yusuke1997/dblp-id-title huggingface dataset:
Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs
On the Impossibility of Reconstructing Ancestral Data and Phylogenies
Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length
The Complexity of Deriving Multi-Labeled Trees from Bipartitions
FedOpenHAR: Federated Multitask Transfer Learning for Sensor-Based Human Activity Recognition
New Approach to Detect Coiled Coil and Leucine Zipper Motifs in Protein Sequences
Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision
PTENpred: A Designer Protein Impact Predictor for PTEN-related Disorders
Partial Immunity and Vaccination for Influenza
Folding 3-Noncrossing RNA Pseudoknot Structures
Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples
Protein Complex Identification Based on Heterogeneous Protein Information Network
Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees
Combinatorics of the Breakage-Fusion-Bridge Mechanism
Repeated Decision Stumping Distils Simple Rules from Single-Cell Data
Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem
Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-Identifiable Distributions
SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation
Large Scale Sequencing by Hybridization
Detection of Recombination in DNA Multiple Alignments with Hidden Markov Models
A New Computational Tool for Establishing Model Parameter Identifiability
A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data
DrML: Probabilistic Modeling of Gene Duplications
Bootstrapping Time-Course Gene Expression Data for Gene Networks: Application to Gene Relevance Networks
Is Tumor Growth Influenced by the Bone Remodeling Process?
Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data
Special RECOMB 2008 Issue
Shared Nearest Neighbor Clustering in a Locality Sensitive Hashing Framework
Note on the Computation of Critical Effective Population Sizes
Directional Association Measurement in Contingency Tables: Genomic Case
New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data
Parallel GPU Implementation of Iterative PCA Algorithms
An R Package for Nonparametric Inference on Dynamic Populations with Infinitely Many Types
A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees
Binary State Pattern Clustering: A Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer
Quantifying Cell-Type-Specific Differences of Single-Cell Datasets Using Uniform Manifold Approximation and Projection for Dimension Reduction and Shapley Additive exPlanations
Enhancing Gibbs Sampling Method for Motif Finding in DNA with Initial Graph Representation of Sequences
An Anytime Local-to-Global Optimization Algorithm for Protein Threading in O(m 2 n 2 ) Space
The Deferred Path Heuristic for the Generalized Tree Alignment Problem
RECOMB Main Conference 2009
Structural Alignment of RNA with Triple Helix Structure
A Faster 1.375-Approximation Algorithm for Sorting by Transpositions*
Discretization of Time Series Data
The Clark Phaseable Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS
An Iterative Method for Improved Protein Structural Motif Recognition
Efficient Error-Correcting Pooling Designs Constructed from Pseudo-Symplectic Spaces Over a Finite Field
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes
Probabilistic Cellular Automata
A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands
Efficient Computation of Longest Common Subsequences with Multiple Substring Inclusive Constraints
Mathematical Model of HIV/AIDS Considering Sexual Preferences Under Antiretroviral Therapy, a Case Study in San Juan de Pasto, Colombia
Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions
Large-Scale Elucidation of Drug Response Pathways in Humans
Detecting Phylogenetic Signals in Eukaryotic Whole Genome Sequences
Identifying Variables Responsible for Clustering in Discriminant Analysis of Data from Infrared Microspectroscopy of a Biological Sample
Hyperdigraph-Theoretic Analysis of the EGFR Signaling Network: Initial Steps Leading to GTP: Ras Complex Formation
Sequence Evolution Under Constraints: Lessons Learned from Sudoku
Structure-Aware Principal Component Analysis for Single-Cell RNA-seq Data
Prospects for a General Theory of Evolutionary Novelty
UPSEC: An Algorithm for Classifying Unaligned Protein Sequences into Functional Families
Numerical Analysis of Split-Step Backward Euler Method with Truncated Wiener Process for a Stochastic Susceptible-Infected-Susceptible Model
Screening for the Biomarkers Associated with Myocardial Infarction by Bioinformatics Analysis
Change-Point Analysis of Paired Allele-Specific Copy Number Variation Data
End-to-End Optimization of High-Throughput DNA Sequencing
All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes
PEM-fitter : A Coarse-Grained Method to Validate Protein Candidate Models
Screening of Prognosis-Related Genes in Primary Breast Carcinoma Using Genomic Expression Data
Adaptive Distance Measures for Resolving K2P Quartets: Metric Separation versus Stochastic Noise
Computing Leapfrog Regularization Paths with Applications to Large-Scale K-mer Logistic Regression
Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds
Regression Approaches for Microarray Data Analysis
Single-Cell Multiomics Integration by SCOT
Preface Special Issue: RECOMB 2019
