yusuke1997/dblp-id-title huggingface dataset:
Hierarchical Organization of Molecular Structure Computations
On Differential Variability of Expression Ratios: Improving Statistical Inference about Gene Expression Changes from Microarray Data
Detection of Structural Variants Involving Repetitive Regions in the Reference Genome
OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method
Manifold Learning in Protein Interactomes
MMG4: Recognition of G4-Forming Sequences Based on Markov Model
Identification of New Members of a Carbohydrate Kinase-Encoding Gene Family
Relative Stability of Wild-Type and Mutant p53 Core Domain: A Molecular Dynamic Study
Combinatorics of RNA Secondary Structures with Base Triples
Efficient Constructions of Disjunct Matrices with Applications to DNA Library Screening
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks
Ancestral Inference from Samples of DNA Sequences with Recombination
Rosalind Franklin Society Proudly Announces the 2023 Award Recipient for Journal of Computational Biology
Efficient Colored de Bruijn Graph for Indexing Reads
SGFNNs: Signed Graph Filtering-based Neural Networks for Predicting Drug-Drug Interactions
MCAT: Motif Combining and Association Tool
Comparison of Analytic Methods for Quantitative Real-Time Polymerase Chain Reaction Data
Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes
On the Complexity of Sorting by Reversals and Transpositions Problems
MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data
CAGE: Combinatorial Analysis of Gene-Cluster Evolution
An Up-Down Bit Pattern Approach to Coregulated and Negative-Coregulated Gene Clustering of Microarray Data
Homology Detection Using Multilayer Maximum Clustering Coefficient
Probabilistic Logic Methods and Some Applications to Biology and Medicine
Selection Probability for Rare Variant Association Studies
Las Vegas Algorithms for Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment
ImagePlane: An Automated Image Analysis Pipeline for High-Throughput Screens Using the Planarian Schmidtea mediterranea
Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion
A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data
Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes
DeepVir: Graphical Deep Matrix Factorization for In Silico Antiviral Repositioning - Application to COVID-19
A Topology-Based Score for Pathway Enrichment
Local Immunodeficiency: Combining Cross-Immunoreactivity Networks
Molecular Markers and Diagnostic Model Specific for Barrett's Esophagus
Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges
PopInf: An Approach for Reproducibly Visualizing and Assigning Population Affiliation in Genomic Samples of Uncertain Origin
Aligning Families of Two-Dimensional Gels by a Combined Multiresolution Forward-Inverse Transformation Approach
Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between Two Genomes with Duplicate Genes
Special Section: 12th International Computational Advances in Bio and Medical Sciences (ICCABS 2023)
Double Cut and Join with Insertions and Deletions
Identification of Candidate Genes for Skeletal Muscle Injury Prevention in Two Different Types
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils
Stochastic Simulation of Notch Signaling Reveals Novel Factors That Mediate the Differentiation of Neural Stem Cells
Word Sense Disambiguation in the Biomedical Domain: An Overview
Integrating Low-Order and High-Order Correlation Information for Identifying Phage Virion Proteins
Algorithms for Selecting Informative Marker Panels for Population Assignment
A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models
Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences
Iterative Stepwise Discriminant Analysis: A Meta-Algorithm for Detecting Quantitative Sequence Motifs
An Approach to Parallel Algorithms for Long DNA Sequences Alignment on Manycore Architecture
A Discriminative Model for Identifying Spatial cis-Regulatory Modules
Linear Regression Models for Solvent Accessibility Prediction in Proteins
Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction
Combination Approaches Improve Predictive Performance of Diagnostic Rules for Mass-Spectrometry Proteomic Data
MetReS, an Efficient Database for Genomic Applications
Comparing the Performance of Three Computational Methods for Estimating the Effective Reproduction Number
Semi-Supervised Cell Detection with Reliable Pseudo-Labels
A Highly Accurate Model for Screening Prostate Cancer Using Propensity Index Panel of Ten Genes
Integrated Analysis of DNA Copy Number Changes and Gene Expression Identifies Key Genes in Gastric Cancer
Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination
Building a Pan-Genome Reference for a Population
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020)
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure
Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor-DNA Interactions with Expression Data: An Entropy-Based Approach
Protein-specific Scoring Method for Ligand Discovery
Score Functions for Determining Regional Conservation in Two-Species Local Alignments
Integrative Bioinformatics Analysis Identifies NEK2 as a Potential Biomarker in Head and Neck Squamous Cell Carcinoma
A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies
An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations
An Efficient Algorithm for Sorting by Block-Interchanges and Its Application to the Evolution of Vibrio Species
Applying Fuzzy Technologies to Equivalence Learning in Protein Classification
On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies
Variational Upper and Lower Bounds for Probabilistic Graphical Models
Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints
A Near-Linear Time Algorithm for Haplotype Determination on General Pedigrees
Nonparametric Regularized Regression for Phenotype-Associated Taxa Selection and Network Construction with Metagenomic Count Data
FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data
gCoda: Conditional Dependence Network Inference for Compositional Data
Inconsistency of Triplet-Based and Quartet-Based Species Tree Estimation under Intralocus Recombination
Learning Multiple Evolutionary Pathways from Cross-Sectional Data
Disease Gene Prioritization Using Network and Feature
A Table-Driven, Full-Sensitivity Similarity Search Algorithm
A New Constant Memory Recursion for Hidden Markov Models
Improved Biological Network Reconstruction Using Graph Laplacian Regularization
Alignment of Phylogenetically Unambiguous Indels in Shewanella
Diagnosis Prediction from Electronic Health Records Using the Binary Diagnosis History Vector Representation
Data Structures for Parsimony Correlation and Biosequence Co-Evolution
A Computational Method for NMR-Constrained Protein Threading
Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints
Chromosome Three-Dimensional Structure Reconstruction: An Iterative ShRec3D Algorithm
Sequencing from Compomers: Using Mass Spectrometry for DNA de novo Sequencing of 200+ nt
Statistical Mitogenome Assembly with RepeaTs
Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks
A Dynamic Programming Approach for Finding Common Patterns in RNAs
Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets
Vavien: An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks
Determination of Bias in the Relative Abundance of Oligonucleotides in DNA Sequences
Understanding Pattern Formation in Embryos: Experiment, Theory, and Simulation
Combinatorial Methods for Epistasis and Dominance
A Joint Bayesian Model for Integrating Microarray and RNA Sequencing Transcriptomic Data
Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny
A Stability Boundary Based Method for Finding Saddle Points on Potential Energy Surfaces
Special Issue Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC) Workshop (2022)
Searching Protein Three-Dimensional Structures in Faster Than Linear Time
Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis
A Fast and Exact Algorithm for the Median of Three Problem: A Graph Decomposition Approach
Codon Optimization Using a Recurrent Neural Network
Revision of Boolean Models of Regulatory Networks Using Stable State Observations
Finding Motifs in Protein Secondary Structure for Use in Function Prediction
De Novo Peptide Sequencing via Tandem Mass Spectrometry
Theory of Morphogenesis
The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus
Finding Approximate Tandem Repeats in Genomic Sequences
Pathway Analysis of Microarray Data via Regression
Aligning a DNA Sequence with a Protein Sequence
Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets
DeepSNP: An End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data
Algorithms for Protein Structural Motif Recognition
Detecting Character Dependencies in Stochastic Models of Evolution
Pathway Realizability in Chemical Networks
Coverage Processes in Physical Mapping by Anchoring Random Clones
Mathematical Modeling of T-Cell Activation Kinetic
1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap
A Power-Performance Perspective to Multiobjective Electroencephalogram Feature Selection on Heterogeneous Parallel Platforms
A Sticker-Based Model for DNA Computation
A Novel Graphlet-Based Community Detection Algorithm
Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures
HetFHMM: A Novel Approach to Infer Tumor Heterogeneity Using Factorial Hidden Markov Models
A Surface-Based Approach to DNA Computation
Finding Motifs in Promoter Regions
Biological Evaluation of d 2 , an Algorithm for High-Performance Sequence Comparison
United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding
FSG: Fast String Graph Construction for De Novo Assembly
An Algorithm to Enumerate Sorting Reversals for Signed Permutations
Simulating Virtual Protein C alpha Traces with Applications
Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching
Sparsity Optimization Method for Multivariate Feature Screening for Gene Expression Analysis
Regression Analysis of Multiple Protein Structures
A Simplified Procedure for Entry of Raw Genotypic Data
Overexpression of miR-101 May Target DUSP1 to Promote the Cartilage Degradation in Rheumatoid Arthritis
Identification of Words in Biological Sequences Under the Semi-Markov Hypothesis
BCtypeFinder: A Semi-Supervised Model with Domain Adaptation for Breast Cancer Subtyping Using DNA Methylation Profiles
Endhered Patterns in Matchings and RNA
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification
MADMX: A Strategy for Maximal Dense Motif Extraction
Prediction of MicroRNA-Disease Potential Association Based on Sparse Learning and Multilayer Random Walks
