yusuke1997/dblp-id-title huggingface dataset:
A Biologically Consistent Model for Comparing Molecular Phylogenies
Permutation Pattern Discovery in Biosequences
Bayesian Normalization and Identification for Differential Gene Expression Data
A Class of Edit Kernels for SVMs to Predict Translation Initiation Sites in Eukaryotic mRNAs
Coding Exon Detection Using Comparative Sequences
Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations
Abstracts from TIGR's Fourth Annual Conference on Computational Genomics November 16-19, 2000, Baltimore, MD
Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach
BiRWDDA: A Novel Drug Repositioning Method Based on Multisimilarity Fusion
Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart
ShRangeSim: Simulation of Single Nucleotide Polymorphism Clusters in Next-Generation Sequencing Data
Genome-Wide Tagging SNPs with Entropy-Based Monte Carlo Method
comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence
Algorithms for Computing and Integrating Physical Maps Using Unique Probes
Nonadaptive Algorithms for Threshold Group Testing with Inhibitors and Error-Tolerance
DTD: An R Package for Digital Tissue Deconvolution
Boolean Models Can Explain Bistability in the lac Operon
Enforcing Temporal Consistency in Migration History Inference
A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l -tuples
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review
Backbone Free Energy Estimator Applied to Viral Glycoproteins
Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction
Modified SuperCurve Method for Analysis of Reverse-Phase Protein Array Data
Model of Morphogenesis
An Improved Model of Nonuniform Coleochaete Cell Division
A Decision Tree System for Finding Genes in DNA
An Efficient Algorithm to Compute the Landscape of Locally Optimal RNA Secondary Structures with Respect to the NussinovJacobson Energy Model
Representing and Reasoning about Protein Families Using Generative and Discriminative Methods
Complete Families of Linear Invariants for Some Stochastic Models of Sequence Evolution, with and without Molecular Clock Assumption
Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences
A New Approach in Applying Systems Engineering Tools and Analysis to Determine Hepatocyte Toxicogenomics Risk Levels to Human Health
Protein Fold Recognition Using Segmentation Conditional Random Fields (SCRFs)
A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware
Fast and Accurate Detection of Multiple Quantitative Trait Loci
UNIPred: Unbalance-Aware Network Integration and Prediction of Protein Functions
Statistical Significance of Large Gene Clusters
Bayesian Estimation of Fold-Changes in the Analysis of Gene Expression: The PFOLD Algorithm
How Does the Regulatory Genome Work?
iRNA-2OM: A Sequence-Based Predictor for Identifying 2′-O-Methylation Sites in Homo sapiens
Alignments without Low-Scoring Regions
A Barrier for Further Approximating Sorting by Transpositions
Time-Series Expression Analysis of Epidermal Stem Cells from High Fat Diet Mice
Identification of Drug Targets in Breast Cancer Metabolic Network
Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules
Drug Repurposing Using Hypergraph Embedding Based on Common Therapeutic Targets of a Drug
On the Convexity of the Effective Reproduction Number
CFINet: Cross-Modality MRI Feature Interaction Network for Pseudoprogression Prediction of Glioblastoma
Reconciliation with Non-Binary Species Trees
rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database
Parallel Tiled Codes Implementing the Smith-Waterman Alignment Algorithm for Two and Three Sequences
Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists
Expectation-Maximization Algorithm for Determining Natural Selection of Y-Linked Genes Through Two-Sex Branching Processes
SuccSPred2.0: A Two-Step Model to Predict Succinylation Sites Based on Multifeature Fusion and Selection Algorithm
Exploration of Novel Biomarkers in Vasculitis by Integrated Bioinfomatic Approaches
Algorithmic Determination of Core Positions in the V L and V H Domains of Immunoglobulin Molecules
Markov Chain Monte Carlo Methods for Radiation Hybrid Mapping
A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing
Multichannel Contribution Aware Network for Prostate Cancer Grading in Histopathology Images
Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes
Genome Halving and Double Distance with Losses
Distinct Molecular Mechanisms Analysis of Three Lung Cancer Subtypes Based on Gene Expression Profiles
PyGTED: Python Application for Computing Graph Traversal Edit Distance
New Genome Similarity Measures based on Conserved Gene Adjacencies
Reconstruction of Genuine Pair-Wise Sequence Alignment
The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs
Three-Dimensional Searching for Recurrent Structural Motifs in Data Bases of Protein Structures
Bayesian Detection of Abnormal Asynchrony of Division Between Sister Cells in Mutant Caenorhabditis elegans Embryos
Joint Analysis of SNP-SNP-Environment Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm
Predicting and Annotating Catalytic Residues: An Information Theoretic Approach
Identification of a Five-CpG Signature with Diagnostic Value in Thyroid Cancer
Faster Multipoint Linkage Analysis Using Fourier Transforms
Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function
The Power of Detecting Enriched Patterns: An HMM Approach
An Optimal Algorithm for Perfect Phylogeny Haplotyping
Exploration of N5-CAIR Mutase Novel Inhibitors from Pyrococcus horikoshii OT3: A Computational Study
Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures
Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods
Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding
Assembling Genes from Predicted Exons In Linear Time with Dynamic Programming
DIsulfide Mapping PLanner Software Tool
RECOMB 2021 Special Issue
Homology Detection via Family Pairwise Search
A Mathematical Framework for Analyzing Wild Tomato Root Architecture
SWsnn: A Novel Simulator for Spiking Neural Networks
Analysis of tRNA Gene Sequences by Neural Network
Inference from Samples of DNA Sequences Using a Two-Locus Model
Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation
Critiquing Protein Family Classification Models Using Sufficient Input Subsets
The Effect of Nonhomogeneous Clone Length Distribution on the Progress of an STS Mapping Project
Emergence of Direction-Selective Retinal Cell Types in Task-Optimized Deep Learning Models
Improvement of Automatic Glioma Brain Tumor Detection Using Deep Convolutional Neural Networks
Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways Using Genomics Information
Statistical Distributions of Pyrosequencing
A Bayesian Evolutionary Distance for Parametrically Aligned Sequences
Improved Versions of Common Estimators of the Recombination Rate
Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data
Identification of Methylation Markers and Differentially Expressed Genes with Prognostic Value in Breast Cancer
Mapping the Nonstructural Transmembrane Proteins of Severe Acute Respiratory Syndrome Coronavirus 2
R/PY-SUMMA: An R/Python Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics
Delayed Stochastic Model of Transcription at the Single Nucleotide Level
Influence of Oscillatory Enzyme Activity on the Reaction Kinetics: Mathematical Model
Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures
An Approximate Maximum Likelihood Approach, Applied to Phylogenetic Trees
Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space
Unveiling Commonalities and Differences in Genetic Regulations via Two-Way Fusion
A Pseudo-Boolean Framework for Computing Rearrangement Distances between Genomes with Duplicates
Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks
Error Tree: A Tree Structure for Hamming and Edit Distances and Wildcards Matching
Bayesian Hierarchical Model for Identifying Changes in Gene Expression from Microarray Experiments
More Is Faster: Why Population Size Matters in Biological Search
Multivariate Analysis of Data Sets with Missing Values: An Information Theory-Based Reliability Function
The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments
New Flexible Approaches for Multiple Sequence Alignment
A Fast Parallel K-Modes Algorithm for Clustering Nucleotide Sequences to Predict Translation Initiation Sites
New Construction for Transversal Design
A Simple Approach to the Reconstruction of a Set of Points from the Multiset of n 2 Pairwise Distances in n 2 Steps for the Sequencing Problem: II. Algorithm
Clustering Gene Expression Patterns
Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence
Harnessing Fuzzy Rule Based System for Screening Major Histocompatibility Complex Class I Peptide Epitopes from the Whole Proteome: An Implementation on the Proteome of Leishmania donovani
Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence
An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes
Selecting "Significant" Differentially Expressed Genes from the Combined Perspective of the Null and the Alternative
Continuous-Time Markov Chain-Based Flux Analysis in Metabolism
Stable Structure-Approximating Inverse Protein Folding in 2D Hydrophobic-Polar-Cysteine (HPC) Model
A Multiomics Graph Database System for Biological Data Integration and Cancer Informatics
Toward a Dynamic Threshold for Quality Score Distortion in Reference-Based Alignment
Reconstructing Reticulate Evolution in SpeciesTheory and Practice
Excerno: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival
The Advantage of Functional Prediction Based on Clustering of Yeast Genes and Its Correlation with Non-Sequence Based Classifications
Comparison of Perturbed Pathways in Two Different Cell Models for Parkinson's Disease with Structural Equation Model
Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data
Representation of k-Mer Sets Using Spectrum-Preserving String Sets
Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data
Wavelet Analysis of DNA Walks
Key Genes Involved in Diabetic Nephropathy Investigated by Microarray Analysis
Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison
Identification of Biomolecular Information in Rotenone-Induced Cellular Model of Parkinson's Disease by Public Microarray Data Analysis
Grohar: Automated Visualization of Genome-Scale Metabolic Models and Their Pathways
Modeling the Hes1 Oscillator
A Ranking Approach for Probe Selection and Classification of Microarray Data with Artificial Neural Networks
Enhanced Over-Representation Analysis for the Differential Regulation of Birc5a and HIF2α-Knockdown Approaches
Lattice Simulations of Aggregation Funnels for Protein Folding
CORaL: Comparison of Ranked Lists for Analysis of Gene Expression Data
Approximate Statistics of Gapped Alignments
Sorting by Reversals, Generalized Transpositions, and Translocations Using Permutation Groups
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks
Exact Learning of RNA Energy Parameters From Structure
An Analysis of a Class of DNA Sequence Reading Molecules
A Computational-Based Method for Predicting Drug-Target Interactions by Using Stacked Autoencoder Deep Neural Network