Tsukuba BB: A Branch and Bound Algorithm for Local Multiple Alignment of DNA and Protein Sequences
Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry
DNA Computing on Surfaces: Encoding Information at the Single Base Level
A Cancer Subpopulation Competition Model Reveals Optimal Levels of Immune Response that Minimize Tumor Size
Numerical Comparison of Several Approximations of the Word Count Distribution in Random Sequences
Toward a Characterization of Landscapes of Combinatorial Optimization Problems, with Special Attention to the Phylogeny Problem
Efficient Algorithms for Quantitative Trait Loci Mapping Problems
Recognition of Translation Initiation Sites of Eukaryotic Genes Based on an EM Algorithm
On Relationship Inference Using Gamete Identity by Descent Data
Sharing Rewards Undermines Coordinated Hunting
CSAM: Using Clustering-Hashing-Signal Anchoring Method to Explore Human Novel Genes
Explaining Gene Expression Using Twenty-One MicroRNAs
Inference in High-Dimensional Parameter Space
On Topological RNA Interaction Structures
On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis
Higher-Order Genomic Organization of Cellular Functions in Yeast
More Accurate Transcript Assembly via Parameter Advising
Scalable Consistency in T-Coffee Through Apache Spark and Cassandra Database
A Random Graph Approach to NMR Sequential Assignment
A New Role for the Nonpathogenic Nonsynonymous Single-Nucleotide Polymorphisms of Acetylcholinesterase in the Treatment of Alzheimer's Disease: A Computational Study
A Statistically Driven Approach for Image Segmentation and Signal Extraction in cDNA Microarrays
Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores
Optimal Search Space for Clustering Gene Expression Data via Consensus
Occurrence Probability of Structured Motifs in Random Sequences
A Fusion Learning Model Based on Deep Learning for Single-Cell RNA Sequencing Data Clustering
Computational Disease Gene Prioritization: An Appraisal
Gene Prioritization in Parkinson's Disease Using Human Protein-Protein Interaction Network
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks
HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis
A Comparative Study of Gene Co-Expression Thresholding Algorithms
A General Edit Distance between RNA Structures
Probing RNA Native Conformational Ensembles with Structural Constraints
Correcting for Observation Bias in Cancer Progression Modeling
Genomic Classification Using an Information-Based Similarity Index: Application to the SARS Coronavirus
A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences
Adaptive Control Model Reveals Systematic Feedback and Key Molecules in Metabolic Pathway Regulation
An Algorithm for Efficient Identification of Branched Metabolic Pathways
A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign and Its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme
Genetic Map Refinement Using a Comparative Genomic Approach
Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach
Combinatorics of γ -Structures
HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data
Fast, Approximate Kinetics of RNA Folding
Evaluation of miRNA Expression Profiles in Schizophrenia Using Principal-Component Analysis-Based Unsupervised Feature Extraction Method
Strong Feature Sets from Small Samples
ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data
New Method for Potential Fusions Detection in Protein-Coding Sequences
Special Issue: Genomic Regulation: Experiments, Computational Modeling, and Philosophy
Prediction of Rare Single-Nucleotide Causative Mutations for Muscular Diseases in Pooled Next-Generation Sequencing Experiments
A Novel Multi-Ensemble Method for Identifying Essential Proteins
On the A-Optimality Criterion for Finding Two-Color Microarray Optimal Designs
Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes
A Six-Point Condition for Ordinal Matrices
Coding Region Prediction Based on a Universal DNA Sequence Representation Method
Analysis of Information Content for Biological Sequences
Model-Based Inference of Haplotype Block Variation
A Hidden-State Markov Model for Cell Population Deconvolution
Timing of Gene Expression Responses to Environmental Changes
Modeling Algae Growth in an Open-Channel Raceway
A Simulation Study to Assess a Variable Selection Method for Selecting Single Nucleotide Polymorphisms Associated with Disease
A Service-Oriented Platform for Approximate Bayesian Computation in Population Genetics
Precise and Parallel Pairwise Metagenomic Comparisons
The 5′-3′ Distance of RNA Secondary Structures
Statistical Development and Evaluation of Microarray Gene Expression Data Filters
HTFSMMA: Higher-Order Topological Guided Small Molecule-MicroRNA Associations Prediction
Longitudinal Genotype-Phenotype Association Study through Temporal Structure Auto-Learning Predictive Model
The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment
Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
Semisupervised Generative Autoencoder for Single-Cell Data
Constructing Phylogenies from Quartets: Elucidation of Eutherian Superordinal Relationships
A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads
A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform
GSEAplot: A Package for Customizing Gene Set Enrichment Analysis in R
Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition
Enumeration of Ancestral Configurations for Matching Gene Trees and Species Trees
Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space
Preface: Research in Computational Molecular Biology (RECOMB 2013)
Robustness Analysis of a Boolean Model of Gene Regulatory Network with Memory
Exact Calculation of Distributions on Integers, with Application to Sequence Alignment
The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study
Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo
Constructing Minimal Ancestral Recombination Graphs
Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning
Bioinformatics Method to Analyze the Mechanism of Pancreatic Cancer Disorder
Picking Alignments from (Steiner) Trees
MAMMLE: A Framework for Phylogeny Estimation Based on Multiobjective Application-aware Multiple Sequence Alignment and Maximum Likelihood Ensemble
Prediction of Drug Target Sensitivity in Cancer Cell Lines Using Apache Spark
QMix: An Efficient Program to Automatically Estimate Multi-Matrix Mixture Models for Amino Acid Substitution Process
Toward Robust Self-Training Paradigm for Molecular Prediction Tasks
Special Issue, Part 2 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022)
Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming
IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data
Effective Integration of Single-Cell Multi-Omics Data Using Improved Network-Based Integrative Clustering with Multigraph Regularization
ThurGood: Evaluating Assembly-to-Assembly Mapping
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics
Nonparametric Model of Smooth Muscle Force Production During Electrical Stimulation
CsSNP: A Web-Based Tool for the Detecting of Comparative Segments SNPs
Defining Low-Dimensional Projections to Guide Protein Conformational Sampling
constNJ: An Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints
cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing
A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem
Zseq: An Approach for Preprocessing Next-Generation Sequencing Data
IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information
DNA Workbench: A Database Package to Manage Regional Physical Mapping
FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules
Contig Selection in Physical Mapping
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function
Re-Evaluating the "Rules" of Protein Topology
Variational Approximation-Based Model Selection for Microbial Network Inference
Deep Learning of Sequence Patterns for CCCTC-Binding Factor-Mediated Chromatin Loop Formation
A Stepwise Approach of Finding Dependent Variables via Coefficient of Intrinsic Dependence
Feature Detection with Controlled Error Rates in LC/MS Images
Convolutional Neural Network for Histopathological Analysis of Osteosarcoma
An Efficient Dual Sampling Algorithm with Hamming Distance Filtration
On Applying Molecular Computation to the Data Encryption Standard
Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies
Ancestral Recombinations Graph: A Reconstructability Perspective Using Random-Graphs Framework
Set Association Analysis of SNP Case-Control and Microarray Data
HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models
A Rigorous Framework to Classify the Postduplication Fate of Paralogous Genes
Shape-Based Feature Matching Improves Protein Identification via LC-MS and Tandem MS
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters
On the Sparse Reconstruction of Gene Networks
Designing Multiple Simultaneous Seeds for DNA Similarity Search
Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions
Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data
Mitochondrial Morphologies Driven by Energy-Consuming Cell Sites in a Spatially and Time-Resolved Quality Model
Phylogeographic Ancestral Inference Using the Coalescent Model on Haplotype Trees
Signal Deconvolution Based Expression-Detection and Background Adjustment for Microarray Data
Compensating for Unknown Confounders in Microarray Data Analysis Using Filtered Permutations
In Silico Prediction of Escherichia coli Proteins Targeting the Host Cell Nucleus, with Special Reference to Their Role in Colon Cancer Etiology
Statistical Distributions of Sequencing by Synthesis with Probabilistic Nucleotide Incorporation
An Algorithmic Framework for Predicting Side Effects of Drugs
Automation on the Generation of Genome-Scale Metabolic Models
Probabilistic Modeling of Pseudorabies Virus Infection in a Neural Circuit
A Self-Organizing Cognitive Network of Antibody Repertoire Development
Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification
Genome Rearrangement Distance with Reversals, Transpositions, and Indels
Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods
Statistical Selection Strategy for Risk and Protective Rare Variants Associated with Complex Traits
Finding an Upper Bound for the Number of Contacts in Hydrophobic-Hydrophilic Protein Structure Prediction Model
Loops in Canonical RNA Pseudoknot Structures
Exploration of DNA Methylation-Driven Genes in Papillary Thyroid Carcinoma Based on the Cancer Genome Atlas
Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing
Preface: MatBio 2021 Special Section
Identification of Potential Hub Genes of Atherosclerosis Through Bioinformatic Analysis
Mass Spectrometry Proteomic Diagnosis: Enacting the Double Cross-Validatory Paradigm
A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks
Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020)
Sequence Alignment on Directed Graphs
Computing Nonoverlapping Inversion Distance Between Two Strings in Linear Average Time
Special Issue, Part II 20th International Symposium on Bioinformatics Research and Applications (ISBRA 2024)
Sequence Alignment of Viral Channel Proteins with Cellular Ion Channels
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design
The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform
Analyzing the LncRNA, miRNA, and mRNA Regulatory Network in Prostate Cancer with Bioinformatics Software
Extended HP Model for Protein Structure Prediction
Comparing Phylogenetic Trees Side by Side Through iPhyloC, a New Interactive Web-Based Framework
A Relational Extension of the Notion of Motifs: Application to the Common 3D Protein Substructures Searching Problem
Matching Reads to Many Genomes with the r-Index
Ballast: A Ball-based Algorithm for Structural Motifs
Structured Motifs Search
Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information
Protein Expression Profile on Differentiation of Bone Marrow Mesenchymal Stem Cells into Retinal Ganglion-Like Cells
iGly-IDN: Identifying Lysine Glycation Sites in Proteins Based on Improved DenseNet
Molecular Dynamics Studies of Histo-Blood Group Antigen Blocking Human Immunoglobulin A Antibody and Escape Mechanism in Noroviruses Upon Mutation
Algorithms for the Design of Maximum Hydropathic Complementarity Molecules
Tabu Search and Binary Particle Swarm Optimization for Feature Selection Using Microarray Data
Modeling Genetic Regulatory Dynamics in Neural Development
A Structure-Based Flexible Search Method for Motifs in RNA
A Graph-Based Machine-Learning Approach Combined with Optical Measurements to Understand Beating Dynamics of Cardiomyocytes
A Simple Approach to the Reconstruction of a Set of Points from the Multiset of Pairwise Distances in n 2 Steps for the Sequencing Problem: III. Noise Inputs for the Beltway Case
Current Limitations to Protein Threading Approaches
Inferring Ancestries Efficiently in Admixed Populations with Linkage Disequilibrium
On Algebraic Properties of Extreme Pathways in Metabolic Networks
DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly
Quantification of Twist from the Central Lines of β-Strands
Hypothesis Generation in Signaling Networks
Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs
Comparison of Minisatellites
Interpretable Numerical Descriptors of Amino Acid Space
Regression-Based Network Estimation for High-Dimensional Genetic Data
Conditional Random Fields with Least Absolute Shrinkage and Selection Operator to Classifying the Barley Genes Based on Expression Level Affected by the Fungal Infection
Asynchronous Stochastic Boolean Networks as Gene Network Models
Asymptotics of RNA Shapes
Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs *
An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats in Biological Sequences
IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology
Distinct Patterns of mRNA and lncRNA Expression Differences Between Lung Squamous Cell Carcinoma and Adenocarcinoma
HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models
Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model
Sorting by Cuts, Joins, and Whole Chromosome Duplications
Duplication and Inversion History of a Tandemly Repeated Genes Family
Haplotyping as Perfect Phylogeny: A Direct Approach
Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language
Toric Ideals of Phylogenetic Invariants
Unveiling Gene Regulatory Networks That Characterize Difference of Molecular Interplays Between Gastric Cancer Drug Sensitive and Resistance Cell Lines
BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations
Adjustable Chain Trees for Proteins
Perfect Phylogenetic Networks with Recombination
A Database for Cell Signaling Networks
An Algorithmic Approach to Multiple Complete Digest Mapping
Generative AI Models for the Protein Scaffold Filling Problem
Trends in Computational Biology: A Summary Based on a RECOMB Plenary Lecture, 1999
Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis
DNA Sequence Evolution with Neighbor-Dependent Mutation
Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting
Genome-Wide Search for Local DNA Segments with Anomalous GC-Content
Simulation Model of Bacterial Resistance to Antibiotics Using Individual-Based Modeling
Constructing Lattice Models of Protein Chains with Side Groups
A Descriptive Analysis of Populations of Three-Dimemsional Structures Calculated from Primary Sequences of Proteins by Osiris
Preface: Special RECOMB'99 Issue
A Learning Method of Hidden Markov Models for Sequence Discrimination
Potential Energy Function for Continuous State Models of Globular Proteins
An S-System Parameter Estimation Method (SPEM) for Biological Networks
Robust Sparse Hyperplane Classifiers: Application to Uncertain Molecular Profiling Data
Information Flow in Interaction Networks
Inference of Population Structure Using Genetic Markers and a Bayesian Model Averaging Approach for Clustering
EasyQC: Tool with Interactive User Interface for Efficient Next-Generation Sequencing Data Quality Control
Bioinformatics: Essential Infrastructure for Global Biology
Finding Motifs Using Random Projections