Identification of Potential Key Genes for Hepatitis B Virus-Associated Hepatocellular Carcinoma by Bioinformatics Analysis
Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm
Bioinformatics Analysis of Key Genes and Pathways in Colorectal Cancer
Reconstruction of a String from Substring Precedence Data
Reverse Engineering Molecular Regulatory Networks from Microarray Data with qp-Graphs
Deep Large-Scale Multitask Learning Network for Gene Expression Inference
ATAC-DEA: A Web-Based ATAC-Seq Data Differential Peak and Annotation Analysis Application
Safe and Complete Contig Assembly Through Omnitigs
Multidimensional Fitting for Multivariate Data Analysis
Group-Penalized Exponential Tilt Model for Identification of Differentially Methylated Genes in Epigenetic Association Studies
Gene Microarray Analysis Using Angular Distribution Decomposition
On Tree-Based Phylogenetic Networks
Sorting by Short Swaps
QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent
Comparative Study Using Neural Networks for 16S Ribosomal Gene Classification
Towards Quality Control for DNA Microarrays
Beyond the Information Maze
Efficient Minimum Flow Decomposition via Integer Linear Programming
Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns
Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs
On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem
A Novel Algorithm for Non-Bonded-List Updating in Molecular Simulations
Modeling Protein Loop Structure by Cyclic Coordinate Descent-based Approach
Estimating the Proportion of Equivalently Expressed Genes in Microarray Data Based on Transformed Test Statistics
Constructing Additive Trees When the Error Is Small
Monotony of Surprise and Large-Scale Quest for Unusual Words
To t -Test or Not to t -Test? A p -Values-Based Point of View in the Receiver Operating Characteristic Curve Framework
Physical Network Models
A Computational Model for the Identification of Biochemical Pathways in the Krebs Cycle
Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification
Threshold Group Testing on Inhibitor Model
Special Issue Preface: 13th International Symposium on BioinformaticsResearch and Applications (ISBRA 2017)
LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins
Preface: RECOMB 2023 Special Issue
Stochastic Modeling and Simulation of the p53-MDM2/MDMX Loop
Protein Structural Motif Prediction in Multidimensional ø - Psi Space Leads to Improved Secondary Structure Prediction
Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery
Stochastic Simulation Algorithm for Gene Regulatory Networks with Multiple Binding Sites
The k Partition-Distance Problem
Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella -Infected and Uninfected Mice
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model
A Novel Approach to Remote Homology Detection: Jumping Alignments
Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion
An Integrative Computational Approach to Evaluate Genetic Markers for Chronic Lymphocytic Leukemia
Live Phylogeny
Mutant-Bin: Unsupervised Haplotype Estimation of Viral Population Diversity Without Reference Genome
The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process
Random Matrix Approach to the Distribution of Genomic Distance
CuMiDa: An Extensively Curated Microarray Database for Benchmarking and Testing of Machine Learning Approaches in Cancer Research
Biological Data Analysis as an Information Theory Problem: Multivariable Dependence Measures and the Shadows Algorithm
Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes
Fast Recovery of Evolutionary Trees with Thousands of Nodes
The Cophylogeny Reconstruction Problem Is NP-Complete
Optimization-based Inference for Temporally Evolving Networks with Applications in Biology
Modeling Biological Oscillations: Integration of Short Reaction Pauses into a Stationary Model of a Negative Feedback Loop Generates Sustained Long Oscillations
Statistically Consistent k -mer Methods for Phylogenetic Tree Reconstruction
Using Bayesian Networks to Analyze Expression Data
A Method for Determining Taxonomical Contributions to Group Differences in Microbiomic Investigations
Integrated Framework for Selection of Additive and Nonadditive Genetic Markers for Genomic Selection
A New Estimator of Significance of Correlation in Time Series Data
Sequencing-by-Hybridization at the Information-Theory Bound: An Optimal Algorithm
The Irredundant Class Method for Remote Homology Detection of Protein Sequences
Zero-Inflated Beta Regression for Differential Abundance Analysis with Metagenomics Data
Three-Dimensional Embryonic Image Segmentation and Registration Based on Shape Index and Ellipsoid-Fitting Method
Statistics of Random Protein Superpositions: p -Values for Pairwise Structure Alignment
Approximation Algorithms for Protein Folding in the Hydrophobic-Polar Model on 3D Hexagonal Prism Lattice
An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a Boolean Network
Microbe Drug Association Prediction with Bernoulli Random Forests
Combining Complementarity and Binding Energetics in the Assessment of Protein Interactions: EnCPdock - A Practical Manual
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems
Preface: RECOMB 2012
Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data
Applying a Modified Wavelet Shrinkage Filter to Improve Cryo-Electron Microscopy Imaging
A New Method for Mapping Discontinuous Antibody Epitopes to Reveal Structural Features of Proteins
Chemical Modeling: From Paul Ehrlich's Dyes to β -Blockers - A Brief History
Betamax: Towards Optimal Sampling Strategies for High-Throughput Screens
UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation
WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment
A Hybrid GNN Approach for Improved Molecular Property Prediction
Chromatin Properties of Regulatory DNA Probed by Manipulation of Transcription Factors
EDoP Distance Between Sets of Incomplete Permutations: Application to Bacteria Classification Based on Gene Order
Prediction of siRNA Potency Using Sparse Logistic Regression
Biological Cluster Evaluation for Gene Function Prediction
Maximum Stacking Base Pairs: Hardness and Approximation by Nonlinear Linear Programming-Rounding
On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models
The Potential Role of Protein Tyrosine Phosphatase, Receptor Type C (CD45) in the Intestinal Ischemia-Reperfusion Injury
Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis
Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays
Kernel Mixed Model for Transcriptome Association Study
Protocol for Designing De Novo Noncanonical Peptide Binders in OSPREY
Compositional Adjustment of Dirichlet Mixture Priors
Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers
Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer
JCB Call for Papers for the Special Issue on "40 Years of Computational Biology: In Honor of Professor Michael Waterman's 80th Birthday": Deadline for Intention to submit: August 1, 2021 Deadline for Manuscript Submission: December 1, 2021
SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data
Categorizing Host-Dependent RNA Viruses by Principal Component Analysis of Their Codon Usage Preferences
Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data
Fast Approximation of Frequent k-Mers and Applications to Metagenomics
LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly
Information Flow in Interaction Networks II: Channels, Path Lengths, and Potentials
bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences
Counting RNA Loop Interaction Networks of Homology Group Rank Zero
Improved Splice Site Detection in Genie
CLHGNNMDA: Hypergraph Neural Network Model Enhanced by Contrastive Learning for miRNA-Disease Association Prediction
The Victor/FRST Function for Model Quality Estimation
Conserved High Free Energy Sites in Human Coronavirus Spike Glycoprotein Backbones
Path Costs in Evolutionary Tree Reconstruction
Potential Inhibitors of the Activity of the Cholesterol-Ester Transfer Protein
High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS)
Exploratory Factor Analysis of Pathway Copy Number Data with an Application Towards the Integration with Gene Expression Data
Bi-Billboard: Symmetrization and Careful Choice of Informant Species Results in Higher Accuracy of Regulatory Element Prediction
Ordering Clone Libraries in Computational Biology
Constructing Consensus Genetic Maps in Comparative Analysis
Efficiently Identifying Significant Associations in Genome-wide Association Studies
Systematic and Fully Automated Identification of Protein Sequence Patterns
Prediction of Membrane Proteins in Mycobacterium tuberculosis Using a Support Vector Machine Algorithm
Dynamic Programming Alignment Accuracy
Fast Molecular Shape Matching Using Contact Maps
RemeDB: Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets
Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue
Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor CIP
Analysis of Gene Sets Based on the Underlying Regulatory Network
A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data
Improving RNA Assembly via Safety and Completeness in Flow Decompositions
Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences
A New Approach for the Identification of Processed Pseudogenes
RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue
A Blind Deconvolution Approach for Improving the Resolution of Cryo-EM Density Maps
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency
K-Boost: A Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data
Reduced-Size Integer Linear Programming Models for String Selection Problems: Application to the Farthest String Problem
Rebuttal to Flaws in the Paper 'Nearly Instantaneous Time-Varying Reproduction Number for Contagious Diseases - a Direct Approach Based on Nonlinear Regression'
Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction
Fast Iterative Gene Clustering Based on Information Theoretic Criteria for Selecting the Cluster Structure
Accurate Estimations of Evolutionary Times in the Context of Strong CpG Hypermutability
Finding Alignments of Conserved Graphlets in Protein Interaction Networks
New t-Gap Insertion-Deletion-Like Metrics for DNA Hybridization Thermodynamic Modeling
A Comparison of Two-Stage Approaches Based on Penalized Regression for Estimating Gene Networks
BLASTphylo: An Interactive Web Tool for Taxonomic and Phylogenetic Analysis of Prokaryotic Genes
Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models
Identifying Subpopulations of Cells in Single-Cell Transcriptomic Data: A Bayesian Mixture Modeling Approach to Zero Inflation of Counts