yusuke1997/dblp-id-title huggingface dataset:
Novel Techniques for Visualizing Biological Information
GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data
TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks
A Computational System for Modeling Flexible Protein-Protein and protein-DNA Docking
A Grammar-Based Unification of Several Alignment and Folding Algorithms
Adding Semantics to Genome Databases: Towards an Ontology for Molecular Biology
SNP Function Portal: a web database for exploring the function implication of SNP alleles
Subclass Approach for Mutational Spectrum Analysis
Efficient multiple genome alignment
Gene Recognition in Cyanobacterium Genomic Sequence Data Using the Hidden Markov Model
Using hidden Markov models to analyze gene expression time course data
Reversal distance for partially ordered genomes
Locomotif: from graphical motif description to RNA motif search
Metrics and Similarity Measures for Hidden Markov Models
Experimental design for three-color and four-color gene expression microarrays
An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
Semi-supervised LC/MS alignment for differential proteomics
Predicting Location and Structure Of beta-Sheet Regions Using Stochastic Tree Grammars
A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation
Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures
Co-clustering of biological networks and gene expression data
Reconstruction of Metabolic Networks Using Incomplete Information
Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment
From Electron Density and Sequence to Structure: Integrating Protein Image Analysis and Threading for Structure Determination
Identifying Chimerism in Proteins Using Hidden Markov Models of Codon Usage
Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library
A motif-based framework for recognizing sequence families
Adaptive String Similarity Metrics for Biomedical Reference Resolution
Quantitative, Scalable Discrete-Event Simulation of Metabolic Pathways
Integrating copy number polymorphisms into array CGH analysis using a robust HMM
An Intelligent System for Comparing Protein Structures
An efficient algorithm for detecting frequent subgraphs in biological networks
Modeling Protein Homopolymeric Repeats: Possible Polyglutamine Structural Motifs for Huntington's Disease
Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity
Mining coherent dense subgraphs across massive biological networks for functional discovery
Kernel methods for predicting protein-protein interactions
TOPITS: Threading One-Dimensional Predictions Into Three-Dimensional Structures
Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature
Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis
Intelligent DNA-Based Molecular Diagnostics Using Linked Genetic Markers
Integrating structured biological data by Kernel Maximum Mean Discrepancy
Pharmaceutical Target Discovery Using Guilt-by-Association: Schizophrenia and Parkinson's Disease Genes
Designing succinct structural alphabets
A physical model for tiling array analysis
Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions
Detection of Correlations in tRNA Sequences with Structural Implications
Remote homology detection: a motif based approach
Accessing bioscience images from abstract sentences
Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS-PROT + TREMBL
Prediction of Primate Splice Junction Gene Sequences with a Cooperative Knowledge Acquisition System
Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data
Genetic Map Construction with Constraints
Multi-way clustering of microarray data using probabilistic sparse matrix factorization
Promoter prediction in the human genome
Stochastic modeling of RNA pseudoknotted structures: a grammatical approach
PALM - A Pattern Language for Molecular Biology
Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions
Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities
DNA Sequence Analysis Using Hierarchical ART-based Classification Network
A procedure for assessing GO annotation consistency
Optimal robust non-unique probe selection using Integer Linear Programming
Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints
Towards the use of argumentation in bioinformatics: a gene expression case study
Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
Automatic genome-wide reconstruction of phylogenetic gene trees
A Restriction Mapping Engine Using Constraint Logic Programming
Summary of the BioLINK Special Interest Group Session on the Future of Scientific Publishing
Classifying Nucleic Acid Sub-Sequences as Introns or Exons Using Genetic Programming
FLASH: A Fast Look-Up Algorithm for String Homology
Identifying cycling genes by combining sequence homology and expression data
A model-based approach for mining membrane protein crystallization trials
Evolution of a Computer Program for Classifying Protein Segments as Transmembrane Domains Using Genetic Programming
Striped sheets and protein contact prediction
Self-Organizing Neural Maps of the Coding Sequences of G-protein-coupled Receptors Reveal Local Domains Associated with Potentially Functional Determinants in the Proteins
Multiple alignment by aligning alignments
Identification of Protein Motifs Using Conserved Amino Acid Properties and Partitioning Techniques
Computational modeling of Caenorhabditis elegans vulval induction
Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences
Analysis of Gene Expression Microarrays for Phenotype Classification
A Modular Learning Environment for Protein Modeling
Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles
Incorporating Global Information into Secondary Structure Prediction with Hidden Markov Models of Protein Folds
Alignment and classification of time series gene expression in clinical studies
Predicting bacterial transcription units using sequence and expression data
A Machine Learning Approach to Acronym Generation
Design of an Object-Oriented Database for Reverse Genetics
Data integration and visualization system for enabling conceptual biology
Protein Model Representation and Construction
Evaluating machine learning approaches for aiding probe selection for gene-expression arrays
Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier
Detecting recombination with MCMC
Using guide trees to construct multiple-sequence evolutionary HMMs
Search for a New Description of Protein Topology and Local Structure
Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis
A Top-Down Approach to Whole Genome Visualization
A graph-based approach to systematically reconstruct human transcriptional regulatory modules
Multiple genome rearrangement: a general approach via the evolutionary genome graph
Protein Design by Optimization of a Sequence-Structure Quality Function
Creating a Knowledge Base of Biological Research Papers
Designing fast converging phylogenetic methods
Beta-Sheet Prediction Using Inter-Strand Residue Pairs and Refinement with Hopfield Neural Network
Identification of functional modules from conserved ancestral protein-protein interactions
Constituting a Receptor-Ligand Information Base from Quality-Enriched Data
Computing the P-value of the information content from an alignment of multiple sequences
Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing
Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping
Discovering Side-Chain Correlations In alpha-Helices
Connecting quantitative regulatory-network models to the genome
An experimental metagenome data management and analysis system
GeneQuiz: A Workbench for Sequence Analysis
Bayesian Protein Family Classifier
Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis
Efficient parameter estimation for RNA secondary structure prediction
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
Code Generation through Annotation of Macromolecular Structure Data
Fully automated ab initio protein structure prediction using I-STES, HMMSTR and ROSETTA
Inductive Logic Programming Used to Discover Topological Constraints in Protein Structures
An Expert System for Processing Sequence Homology Data
Corpus Design for Biomedical Natural Language Processing
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling
Protein Sequencing Experiment Planning Using Analogy
HyBrow: a prototype system for computer-aided hypothesis evaluation
ISMB/ECCB 2007 Organization
Systematic discovery of functional modules and context-specific functional annotation of human genome
Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005
The metric space of proteins-comparative study of clustering algorithms
Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models
Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences
Gene selection via the BAHSIC family of algorithms
A Constraint Reasoning System for Automating Sequence-Specific Resonance Assignments from Multidimensional Protein NMR Spectra
Finding novel genes in bacterial communities isolated from the environment
A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops
Inference of Molecular Phylogenetic Tree Based on Minimum Model-Based Complexity Method
Marginalized kernels for biological sequences
Protein function prediction via graph kernels
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy
HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae
Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
High-throughput inference of protein-protein interfaces from unassigned NMR data
Translation initiation site prediction on a genomic scale: beauty in simplicity
Application of a new probabilistic model for recognizing complex patterns in glycans
Multiple Structural Alignment and Core Detection by Geometric Hashing
A Surface Measure for Probabilistic Structural Computations
Recognising Promoter Sequences Using An Artificial Immune System
Mining frequent patterns in protein structures: a study of protease families
Assigning transmembrane segments to helices in intermediate-resolution structures
A Partial Digest Approach to Restriction Site Mapping
A tree kernel to analyse phylogenetic profiles
Bayesian gene/species tree reconciliation and orthology analysis using MCMC
Efficient approximations for learning phylogenetic HMM models from data
ISMB/ECCB 2004 Organization
Using Temporal Reasoning for Genome Map Assembly
Tag SNP selection in genotype data for maximizing SNP prediction accuracy
Using dynamic programming to create isotopic distribution maps from mass spectra
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
High-recall protein entity recognition using a dictionary
Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming
Applications of GeneMark in Multispecies Environments
Distance based algorithms for small biomolecule classification and structural similarity search
Gene Prediction by Pattern Recognition and Homology Search
A computational approach toward label-free protein quantification using predicted peptide detectability
The POPPs: clustering and searching using peptide probability profiles
An HMM posterior decoder for sequence feature prediction that includes homology information
ISMB 2002
Relative contributions of structural designability and functional diversity in molecular evolution of duplicates
A tool to assist the study of specific features at protein binding sites
Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks
A CORBA Server for the Radiation Hybrid Database
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data
Molecular classification of multiple tumor types
A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors
Ontological Foundations for Biology Knowledge Models
Integrating Order and Distance Relationships from Heterogeneous Maps
Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood
Protein network inference from multiple genomic data: a supervised approach
In search of lost introns
Selecting Optimal Oligonucleotide Primers for Multiplex PCR
Detection of IUPAC and IUPAC-like chemical names
Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation
Inferring Functional Pathways from Multi-Perturbation Data
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
Compression of Strings with Approximate Repeats
Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, July 21-25, 2001, Copenhagen, Denmark
VQLM: A Visual Query Language for Macromolecular Structural Databases
Separating real motifs from their artifacts
Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences
Spectrum : joint bayesian inference of population structure and recombination events
UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences
Probabilistic Structure Calculations: A Three-Dimensional tRNA Structure from Sequence Correlation Data
Extracting synonymous gene and protein terms from biological literature
Representations of Metabolic Knowledge
Symbolic Generation and Clustering of RNA 3-D Motifs
Prediction of the coupling specificity of G protein coupled receptors to their G proteins
Building Dictionaries of 1D and 3D Motifs by Mining the Unaligned 1D Sequences of 17 Archaeal and Bacterial Genomes
Clustering short time series gene expression data
Protein complex identification by supervised graph local clustering
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Position-Specific Annotation of Protein Function Based on Multiple Homologs
Analysis of Ribosomal RNA Sequences by Combinatorial Clustering
Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28 - July 1, 1998
BaCelLo: a balanced subcellular localization predictor
Detecting coevolving amino acid sites using Bayesian mutational mapping
Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem
Rapid knot detection and application to protein structure prediction
A Distance-Based Block Searching Algorithm
Inferring sub-cellular localization through automated lexical analysis
Sequence Comparisons via Algorithmic Mutual Information
Methods for optimizing antiviral combination therapies
Mining MEDLINE for implicit links between dietary substances and diseases
The Prediction of Human Exons By Oligonucleotide Composition and Disriminant Analysis of Spliceable Open Reading Frames
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
Nested effects models for high-dimensional phenotyping screens
Calculating the Exact Probability of Language-Like Patterns in Biomolecular Sequences
Optimized design and assessment of whole genome tiling arrays
Prediction of the Number of Residue Contacts in Proteins
Bayesian Adaptive Alignment and Inference
Finding composite regulatory patterns in DNA sequences
Conservative extraction of over-represented extensible motifs
Linear Modeling of Genetic Networks from Experimental Data
A Knowledge-Based Method for Protein Structure Refinement and Prediction
ISMB 2001
Information theory applied to the sparse gene ontology annotation network to predict novel gene function
Genomic characterization of perturbation sensitivity
Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP
Functional annotation of regulatory pathways
MedTag: A Collection of Biomedical Annotations
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences
Inference of Order in Genetic Systems
The Value of Prior Knowledge in Discovering Motifs with MEME
Statistics of local multiple alignments
Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes
A Statistical Method for Finding Transcription Factor Binding Sites
Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms
Predicting protein thermostability changes from sequence upon multiple mutations
Inferring subnetworks from perturbed expression profiles
High Speed Pattern Matching in Genetic Data Base with Reconfigurable Hardware
Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations
Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains
MASS: multiple structural alignment by secondary structures
Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design
Inferring protein-DNA dependencies using motif alignments and mutual information
Bistable switching and excitable behaviour in the activation of Src at mitosis
Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design
Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity
Beyond tandem repeats: complex pattern structures and distant regions of similarity
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis
Learning kernels from biological networks by maximizing entropy
Knowledge Discovery of Multilevel Protein Motifs
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species
Nucleotide variation of regulatory motifs may lead to distinct expression patterns
Integrating image data into biomedical text categorization
Inferring Gene Structures in Genomic Sequences Using Pattern Recognition and Expressed Sequence Tags
Detecting protein sequence conservation via metric embeddings
Segmentation and Interpretation of 3D Protein Images
Continuous hidden process model for time series expression experiments
SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
Hierarchical Minimization with Distance and Angle Constraints
Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns
Protein Topology Prediction through Parallel Constraint Logic Programming
SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database
In silico identification of functional regions in proteins
Spatio-Temporal Registration of the Expression Patterns of Drosophila Segmentation Genes
A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data
The cell graphs of cancer
Gene structure-based splice variant deconvolution using a microarry platform
CONTRAfold: RNA secondary structure prediction without physics-based models
PseudoViewer: automatic visualization of RNA pseudoknots
Context-specific independence mixture modeling for positional weight matrices
Constraint Satisfaction Techniques for Modeling Large Complexes: Application to the Central Domain of 16S Ribosomal RNA
Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families
Classification and feature selection algorithms for multi-class CGH data
Biases induced by pooling samples in microarray experiments
Annotating proteins by mining protein interaction networks
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries
Comparative genomics reveals unusually long motifs in mammalian genomes
Predicting protein-protein interaction by searching evolutionary tree automorphism space
Neural Net Representations of Empirical Protein Potentials
Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites
A neural-network-based method for predicting protein stability changes upon single point mutations
Graph-Theoretic Approach to RNA Modeling Using Comparative Data
Segment-Based Scores for Pairwise and Multiple Sequence Alignments
An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequence
Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006
High density linkage disequilibrium mapping using models of haplotype block variation
The Induction of Rules for Predicting Chemical Carcinogenesis in Rodents
Protein Secondary Structure Prediction Using Two-Level Case-Based Reasoning
Dead-End Elimination with Backbone Flexibility
Using the Fisher Kernel Method to Detect Remote Protein Homologies
A Multi-Level Description Scheme of Protein Conformation
Manual curation is not sufficient for annotation of genomic databases
Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone
ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins
Annotating gene function by combining expression data with a modular gene network
The multiple gene duplication problem revisited
Petri Net Representations in Metabolic Pathways
Identification of Human Gene Functional Regions Based on Oligonucleotide Composition
Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008
Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold
Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes
MMDB: An ASN.1 Specification for Macromolecular Structure
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
APIC : A Generic Interface for Sequencing Projects
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets
Design of a compartmentalized shotgun assembler for the human genome
A Flexible Approach to Genome Map Assembly
Kinematic Manipulation of Molecular Chains Subject to Rigid Constraint
Alignment of Flexible Protein Structures
Computationally Efficient Cluster Representation in Molecular Sequence Megaclassification
Modeling Transcription Factor Binding Sites with Gibbs Sampling and Minimum Description Length Encoding