yusuke1997/dblp-id-title huggingface dataset:
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
Optimized Fluorescence-Based Detection in Single Molecule Synthesis Process
A Polyhedral Approach to RNA Sequence Structure Alignment
Modelling and Simulation of Motility in Actomyosin Systems
DNA Sequencing by Hybridization Using Semi-Degenerate Bases
Genomewide Conserved Epitope Profiles of HIV-1 Predicted by Biophysical Properties of MHC Binding Peptides
Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model
New Approximate Statistical Significance of Gapped Alignments Based on the Greedy Extension Model
Protein Network Analysis of the Fifth Chromosome of Zebrafish
Design and Construction of a Versatile Synthetic Network for Bistable Gene Expression in Mammalian Systems
A Deterministic Finite Automaton for Faster Protein Hit Detection in BLAST
Maximum Similarity: A New Formulation of Phylogenetic Reconstruction
Pairwise Distances and the Problem of Multiple Optima
NMR Structural Inference of Symmetric Homo-Oligomers
New, Improved, and Practical k-Stem Sequence Similarity Measures for Probe Design
Kinship Solutions for Partially Observed Multiphenotype Data
BCL: : Contact-Low Confidence Fold Recognition Hits Boost Protein Contact Prediction and De Novo Structure Determination
Knowledge-based Generalization of Metabolic Models
The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches
A Simulation Approach for Change-Points on Phylogenetic Trees
A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes
Multiresolution Topological Simplification
Identify Cross Talk Between Circadian Rhythm and Coronary Heart Disease by Multiple Correlation Analysis
Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction
Efficient Detection of Unusual Words
Detecting Conserved Interaction Patterns in Biological Networks
Spectrum-Based De Novo Repeat Detection in Genomic Sequences
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification
Heterogeneous Molecular Biology Databases
Retraction of: Screening of Clinical Factors Related to Prognosis of Breast Cancer Based on the Cox Proportional Risk Model (doi: 10.1089/cmb.2019.0110)
Interpreting Chromosome Aberration Spectra
DERNA Enables Pareto Optimal RNA Design
Fast Context-Aware Analysis of Genome Annotation Colocalization
Microarrays: How Many Do You Need?
Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact
Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility
The Power of Population Effect in Temnothorax Ant House-Hunting: A Computational Modeling Approach
On Stable States in a Topologically Driven Protein Folding Model
Mining Genetic Epidemiology Data with Bayesian Networks Application to APOE Gene Variation and Plasma Lipid Levels
Identification of Key Biomarkers and Potential Molecular Mechanisms in Oral Squamous Cell Carcinoma by Bioinformatics Analysis
Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects
CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation
PROSES: A Web Server for Sequence-Based Protein Encoding
A Note on the Linear Memory Baum-Welch Algorithm
ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes
Protein Sequence Classification Using Natural Vector and Convex Hull Method
A Secure Alignment Algorithm for Mapping Short Reads to Human Genome
Finding Motifs with Insufficient Number of Strong Binding Sites
Development of Computer Algorithm for Editing of Next Generation Sequencing Metagenome Data
Special Issue: Biological Distributed Algorithms 2021
Recent Developments in Linear-Space Alignment Methods: A Survey
In Silico Approach to Investigate the Structural and Functional Attributes of Familial Hypercholesterolemia Variants Reported in the Saudi Population
Use of Wrapper Algorithms Coupled with a Random Forests Classifier for Variable Selection in Large-Scale Genomic Association Studies
An Integrative Transcriptome Analysis Reveals Consistently Dysregulated Long Noncoding RNAs and Their Transcriptional Regulation Relationships in Heart Failure
Evolution and Vaccination of Influenza Virus
Identification of Amino Acid Latent Periodicity within 94 Protein Families
Positional Statistical Significance in Sequence Alignment
An Overview of Population Genetic Data Simulation
Maximal Acyclic Agreement Forests
The Application of the Weighted k -Partite Graph Problem to the Multiple Alignment for Metabolic Pathways
pSuc-PseRat: Predicting Lysine Succinylation in Proteins by Exploiting the Ratios of Sequence Coupling and Properties
A Construction of Pooling Designs with Some Happy Surprises
Discovering Interesting Motif-Sets for Multi-Class Protein Sequence Classification
Special Issue: Professor Michael Waterman's 80th Birthday, Part 1
Predicting Designability of Small Proteins from Graph Features of Contact Maps
Speeding Up the Structural Analysis of Metabolic Network Models Using the Fredman-Khachiyan Algorithm B
A Cluster Pattern Algorithm for the Analysis of Multiparametric Cell Assays
Translation Conditional Models for Protein Coding Sequences
Mining Subspace Clusters from DNA Microarray Data Using Large Itemset Techniques
The Integration of Genetic Maps Using Bayesian Inference
Recombination Processes and Nonlinear Markov Chains
Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop
A Provably Efficient Algorithm for the k -Mismatch Average Common Substring Problem
VTrans: A VAE-Based Pre-Trained Transformer Method for Microbiome Data Analysis
GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction
Machine-Learning Models for Multicenter Prostate Cancer Treatment Plans
Exploring the Influence of Gene Networks on Driver Gene Classification
Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model
Markov Logic Networks in the Analysis of Genetic Data
Sorting Genomes with Centromeres by Translocations
Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation
Detection and Segmentation of Glioma Tumors Utilizing a UNet Convolutional Neural Network Approach with Non-Subsampled Shearlet Transform
Recognizing Circular Decompossible Metrics
Computing Maximal Covers for Protein Sequences
Learning Gene Functional Classifications from Multiple Data Types
A Boltzmann Sampler for 1-Pairs with Double Filtration
AFMDD: Analyzing Functional Connectivity Feature of Major Depressive Disorder by Graph Neural Network-Based Model
FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions
Order of Precedence and Age of Y-DNA Haplotypes
Feature Selection by Hybrid Brain Storm Optimization Algorithm for COVID-19 Classification
MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins
RNA Instant Quality Check: Alignment-Free RNA-Degradation Detection
Robust Sample-Specific Stability Selection with Effective Error Control
Extracting Information from Gene Coexpression Networks of Rhizobium leguminosarum
EnrichVisBox: A Versatile and Powerful Web Toolbox for Visualizing Complex Functional Enrichment Results of Omics Data
A Greedy Algorithm for Aligning DNA Sequences
RDscan: A New Method for Improving Germline and Somatic Variant Calling Based on Read Depth Distribution
Identification of Repurpose Drugs by Computational Analysis of Disease-Gene-Drug Associations
QGB: A System for Querying Sequence Database Fields and Features
A Conceptual Database Model for Genomic Research
A Bayesian Network Classification Methodology for Gene Expression Data
Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling
Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss
How to Synchronize Biological Clocks
The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions
Using PQ Structures for Genomic Rearrangement Phylogeny
Structural Bistability of the GAL Regulatory Network and Characterization of its Domains of Attraction
Characterizing the Empirical Distribution of Prokaryotic Genome n -mers in the Presence of Nullomers
RASCAL: A Randomized Approach for Coevolutionary Analysis
Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data
Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype
Determining a Reasonable Range of Relative Numerical Tolerance Values for Simulating Deterministic Models of Biochemical Reactions
Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data
Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions
Computational Analysis of Gene Identification with SAGE
Transformations that Preserve Detailed Balance in Markov Models
HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking
Challenges in Integrating Biological Data Sources
Statistical Significance of Threading Scores
Enhanced Compression of k -Mer Sets with Counters via de Bruijn Graphs
Contrast Normalization of Oligonucleotide Arrays
Selected Papers from the Workshop on Computational Biology: Joint with the International Joint Conference on Artificial Intelligence and the International Conference on Machine Learning, 2018
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics
On the Parameterized Complexity of Pooling Design
A Mapper Algorithm with Implicit Intervals and Its Optimization
Privacy-Preserving Identification of Cancer Subtype-Specific Driver Genes Based on Multigenomics Data with Privatedriver
IMFLer: A Web Application for Interactive Metabolic Flux Analysis and Visualization
U 50 : A New Metric for Measuring Assembly Output Based on Non-Overlapping, Target-Specific Contigs
A Combinatorial Approach to Protein Docking with Flexible Side Chains
Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array
Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism
DNA Motif Match Statistics Without Poisson Approximation
Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem
Special Issue, Part I 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023)
Discerning Functional Connections in the Pulsed Neural Networks with the Dynamic Bayesian Network Structure Search Method Based on a Genetic Algorithm
Enhanced Interpretable Neural Network Approach for Unified Batch Effect Mitigation and Disease Classification Using Cross-Cohort Microbiome Profiles
Privacy-Preserving Statistical Analysis of Genomic Data Using Compressive Mechanism with Haar Wavelet Transform
Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-Integer Linear Programming for Metabolite Production in Constraint-Based Models: gDel_minRN
Robust E-Values for Gapped Local Alignments
Effloc: An Efficient Locating Algorithm for Mass-Occurrence Biological Patterns with FM-Index
Multi-Species Network Inference Improves Gene Regulatory Network Reconstruction for Early Embryonic Development in Drosophila
Adaptive Arithmetic Coding-Based Encoding Method Toward High-Density DNA Storage
Real-Time Gene Expression: Statistical Challenges in Design and Inference
A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k -Mer Distances
On the Relation Between Linear Autoencoders and Non-Negative Matrix Factorization for Mutational Signature Extraction
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny
Identifying the Impact of Inframe Insertions and Deletions on Protein Function in Cancer
Human Splice-Site Prediction with Deep Neural Networks
A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae
Toward a Three-Dimensional Chromosome Shape Alphabet
Michael Waterman's Contributions to Computational Biology and Bioinformatics
MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species
SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis
Exploiting Genome Structure in Association Analysis
A General Coverage Theory for Shotgun DNA Sequencing
Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump Markov Chain Monte Carlo
Performance of Threading Scoring Functions Designed Using New Optimization Method
Krylov Subspace Algorithms for Computing GeneRank for the Analysis of Microarray Data Mining
An Information Measure of the Quality of Protein Secondary Structure Prediction
Conformational Sampling Reveals Amino Acids with a Steric Influence on Specificity
Fast, Sensitive Discovery of Conserved Genome-Wide Motifs
3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data
Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets
Investigation of Potential Mechanisms Associated with Non-small Cell Lung Cancer
RESISTOR: A New OSPREY Module to Predict Resistance Mutations
MONI: A Pangenomic Index for Finding Maximal Exact Matches
Exact Algorithms for Planted Motif Problems
Approximation of Protein Structure for Fast Similarity Measures
Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology
VERSE: A Varying Effect Regression for Splicing Elements Discovery
T-Cell Epitope Prediction with Combinatorial Peptide Libraries
Mining Protein Sequences for Motifs
Markov-Modulated Markov Chains and the Covarion Process of Molecular Evolution
On Near-Optimal Alignments of Biological Sequences
A Finite Population Model of Molecular Evolution: Theory and Computation
Blind Source Separation and the Analysis of Microarray Data
A Model for Measurement Error for Gene Expression Arrays
A Mixed Polyploid Model for Linkage Analysis in Outcrossing Tetraploids Using a Pseudo-Test Backcross Design
Spline Methods for the Comparison of Physical and Genetic Maps
Finding Short DNA Motifs Using Permuted Markov Models
Transforming Rooted Agreement into Unrooted Agreement
Graph-Based Reconstruction and Analysis of Disease Transmission Networks Using Viral Genomic Data
Orthology and Paralogy Relationships at Transcript Level
Data Set-Adaptive Minimizer Order Reduces Memory Usage in k -Mer Counting
Tissue Classification with Gene Expression Profiles
BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level
A Segment-Based Dynamic Programming Algorithm for Predicting Gene Structure
Restructuring the Genome Data Base: A Model for a Federation of Biological Databases
virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2
On the Maximal Interval Subgraph of a Tree
Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes
Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory
Counting RNA Pseudoknotted Structures
Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads
Constructing and Counting Phylogenetic Invariants
GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome
A Systematic Bioinformatics Approach to Motif-Based Analysis of Human Locus Control Regions
Counting Coalescent Histories
An Algorithm for an Automatic NOE Pathways Analysis of 2D NMR Spectra of RNA Duplexes
Pairwise Alignment of Protein Interaction Networks
On Distinguishing Unique Combinations in Biological Sequences
Base Pairing Probabilities in a Complete HIV-1 RNA
The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion
cDREM: Inferring Dynamic Combinatorial Gene Regulation
ORFs and Genes: How Strong a Connection?
Species Tree Inference by the STAR Method and Its Generalizations
Prediction of Virus-Receptor Interactions Based on Improving Similarities
A Two-Level Scheme for Quality Score Compression
DNA Sequencing with Transposons
Efficient q -Gram Filters for Finding All epsilon -Matches over a Given Length
Polynomial-Time Algorithms for Building a Consensus MUL-Tree
Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes
Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs
Resolving Conflicting Predictions from Multimapping Reads
The Role of Significantly Deregulated MicroRNAs in Recurrent Cervical Cancer Based on Bioinformatic Analysis of the Cancer Genome Atlas Data
POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations
Properties of Balanced Permutations
Automatic International Classification of Diseases Coding via Note-Code Interaction Network with Denoising Mechanism
An Upper and Lower Bound for the Convergence Time of House-Hunting in Temnothorax Ant Colonies
The Insight into Protein-Ligand Interactions, a Novel Way of Buffering Protein Noise in Gene Expression
A Subgraph Problem from Restriction Maps of DNA
Estimation of Ordinary Differential Equation Models for Gene Regulatory Networks Through Data Cloning
Shift-Invariant Adaptive Double Threading: Learning MHC II-Peptide Binding
Alignment Constrained Sampling
A Viability Approach for Robustness Measurement, Organizational Autopoiesis, and Cell Turnover in a Multicellular System
A Graph Representation Approach Based on Light Gradient Boosting Machine for Predicting Drug-Disease Associations
Building Human Genome Maps with Radiation Hybrids
Learning Robust Multilabel Sample Specific Distances for Identifying HIV-1 Drug Resistance
Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data
Identification of Disease-Associated MicroRNAs Via Locality-Constrained Linear Coding-Based Ensemble Learning
Separating Significant Matches from Spurious Matches in DNA Sequences
Combining Algorithms to Find Signatures That Predict Risk in Early-Stage Stomach Cancer
Protein Engineering Study of Protein L by Simulation
Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm
A Fast and Simple Pattern Matching with Hamming Distance on Large Alphabets
Novel MicroRNA Biomarkers, miR-142-5p, miR-550a, miR-1826, and miR-1201, Were Identified for Primary Melanoma
On the Inference of Dirichlet Mixture Priors for Protein Sequence Comparison
Duplication Models for Biological Networks
Motif-Based Protein Sequence Classification Using Neural Networks
Disease Spread Model in Structurally Complex Spaces: An Open Markov Chain Approach
Separating Biological Variance from Noise by Applying Expectation-Maximization Algorithm to Modified General Linear Model
A Physical Analogy of the Genetic Toggle Switch
Inferring Transcription Factor Targets from Gene Expression Changes and Predicted Promoter Occupancy
A Novel Algorithm for Enhanced Structural Motif Matching in Proteins
cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design
The Probability of Unique Solutions of Sequencing by Hybridization
Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k-Mer Annotation
A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta
The Noncompacted Folding of Proteins by Modified Elastic Net Algorithm
MELC Genomics: A Framework for De Novo Genome Assembly
Prediction of Function in DNA Sequence
Intra-Exon Motif Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in RNA-Seq
Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression
Exceptional Motifs in Different Markov Chain Models for a Statistical Analysis of DNA Sequences