HOPE: A Homotopy Optimization Method for Protein Structure Prediction
A Protective Role for RHOJ in NonSmall Cell Lung Cancer Based on Integrated Bioinformatics Analysis
Simultaneously Learning DNA Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm
A Workflow to Improve Variant Calling Accuracy in Molecular Barcoded Sequencing Reads
Studies on the Clustering Algorithm for Analyzing Gene Expression Data with a Bidirectional Penalty
Spatial Codes and the Hardness of String Folding Problems
Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny
Amino Acid Substitution Matrices from an Artificial Neural Network Model
Locally Learning Biomedical Data Using Diffusion Frames
Biological Network Edit Distance
Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data
MetaProb 2: Metagenomic Reads Binning Based on Assembly Using Minimizers and K-Mers Statistics
Cytopede: A Three-Dimensional Tool for Modeling Cell Motility on a Flat Surface
A Bayesian Sampler for Optimization of Protein Domain Hierarchies
Comparing DNA Damage-Processing Pathways by Computer Analysis of Chromosome Painting Data
Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models
Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes
BLUP Genotype Imputation for Case-Control Association Testing with Related Individuals and Missing Data
Theory and Practice of Ultra-Perfection
Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length
RNA Secondary Structures Having a Compatible Sequence of Certain Nucleotide Ratios
Integrating Biological Knowledge Into Case-Control Analysis Through Iterated Conditional Modes/Medians Algorithm
Evaluation Measures of Multiple Sequence Alignments
deepMc: Deep Matrix Completion for Imputation of Single-Cell RNA-seq Data
A Mathematical Solution to a Network Designing Problem
Identification of Differentially Expressed Genes Associated with Idiopathic Pulmonary Arterial Hypertension by Integrated Bioinformatics Approaches
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis
Bayesian Inference for Duplication-Mutation with Complementarity Network Models
Group Testing with Multiple Inhibitor Sets and Error-Tolerant and Its Decoding Algorithms
Biases in Amino Acid Replacement Matrices and Alignment Scores Due to Rate Heterogeniety
Optimal Solution of a Fractional HIV/AIDS Epidemic Mathematical Model
A 2-Approximation for the Minimum Duplication Speciation Problem
On the Structure of the Scaffolding Core of Bacteriophage T4
Minimal-Risk Scoring Matrices for Sequence Analysis
Automatic Parameter Learning for Multiple Local Network Alignment
Reconstruction of Ancestral Genomic Sequences Using Likelihood
Simpler and Faster Development of Tumor Phylogeny Pipelines
Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns
Path Matching and Graph Matching in Biological Networks
The Inverse Problems for Some Topological Indices in Combinatorial Chemistry
An Automaton Approach for Waiting Times in DNA Evolution
Fast Metagenomic Binning via Hashing and Bayesian Clustering
MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes
A Fixed-Parameter Tractable Algorithm for Finding Agreement Cherry-Reduced Subnetworks in Level-1 Orchard Networks
A Pairwise Alignment Algorithm Which Favors Clusters of Blocks
ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs
An Efficient Test for Comparing Sequence Diversity between Two Populations
Short Superstrings and the Structure of Overlapping Strings
Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets
The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data
A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions
A New Structure Feature Introduced to Predict Protein-Protein Interaction Sites
Predicting the Beta-Helix Fold from Protein Sequence Data
Special Issue: RECOMB 2022, Part 1
Identifying Differentially Expressed Genes in cDNA Microarray Experiments
Network-Constrained Eigen-Single-Cell Profile Estimation for Uncovering Crucial Immunogene Regulatory Systems in Human Bone Marrow
MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall
Bounding Volumes for Proteins: A Comparative Study
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics
TRANSFAC Retrieval Program: A Network Model Database of Eukaryotic Transcription Regulating Sequences and Proteins
Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency
Computational Framework for Modeling Multiple Noncooperative Transcription Factor Binding and Its Application to the Analysis of Nuclear Factor Kappa B Oscillatory Response
Comparison between Molecular Dynamic Based and Knowledge Based Potentials for Protein Side Chains
SDGCCA: Supervised Deep Generalized Canonical Correlation Analysis for Multi-Omics Integration
Mosaic Graphs and Comparative Genomics in Phage Communities
A Note on the Relations Between Spatio-Genetic Models
Optimal Sparsity Criteria for Network Inference
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data
Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families
Score Distributions for Simultaneous Matching to Multiple Motifs
Canonical RNA Pseudoknot Structures
A Phase Transition in Energy-Filtered RNA Secondary Structures
Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-Based Cell Segmentation in Microscopy Images
On the Representation of De Bruijn Graphs
A Time to Model and a Time to Experiment
Representations of Search Spaces in the Problem of Mutational Pressure Optimization According to Protein-Coding Sequences
Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates
A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees
Where Do We Stand in Regularization for Life Science Studies?
Maximal Information Transfer and Behavior Diversity in Random Threshold Networks
Identification of Marker Genes and Pathways in Patients with Primary Biliary Cholangitis
A Genetic Algorithm to Optimize Weighted Gene Co-Expression Network Analysis
On the Complexity of Fundamental Computational Problems in Pedigree Analysis
Improvements to a Class of Distance Matrix Methods for Inferring Species Trees from Gene Trees
DAHNGC: A Graph Convolution Model for Drug-Disease Association Prediction by Using Heterogeneous Network
Classifier Assessment and Feature Selection for Recognizing Short Coding Sequences of Human Genes
Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks
Complex Variant Discovery Using Discordant Cluster Normalization
Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots
Haplotype Inference by Pure Parsimony: A Survey
Fast Algorithms for Inferring Evolutionary Trees
Application of Time-Frequency Domain Transform to Three-Dimensional Interpolation of Medical Images
Downregulations of miR-449a and miR-145-5p Act as Prognostic Biomarkers for Endometrial Cancer
Modeling Amino Acid Replacement
LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures
Fast Detection of Common Geometric Substructure in Proteins
Central Limit Theorem from Renewal Theory for Several Patterns
Statistical Models for Local Occurrences of RNA Structures
Duplication-Based Measures of Difference Between Gene and Species Trees
Tests for Gene Clustering
Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error
Bayesian Estimation of Transcript Levels Using a General Model of Array Measurement Noise
De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning
Structure-Approximating Inverse Protein Folding Problem in the 2D HP Model
An Algorithm for Haplotype Analysis
A Faster Algorithm for Simultaneous Alignment and Folding of RNA
A Complex Prime Numerical Representation of Amino Acids for Protein Function Comparison
Phylogenetic Stochastic Mapping Without Matrix Exponentiation
Identification of Specific Candidate Diagnostic Biomarkers for Lung Squamous Cell Carcinoma Based on Methylation
The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules
A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA)
Heuristic Approach to Sparse Approximation of Gene Regulatory Networks
Seqeunce Alignment in Molecular Biology
Evaluation of Experimental Designs for Two-Color cDNA Microarrays
The Reasoning Engine: A Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models
New Constructions of One- and Two-Stage Pooling Designs
DNA Segmentation Through the Bayesian Approach
Gene Maps Linearization Using Genomic Rearrangement Distances
Initial Cluster Analysis
Reconstruction of Biological Networks by Incorporating Prior Knowledge into Bayesian Network Models
A Scalable Method for Molecular Network Reconstruction Identifies Properties of Targets and Mutations in Acute Myeloid Leukemia
Significance of Gapped Sequence Alignments
NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees
Clustered Sequence Representation for Fast Homology Search
A Local Alignment Metric for Accelerating Biosequence Database Search
Combinatorial Structure of Genome Rearrangements Scenarios
Simultaneous Class Discovery and Classification of Microarray Data Using Spectral Analysis
Importance Sampling of Word Patterns in DNA and Protein Sequences
Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent Rates
Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads
Analysis of Gene Expression in Bladder Cancer: Possible Involvement of Mitosis and Complement and Coagulation Cascades Signaling Pathway
Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach
miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines
Normalization of DNA-Microarray Data by Nonlinear Correlation Maximization
Accurate Prediction of Docked Protein Structure Similarity
Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins
Insights into Bacterial Genome Composition through Variable Target GC Content Profiling
Coalescent Histories for Lodgepole Species Trees
Two Lower Bounds for Self-Assemblies at Temperature 1
Identification of Hub Genes in Duchenne Muscular Dystrophy: Evidence from Bioinformatic Analysis
Transformer Neural Networks for Protein Family and Interaction Prediction Tasks
A Fast Algorithm for Computing the Fourier Spectrum of a Fractional Period
The Flux Model of the Movement of Tumor Cells and Healthy Cells Using a System of Nonlinear Heat Equations
PyPathway: Python Package for Biological Network Analysis and Visualization