yusuke1997/dblp-id-title huggingface dataset:
A Dataset Generator for Whole Genome Shotgun Sequencing
Advanced Query Mechanisms for Biological Databases
Automatic Derivation of Substructures Yields Novel Structural Building Blocks in Globular Proteins
ANOLEA: A WWW Server to Assess Protein Structures
Identification of CDNA Sequences by Specific Oligonucleotide Sets - A Computer Tool and Application
Nearest Neighbor Classification in 3D Protein Databases
A geometric approach for the alignment of liquid chromatography - mass spectrometry data
Genome-Scale DNA Sequence Recognition by Hybridization to Short Oligomers
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree
MultiMap: An Expert System for Automated Genetic Linkage Mapping
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins
Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, Glasgow, UK, July 31-August 4, 2004
Grammatical Formalization of Metabolic Processes
Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics
Filtering erroneous protein annotation
The effectiveness of position- and composition-specific gap costs for protein similarity searches
Talisman - rapid application development for the grid
An Efficient Method for Multiple Sequence Alignment
Assigning Function to CDS Through Qualified Query Answering: Beyond Alignment and Motifs
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo
Efficient Attractor Analysis Based on Self-Dependent Subsets of Elements An Application to Signal Transduction Studies
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences
Protein Structure Prediction: Selecting Salient Features from Large Candidate Pools
Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data
Characterizing Oriented Protein Structural Sites Using Biochemical Properties
Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model
Identifying splits with clear separation: a new class discovery method for gene expression data
A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion
Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images
Dynamite: A Flexible Code Generating Language for Dynamic Programming Methods Used in Sequence Comparison
Flow Cytometry Data Analysis: Comparing Large Multivariate Data Sets Using Classification Trees
A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations
The iRMSD: a local measure of sequence alignment accuracy using structural information
Combinatorial influence of environmental parameters on transcription factor activity
Splice site identification by idlBNs
GEST: a gene expression search tool based on a novel Bayesian similarity metric
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins
A Map of the Protein Space: An Automatic Hierarchical Classification of all Protein Sequences
Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models
Protein Secondary-Structure Modeling with Probabilistic Networks
ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences
A Phylogenetic Approach to RNA Structure Prediction
An algorithm for finding signals of unknown length in DNA sequences
The Prediction of the Degree of Exposure to Solvent of Amino Acid Residues Via Genetic Programming
Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements
Using genome-context data to identify specific types of functional associations in pathway/genome databases
Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data
Robust classification modeling on microarray data using misclassification penalized posterior
Analysis of Gene Expression Data with Pathway Scores
A New Approach to Primer Selection in Polymerase Chain Reaction Experiments
Interpreting anonymous DNA samples from mass disasters - probabilistic forensic inference using genetic markers
Application of Genetic Search in Derivation of Matrix Models of Peptide Binding to MHC Molecules
Kinetics analysis methods for approximate folding landscapes
DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations
Fidelity Probes for DNA Arrays
Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System
Constructing Near-Perfect Phylogenies with multiple homoplasy events
Crystallographic Threading
Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins
Quantification of transcription factor expression from Arabidopsis images
Prediction of DNA-binding residues from sequence
IMGT/LIGM-DB: A Systematized Approach for ImMunoGeneTics Database Coherence and Data Distribution Improvement
Automatic Quality Assessment of Peptide Tandem Mass Spectra
Robust inference of groups in gene expression time-courses using mixtures of HMMs
Protein structure prediction via combinatorial assembly of sub-structural units
Automated Clustering and Assembly of Large EST Collections
ISMB 2003 - Editorial
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
A Small Automaton for Word Recognition in DNA Sequences
Finding an Average Core Structure: Application to the Globins
Parallel Sequence Alignment in Limited Space
Discovering regulatory and signalling circuits in molecular interaction networks
Comparison of Two Variations of Neural Network Approaches to the Prediction of Protein Folding Pattern
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics@ISMB 2005, Detroit, MI, USA June 24, 2005
SCOPEC: a database of protein catalytic domains
Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes
RASE: recognition of alternatively spliced exons in C.elegans
Identification of Human Gene Structure Using Linear Discriminant Functions and Dynamic Programming
IntEx: A Syntactic Role Driven Protein-Protein Interaction Extractor for Bio-Medical Text
New approaches for reconstructing phylogenies from gene order data
A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk
Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens
Increasing Consensus Accuracy in DNA Fragment Assemblies by Incorporating Fluorescent Trace Representations
Computational Applications of DNA Structural Scales
Modeling Antibody Side Chain Conformations Using Heuristic Database Search
Seamless Integration of Biological Applications within a Database Framework
Tracking repeats using significance and transitivity
Create and assess protein networks through molecular characteristics of individual proteins
Reconstructing sibling relationships in wild populations
Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins
A probabilistic approach to protein backbone tracing in electron density maps
Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology
A variance-stabilizing transformation for gene-expression microarray data
MACHOS: Markov clusters of homologous subsequences
A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins
The Context-Dependence of Amino Acid Properties
Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome Analysis
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies
Integrating high dimensional bi-directional parsing models for gene mention tagging
Estimating true evolutionary distances under the DCJ model
Of truth and pathways: chasing bits of information through myriads of articles
Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes
Combining multiple microarray studies and modeling interstudy variation
Predicting protein function from protein/protein interaction data: a probabilistic approach
BLASTing small molecules - statistics and extreme statistics of chemical similarity scores
Reconstruction of highly heterogeneous gene-content evolution across the three domains of life
Softening Constraints in Constraint-Based Protein Topology Prediction
Inferring quantitative models of regulatory networks from expression data
Aligning Genomes with Inversions and Swaps
Choosing where to look next in a mutation sequence space: Active Learning of informative p53 cancer rescue mutants
Fragment assembly with double-barreled data
Gene recognition based on DAG shortest paths
Designing better phages
The Gene-Finder Computer Tools for Analysis of Human and Model Organisms Genome Sequences
Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution
Improving the Quality of Automatic DNA Sequence Assembly Using Fluorescent Trace-Data Classifications
Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature
The Gene Ontology Categorizer
Prototyping a Genetics Deductive Database
springScape : visualisation of microarray and contextual bioinformatic data using spring embedding and an "information landscape"
Neural Networks for Molecular Sequence Classification
SENEX: A CLOS/CLIM Application for Molecular Pathology
A Motion Planning Approach to Flexible Ligand Binding
A Fast Heuristic Algorithm for a Probe Mapping Problem
Assigning probes into a small number of pools separable by electrophoresis
Feature selection for DNA methylation based cancer classification
Accelerating Protein Classification Using Suffix Trees
The Megaprior Heuristic for Discovering Protein Sequence Patterns
Polyploids, genome halving and phylogeny
Learning MHC I - peptide binding
Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup
Solving Large Scale Phylogenetic Problems using DCM2
Identification of metabolic units induced by environmental signals
Disambiguating proteins, genes, and RNA in text: a machine learning approach
Pair hidden Markov models on tree structures
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
A Chado case study: an ontology-based modular schema for representing genome-associated biological information
Compact Encoding Strategies for DNA Sequence Similarity Search
Towards an Intelligent System for the Automatic Assignment of Domains in Globular Proteins
Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data
Beyond the clause: extraction of phosphorylation information from medline abstracts
PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank)
Predicting the in vivo signature of human gene regulatory sequence
Fast identification and statistical evaluation of segmental homologies in comparative maps
Functional inference from non-random distributions of conserved predicted transcription factor binding sites
The LabFlow System for Workflow Management in Large Scale Biology Research Laboratories
Chain functions and scoring functions in genetic networks
Representations of Metabolic Knowledge: Pathways
SEALS: A System for Easy Analysis of Lots of Sequences