Adaptive Local Realignment of Protein Sequences
Analyzing Apomorphine-Mediated Effects in a Cell Model for Parkinson's Disease with Partial Least Squares Structure Equation Modeling
ViDis: A Platform for Constructing and Sharing of Medical Algorithms
Metrics on RNA Secondary Structures
HF-DDI: Predicting Drug-Drug Interaction Events Based on Multimodal Hybrid Fusion
Simultaneous Folding of Alternative RNA Structures with Mutual Constraints: An Application to Next-Generation Sequencing-based RNA Structure Probing
The Floor Is Lava: Halving Natural Genomes with Viaducts, Piers, and Pontoons
Detection of Copy Number Variation Regions Using the DNA-Sequencing Data from Multiple Profiles with Correlated Structure
Tracing the Most Parsimonious Indel History
Fold Recognition via a Tree
Ancestral Genome Organization: An Alignment Approach
Human MicroRNA Target Prediction via Multi-Hypotheses Learning
A Simple Linear Space Algorithm for Computing Nonoverlapping Inversion and Transposition Distance in Quadratic Average Time
A Hybrid BPSO-CGA Approach for Gene Selection and Classification of Microarray Data
On the Hardness of Sequence Alignment on De Bruijn Graphs
The Complexity of the Dirichlet Model for Multiple Alignment Data
Randomness in Cancer Breakpoint Prediction
Weighted Selection Probability to Prioritize Susceptible Rare Variants in Multi-Phenotype Association Studies with Application to a Soybean Genetic Data Set
Microarray Analysis for Differentially Expressed Genes Between Stromal and Epithelial Cells in Development and Metastasis of Invasive Breast Cancer
A System Architecture for Efficient Transmission of Massive DNA Sequencing Data
Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function
Finding Anchors for Genomic Sequence Comparison
Drug-Target Interaction Network Analysis of Gene-Phenotype Connectivity Maintained by Genistein
Sure Joint Screening for High Dimensional Cox's Proportional Hazards Model Under the Case-Cohort Design
Labeled Cycle Graph for Transposition and Indel Distance
Positivity and Boundedness Preserving Numerical Scheme for a Stochastic Multigroup Susceptible-Infected-Recovering Epidemic Model with Age Structure
Comprehensive Analysis of Core Genes and Potential Mechanisms in Rectal Cancer
Preface: Special Issue
An Efficient Computational Method for Globally Optimal Threading
Biological Network Querying Techniques: Analysis and Comparison
The Distribution of Word Matches Between Markovian Sequences with Periodic Boundary Conditions
Preface: Selected Articles of the Second International Conference on Algorithms for Computational Biology (AlCoB 2015)
Assessing the Exceptionality of Network Motifs
Alignment-Free Sequence Comparison (I): Statistics and Power
Identification and Classification Problems on Pooling Designs for Inhibitor Models
Toward a Better Compression for DNA Sequences Using Huffman Encoding
Towards Integration of Multiple Alignment and Phylogenetic Tree Construction
Preface: Special RECOMB 2004 Issue
A New ℓ0-Regularized Log-Linear Poisson Graphical Model with Applications to RNA Sequencing Data
Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in Java Library
Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models
MixProTool: A Powerful and Comprehensive Web Tool for Analyzing and Visualizing Multigroup Proteomics Data
Algorithm for Haplotype Inference via Galled-Tree Networks with Simple Galls
Inference from Clustering with Application to Gene-Expression Microarrays
The Mutation Process of Microsatellites During the Polymerase Chain Reaction
Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming