Cells in Order to Better Understand the Basics of Biological Processes and to Predict Their Likely Behaviors
A Hierarchical Mixture of Markov Models for Finding Biologically Active Metabolic Paths Using Gene Expression and Protein Classes
Discriminative Discovery of Transcription Factor Binding Sites from Location Data
Simulated Pharmacogenomics Exercises for the Cybertory Virtual Molecular Biology Laboratory
Operon Prediction in Cyanobacteria using Comparative Genomics
Automated Protein NMR Resonance Assignments
A Symbolic Logic Strategy For Mapping Biological Concepts in the HERBE Prototype
A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data
Multiple Protein Structure Alignment by Deterministic Annealing
Inferring Genetic Networks from Microarray Data
Robust and Accurate Cancer Classification with Gene Expression Profiling
Computational prediction of DtxR regulon-A Dissection of physiological process controlled by DtxR in Corynebacterium species
Two operative concepts for the post-genomic era: the "me'moire vive" of the cell and a molecular algebra
Creating a Protein Ontology Resource
Consensus Methods Using Phylogenetic Databases
Gene Function, Metabolic Pathways and Comparative Genomics in Yeast
An Application of a Pathway Alignment Method to Comparative Analysis between Genome and Pathways
Discover True Association Rates in Multi-protein Complex Proteomics Data Sets
MassTRAQ: a Fully Automated Tool for iTRAQ-labeled Protein Quantification
A Finite Model Theory for Biological Hypotheses
Extracting Characteristic Patterns from Genome - Wide Expression Data by Non-Negative Matrix Factorization
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation - A Graph-Theoretic Approach
Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways
A New Method of Secondary Structure Assignment Based on the Delaunay Tessellation of Protein Structures
Using Enhancing Signals to Improve Specificity of ab initio Splice Site Sensors
Are We There Yet? Genomic Profiling and Mechanism in Cancer Research
Rule Clustering and Super-rule Generation for Transmembrane Segments Prediction
Cluster Utility: A New Metric for Clustering Biological Sequences
Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment
A Semantic Mediation Approach for Problems in Computational Molecular Biology
Computational Simulation of Lipid Bilayer Reorientation at Gaps
Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases
Application of a Genetic Algorithm/K-Nearest Neighbor Method to the Classification of Renal Cell Carcinoma
Large-Scale Testing of Chemical Shift Prediction Algorithms and Improved Machine Learning-Based Approaches to Shift Prediction
Motif Extraction and Protein Classification
Identifying Simple Discriminatory Gene Vectors with an Information Theory Approach
Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra
Iterative Rank based Methods for Clustering
Analysis of four different sets of predictive features for metalloproteins
HIV Protease Structural Database
Analysis of SNP-Expression Association Matrices
Eulerian Path Methods for Multiple Sequence Alignment
EcMLST: An Online Database for Multi Locus Sequence Typing of Pathogenic Escherichia coli
An Evolutionary Approach to Finding Schemas for 3-Class Protein Secondary Structure Prediction
Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating
A Theoretical Analysis of Gene Selection
Navigating through the Biological Maze
DASH: Localising Dynamic Programming for Order of Magnitude Faster, Accurate Sequence Alignment
Accelerating the Kernels of BLAST with an Efficient PIM (Processor-In-Memory) Architecture
Multivariate gene selection: Does it help
Autonomicity An Antidote for Complexity?
PSIST: Indexing Protein Structures Using Suffix Trees
Pathway Bioinformatics
Statistical Resynchronization and Detection of Periodic Transcripts
MedfoLink: Bridging the Gap between IT and the Medical Community
MinPD: Distance-Based Phylogenetic Analysis and Recombination Detection of Serially-Sampled HIV Quasispecies
Oscillatory dynamics in the mitogen-activated protein kinase cascade
High Performance Computational Biology - Past Progress and Future Promise
Accelerating Approximate Subsequence Search on Large Protein Sequence Databases
On Discriminating a TATA-box from putative TATA boxes: A Case Study Using Plant Genome
Towards Automatic Clustering of Protein Sequences
In-Silico Prediction of Surface Residue Clusters for Enzyme-Substrate Specificity
A Comparison of Particle Swarms Techniques for the Development of Quantitative Structure-Activity Relationship Models for Drug Design
Considerations in Making Microarray Cross-Platform Correlations
CUBIC: Identification of Regulatory Binding Sites Through Data Clustering
Automated Characterization of cellular migration phenomena
Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach
HIV Structural and Biothermodynamics Databases: a Resource for the Pharmaceutical and Biotechnology Industry
Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes
A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites
MageBuilder: A Schema Translation Tool for Generating MAGE-ML from Tabular Microarray Data
Contraction Graphs for Representation and Analysis of RNA Secondary Structure
A Block Coding Method that Leads to Significantly Lower Entropy Values for the Proteins and Coding Sections of Haemophilus influenzae
Agent-Oriented Approach to DNA Computing
Comparison of Two Schemes for Automatic Keyword Extraction from MEDLINE for Functional Gene Clustering
Adapting Support Vector Machines to Predict Translation Initiation Sites the Human Genome
A Parallel Algorithm for Clustering Protein-Protein Interaction Networks
Parallelizing a DNA Simulation Code for the Cray MTA-2
A Knowledge Base for Computational Pathway Reconstruction
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error
Meanshift Clustering for DNA Microarray Analysis
Head and Neck Cancer Metastasis Prediction via Artificial Neural Networks
A Novel Computational Framework for Structural Classification of Proteins Using Local Geometric Parameter Matching
Design of Genetic Switches with Only Positive Feedback Loops
Riptide: Fast Protein Identification from Mass Spectrometer Data
Computational identification and characterization of Type III secretion substrates
Noise Propagation in Transcriptional Cascades
A Bayesian Modeling Framework for Genetic Regulation
Multiple RNA Structure Alignment
Inference of Gene Regulatory Network Based on Module Network Model with Gene Functional Classifications
Consensus Genetic Maps: A Graph Theoretic Approach
Imputation of Missing Values in DNA Microarray Gene Expression Data
A New Approach to Clustering Biological Data Using Message Passing
P-quasi Complete Linkage Analysis for Gene-Expression Data
A Java Program to Create Simulated Microarray Images
The Center for Computational Biology
TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
A Security System for Personal Genome Information at DNA Level
A Self-Tuning Method for One-Chip SNP Identification
Automatic Construction of 3D Structural Motifs for Protein Function Prediction
An Index Structure for Pattern Similarity Searching in DNA Microarray Dat
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data
Pathway Mapping with Operon Information: An Integer-Programming Method
Artificial Neural Networks to Predict Daylily Hybrids
Decoding Noncoding Regulatory DNAs in Metazoan Genomes
State-Space Model for Gene Regulatory Networks with Time Delays
Multispectral Multidimensional Multiplexed Data: The More, the Merrier
Oncogenetics Tree Models - An Estimation
Statistical issues in the analysis of the array CGH data
A rule-based framework for gene regulation pathways discovery
PTC: An Interactive Tool for Phylogenetic Tree Construction
Molecular Evaluation using Comparative Molecular Interaction Profile Analysis system
Identifying Orthologs: Cycle Splitting on the Breakpoint Graph
K-means+ Method for Improving Gene Selection for Classification of Microarray Data
A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns
Multi-Knockout Genetic Network Analysis: The Rad6 Example
Minimal Marker Sets to Discriminate Among Seedlines
Profile-Based String Kernels for Remote Homology Detection and Motif Extraction
Genome on Demand: Interactive Substring Searching
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network
Complexity and Application of Pedigree Analysis Programme GTree
A Linear Programming Based Algorithm for Multiple Sequence Alignments
An Exhaustive Genome Assembly Algorithm Using K-Mers to Indirectly Perform N-Squared Comparisons in O(N)
Molecular Modeling of Full-Length OxyR from Shewanella oneidensis MR-1 and Molecular Dynamics Studies of the Activation Domain
Towards Interactive Exploration of Images, Meta-Data, and Analytic Results in the Open Microscopy Environment
Identification of Contaminants in Proteomics Mass Spectrometry Data
Locating All Tandem Repeat Families in a Sequence
BioSPRINT: Classification of Intron and Exon Sequences Using the SPRINT Algorithm
PROMOCO: a New Program for Prediction of cis Regulatory Elements: From High-Information Content Analysis to Clique Identification
Combinatorial method of splice sites prediction
Epitope Prediction Algorithms for Peptide based Vaccine Design
Accurate Prediction of Orthologous Gene Groups in Microbes
Automatic Recognition of Regions of Intrinsically Poor Multiple Alignment Using Machine Learning
A Prediction Model for the Drug Efficacy of Interferon in CHC Patients Based on SNPs
Key Features of the UCSC Genome Site
Segmental Duplications Containing Tandem Repeated Genes Encoding Putative Deubiquitinating Enzymes
Search for Evolution-Related-Oligonucleotides and Conservative Words in rRNA Sequences
PET Imaging of Tumor Integrin Expression
Reconstructing Phylogenetic Networks Using Maximum Parsimony
The GeneCardsTM Family of Databases: GeneCards, GeneLoc, GeneNote and GeneAnnot
Large-scale Drug Function Prediction by Integrating QIS D2 and BioSpice
Suffix Trees (and Relatives) Come of Age in Bioinformatics
Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes
LOGOS: a modular Bayesian model for de novo motif detection
Clustering Gene Expression Data using Continuous Markov Models
Selection of Putative Cis-Regulatory Motifs through Regional and Global Conservation
Lossless Compression of DNA Microarray Images
PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences
Estimating Recombination Rate Distribution by Optimal Quantization
Fourier Harmonic Approach for Visualizing Temporal Patterns of Gene Expression Data
Compressed Pattern Matching in DNA Sequences
Boosted PRIM with Application to Searching for Oncogenic Pathway of Lung Cancer
SMASHing regulatory sites in DNA by human
Towards Index-based Similarity Search for Protein Structure Databases
RNA Motif Search Using the Structure to String (STR 2 ) Method
Local Minima-Based Exploration for Off-Lattice Protein Folding
Gene Selection for Cancer Classification Using Bootstrapped Genetic Algorithms and Support Vector Machines
An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes
Exploring Genomic Context Patterns for Rhodobacter Sphaeroides in the HERBE Knowledge Discovery Environment
An Algebraic Geometry Approach to Protein Structure Determination from NMR Data
Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system
A Personalized and Automated dbSNP Surveillance System
An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings
MiCA: Web-Based Computational Tools for the Analysis of Microbial Community Structure and Compisition Based on T-RFLP of 16S rRNA Gene
Unravelling the murine osteoblast differentiation pathway by network structure analysis using time-series microarray data
Representing and reasoning about signal networks: an illustration using NF\kappaB dependent signaling pathways
Nonlinear Modeling on Protein Kinase C(PKC)-Epsilon Inverse Regulation of Stress Fibers in Oncogenically Transformed Cells
Semantic Similarity-based Validation of Human Protein-Protein Interactions
Designing Oscillators in Synthetic Gene Networks Based on Multi-Scale Dynamics
Assigning Gene Ontology Categories (GO) to Yeast Genes Using Text-Based Supervised Learning Methods
ANTICLUSTAL: Multiple Sequence Alignment by Antipole Clustering and Linear Approximate 1-Median Computation
Finding Higher Order Motifs under the Levenshtein Measure
Designing Synthetic Biological Systems by Multiple Time Scale Networks
Identification of Post-Translational Modifications via Blind Search of Mass-Spectra
Shannon Information in Complete Genomes
A Pattern Matching Algorithm for Codon Optimization and CpG Motif-Engineering in DNA Expression Vectors
A Computational Approach to Reconstructing Gene Regulatory Networks
CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Feature
cWINNOWER Algorithm for Finding Fuzzy DNA Motifs
A Method for Tight Clustering: with Application to Microarray
Initial Large-scale Exploration of Protein-protein Interactions in Human Brain
Computing for the DOE Genomes to Life Program
Automatic Protein Function Annotation through Candidate Ortholog Clusters from Incomplete Genomes
Fast and Sensitive Alignment of Large Genomic Sequences
Dynamical Robustness in Gene Regulatory Networks
Recognition of Exon/Intron Boundaries Using Dynamic Ensembles
2nd IEEE Computer Society Bioinformatics Conference, CSB 2003, Stanford, CA, USA, August 11-14, 2003
A Probabilistic Model for Identifying Protein Names and their Name Boundaries
Reconstruction of Ancient Operons From Complete Microbial Genome Sequences
Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons
A Graph Analysis Method to Detect Metabolic Sub-Networks Based on Phylogenetic Profile
Probabilistic Consistency Analysis for Gene Selection
An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings
Incremental and Decremental Least Squares Support Vector Machine and Its Application to Drug Design
Evidence for Growth of Microbial Genomes by Short Segmental Duplications
Noise-Attenuation in Artificial Genetic Networks
Biclustering in Gene Expression Data by Tendency
Biclustering Gene-Feature Matrices for Statistically Significant Dense Patterns
A General Methodology for Integration of Microarray Data
Bacillus Subtilis Protein Interaction Network Analysis
Predicting functional gene-links from phylogenetic-statistical analyses of whole genomes
An Intelligent Digital Library System for Biologists
A New Approach for Gene Annotation Using Unambiguous Sequence Joining
The National Alliance for Medical Imaging Computing (NA-MIC)
Patterns of Gene Deletion following Genome Duplication in Yeast
Protein Structure Prediction Using Physical-Based Global Optimization and Knowledge-Guided Fragment Packing
A Topological Measurement for Weighted Protein Interaction Network
Identifying Local Gene Expression Patterns in Biomolecular Networks
TPR Packing Analysis and 3D Modeling for the HAT Domain of Human Crooked Neck Protein
Two-way clustering of gene expression profiles by sparse matrix factorization
Statistical Inference for Well-ordered Structures in Nucleotide Sequences
Genetic Algorithm Approach for the Closest String Problem
A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST
Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs
EST-Based Analysis of Gene Expression in the Human Cochea
A New Clustering Strategy with Stochastic Merging and Removing Based on Kernel Functions
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees
Weighting Features to Recognize 3D Patterns of Electron Density in X-Ray Protein Crystallography
GeneTide: Terra Incognita Discovery Endeavor Mining ESTs and Expression Data to Elucidate Known and De-Novo GeneCards Genes
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment
CoMRI: A Compressed Multi-Resolution Index Structure for Sequence Similarity Queries
A Novel Approach for Prediction of Multi-Labeled Protein Subcellular Localization for Prokaryotic Bacteria
A New Method for Predicting RNA Secondary Structure
Clustering Genes Using Gene Expression and Text Literature Data
Parallel Monte Carlo Methods for Physical Mapping of Chromosones
Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation
Gene Teams with Relaxed Proximity Constraint
Subspace Clustering for Microarray Data Analysis: Multiple Criteria and Significance Assessment
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity
Sequential Diagonal Linear Discriminant Analysis (SeqDLDA) for Microarray Classification and Gene Identification
Development of a Knowledge-Based Multi-Scheme Cancer Microarray Data Analysis System
A Polynomial Algorithm for the Minimum Quartet Inconsistency Problem with O(n) Quartet Errors
EGOMinor: A Genomics and Proteomics Data Computation and Interpretation System for Biomedical Applications
Comparative Genomics of Cyclin-Dependent Kinases Suggest Co-Evolution of the RNAP II C-Terminal Domain and CTD-Directed CDKs
Application of Singular Value Decomposition and Functional Clustering to Analyzing Gene Expression Profiles of Renal Cell Carcinoma
Learning Yeast Gene Functions from Heterogeneous Sources of Data Using Hybrid Weighted Bayesian Networks
On Gene Prediction by Cross-Species Comparative Sequence Analysis
Maximum Sequence Alignment Fails to Predict Off-targeted Gene Regulation by RNAi
MISAE: A New Approach for Regulatory Motif Extraction
Structure Elucidation and Visualization of Reconstructed 3D Maps of Macromolecular Complexes
Promoter Recognition for E. coli DNA Segments by Independent Component Analysis
An SVM-based Algorithm for Identification of Photosynthesis-specific Genome Features
The Role of Algorithmic Research in Computational Genomics
Current Challenges in Bioimage Database Design
Predicting Continuous Epitopes in Proteins
Environment-based Development of Reactive Systems
Refinement in Object-Oriented Specification Languages
Implementing Promoted Operations in Z
Proving Total Correctness with Respect to a Fair (Shared-State) Parallel Language
Machine Code Programs are Predicates Too
A Model of the Refinement Process
Using Metavariables in Natural Deduction Proofs
Testing and Safety Analysis of AM (Abstract Machine) Specifications
Deriving language recognition algorithms: A case study in combining program specialisation and data refinement
Laws of Parallel Programming with Shared Variables
A Window Inference Tool for Refinement
A Note on Compositional Refinement
6th Refinement Workshop, Proceedings of the 6th Refinement Workshop, organised by BCS-FACS, London, UK, 5-7 January 1994
Software Reification using the SETS Calculus
Program Refinement by Theorem Prover
BCS FACS Refinement Workshop 2002, Refine 2002, Satellite Event of FLoC 2002, Copenhagen, Denmark, July 20-21, 2002
A Recursion Removal Theorem
Refinement and Confidentiality
Classification of Refinements in VDM
5th Refinement Workshop, Proceedings of the 5th Refinement Workshop, organised by BCS-FACS, London, 8-10 January 1992
A Tactic Driven Refinement Tool
Constructive Refinement of First Order Specifications
A case study in formally developing state-based parallel programs - the Dutch National Torus
Revisiting Abstraction Functions For Reasoning About Concurrency
Proceedings of the REFINE 2005 Workshop, REFINE 2005, Guildford, UK, April 2005
Metavariables and Conditional Refinements in the Refinement Calculus
Proceedings of the BCS-FACS Refinement Workshop, REFINE@IFM 2007, Oxford, UK, July 2007
Demonstrating the Compliance of Ada Programs with Z Specifications
Using Refinement to Understand Architectural Connection
Concurrent Processes as Objects
Formal Development of Authentication Protocols
Methods and Tools for the Verification of Critical Properties
Proceedings of the 14th BCS-FACS Refinement Workshop, REFINE@FMWeek 2009, Eindhoven, The Netherlands, November 2009
Improving the Process of System Specification and Refinement in B
Proceedings of the 11th Refinement Workshop, Refine@ICFEM 2006, Macao, October 31, 2006
Proceedings of the 13th BAC-FACS Refinement Workshop, Refine@FM 2008, Turku, Finland, May 27, 2008
Formal Semantics for Ward & Mellor's Transformation Schemas
Operation Semantics with Read and Write Frames
Proof Obligations for Real-Time Refinement
Co-Refinement
Formalising Dijkstra's Development Strategy within Stark's Formalism
Applied Soft Computing Technologies: The Challenge of Complexity, Proceedings of the 9th Online World Conference on Soft Computing in Industrial Applications (WSC9), September 20th - October 8th, 2004, held on the World Wide Web
Closed Loop Control for Common Rail Diesel Engines based on Rate of Heat Release
Research of Mapped Least Squares SVM Optimal Configuration
Optimization of Co-rotating Twin-Screw Extruders Using Pareto Local Search
Fuzzy C-Means Based Stop Line and Crosswalk Placement at Right Turn Vehicle Exclusive Lane
Classification of Pressure Drop Devices of Proto Type Fast Breeder Reactor through Seven Layered Feed Forward Neural Network