A top-level ontology of functions and its application in the Open Biomedical Ontologies
A Divide and Conquer Approach to Multiple Alignment
Discovering Sequence Similarity by the Algorithmic Significance Method
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
Mining viral protease data to extract cleavage knowledge
A Specification for Defining and Annotating Regions of Macromolecular Structures
Exploring Williams-Beuren syndrome using my Grid
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
Predicting Protein Folding Classes without Overly Relying on Homology
Efficient inference of bacterial strain trees from genome-scale multilocus data
Domain Identification by Clustering Sequence Alignments
A probabilistic method to detect regulatory modules
Sequence Database Search Using Jumping Alignments
Genomic Fold Assignment and Rational Modeling of Proteins of Biological Interest
De novo identification of repeat families in large genomes
Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains
Protein Structure Prediction System Based on Artificial Neural Networks
Finding disease specific alterations in the co-expression of genes
A Constraint-Based Assignment System for Automating Long Side Chain Assignments in Protein 2D NMR Spectra
Homology search for genes
Genomics via Optical Mapping III: Contiging Genomic DNA
Robust Parametric and Semi-Parametric Spot Fitting for Spot Array Images
RNA Modeling Using Gibbs Sampling and Stochastic Context Free Grammars
MotifCut: regulatory motifs finding with maximum density subgraphs
Weakly Supervised Learning Methods for Improving the Quality of Gene Name Normalization Data
Supervised enzyme network inference from the integration of genomic data and chemical information
Data Mining for Regulatory Elements in Yeast Genome
Differential variability analysis of gene expression and its application to human diseases
Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study
Deriving phylogenetic trees from the similarity analysis of metabolic pathways
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors
Search for folding nuclei in native protein structures
Finding the evidence for protein-protein interactions from PubMed abstracts
Into the heart of darkness: large-scale clustering of human non-coding DNA
Optimally Parsing a Sequence into Different Classes Based on Multiple Types of Evidence
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, August 14-17, 1994, Stanford University, Stanford, California, USA
DNA Sequence Assembly and Genetic Algorithms - New Results and Puzzling Insights
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
Modelling regulatory pathways in E. coli from time series expression profiles
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
Statistically based postprocessing of phylogenetic analysis by clustering
A Statistical Theory of Sequence Alignment with Gaps
Dense subgraph computation via stochastic search: application to detect transcriptional modules
Selecting anti-HIV therapies based on a variety of genomic and clinical factors
Comparative footprinting of DNA-binding proteins
Identity by Descent Genome Segmentation Based on Single Nucleotide Polymorphism Distributions
Learning to extract relations for protein annotation
Rapid Assessment of Extremal Statistics for Gapped Local Alignment
Automatic detection of subsystem/pathway variants in genome analysis
Object-Oriented Knowledge Bases for the Analysis of Prokaryotic and Eukaryotic Genomes
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data
Selecting biomedical data sources according to user preferences
A Knowledge Base for D. melanogaster Gene Interactions Involved in Pattern Formation
IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs
ANOSVA: a statistical method for detecting splice variation from expression data
Efficiently detecting polymorphisms during the fragment assembly process
Multi-Body Interactions within the Graph of Protein Structure
YeastHub: a semantic web use case for integrating data in the life sciences domain
Maximum Entropy Weighting of Aligned Sequences of Proteins or DNA
Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions
ExonHunter: a comprehensive approach to gene finding
Computational expansion of genetic networks
Predicting genetic regulatory response using classification
Automatic Construction of Knowledge Base from Biological Papers
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification
Evaluating functional network inference using simulations of complex biological systems
TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources
Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization
Automated interpretation of MS/MS spectra of oligosaccharides
GeneLoc: exon-based integration of human genome maps
Non-symmetric score matrices and the detection of homologous transmembrane proteins
ISMB 2006
DNA sequence and structure: direct and indirect recognition in protein-DNA binding
Good Maps Are Straight
Indel seeds for homology search
Knowledge-Based Generation of Machine-Learning Experiments: Learning with DNA Crystallography Data
How old is your fold?
Improved prediction of the number of residue contacts in proteins by recurrent neural networks
Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars
Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer
Contact replacement for NMR resonance assignment
Multiple Alignment Using Hidden Markov Models
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, August 3-7, 2002, Edmonton, Alberta, Canada
A two-stage classifier for identification of protein-protein interface residues
The ontology of biological taxa
An integrative approach for causal gene identification and gene regulatory pathway inference
Rich probabilistic models for gene expression
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, St. Louis, MO, USA, June 12-15 1996
A computational framework to empower probabilistic protein design
Identification of Localized and Distributed Bottlenecks in Metabolic Pathways
Representation for Discovery of Protein Motifs
Combining NLP and probabilistic categorisation for document and term selection for Swiss-Prot medical annotation
Extraction of Substructures of Proteins Essential to their Biological Functions by a Data Mining Technique
Probabilistic approaches to the use of higher order clone relationships in physical map assembly
Centralization: a new method for the normalization of gene expression data
Minimizing Complexity in Cellular Automata Models of Self-Replication
Glocal alignment: finding rearrangements during alignment
Induction of Rules for Biological Macromolecular Crystallization
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm
A statistical method for alignment-free comparison of regulatory sequences
Describing Multiple Levels of Abstraction in the Metabolism
Inferring differentiation pathways from gene expression
Efficient identification of DNA hybridization partners in a sequence database
The EXACT description of biomedical protocols
ISMB/ECCB 2004
Discovering statistically significant biclusters in gene expression data
The Ribosome Scanning Model for Translation Initiation: Implications for Gene Prediction and Full-Length cDNA Detection
Neweyes: A System for Comparing Biological Sequences Using the Running Karp-Rabin Greedy String-Tiling Algorithm
Computation and Visualization of Degenerate Repeats in Complete Genomes
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Viewing Genome Data as Objects for Application Development
Negation of protein-protein interactions: analysis and extraction
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, August 19-23, 2000, La Jolla / San Diego, CA, USA
Reconstructing tumor amplisomes
STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, Bethesda, MD, USA, July 1993
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany
ISMB 2005
Probabilistic divergence measures for detecting interspecies recombination
Classification of arrayCGH data using fused SVM
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles
Integrative Analysis of Protein Interaction Data
Algorithm for backrub motions in protein design
Modeling recurrent DNA copy number alterations in array CGH data
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks
A nucleotide substitution model with nearest-neighbour interactions
Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model
Protein Fold Class Prediction: New Methods of Statistical Classification
Identification of new drug classification terms in textual resources
A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser
Detection and validation of single gene inversions
Pattern Discovery in Gene Regulation: Designing an Analysis Environment
Two Methods for Improving Performance of a HMM and their Application for Gene Finding
Cooperative Computer System For Genome Sequence Analysis
Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods
An Optimized Parsing Algorithm Well Suited to RNA Folding
TEXTAL: A Pattern Recognition System for Interpreting Electron Density Maps
Database Search Based on Bayesian Alignment
CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts
A Service-Oriented Information Sources Database for the Biological Sciences
Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis
ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
An equilibrium partitioning model connecting gene expression and cis -motif content
Toward Multi-Strategy Parallel & Distributed Learning in Sequence Analysis
Solvent Accessible Surface Representation in a Database System for Protein Docking
Regulatory Element Detection Using a Probabilistic Segmentation Model
Integrating genomic homology into gene structure prediction
Partial Cox regression analysis for high-dimensional microarray gene expression data
On counting position weight matrix matches in a sequence, with application to discriminative motif finding
Modelling sequential protein folding under kinetic control
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
Predicting Enzyme Function from Sequence: A Systematic Appraisal
Reconstructing the Duplication History of a Tandem Repeat
Protein Family Classification Using Sparse Markov Transducers
Peptide sequence tag-based blind identification of post-translational modifications with point process model
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli