yusuke1997/dblp-id-title huggingface dataset:
Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks
The Probability of Joint Monophyly of Samples of Gene Lineages for All Species in an Arbitrary Species Tree
CerviNet: A Novel Approach for Cervical Cancer Classification Using Pap-Smear Images
Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions
RNA Pseudoknot Prediction in Energy-Based Models
Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer
GBA Manager: An Online Tool for Querying Low-Complexity Regions in Proteins
Corrigendum to: CerviNet: A Novel Approach for Cervical Cancer Classification Using Pap-Smear Images
Hitch-Hiking: A Parallel Heuristic Search Strategy, Applied to the Phylogeny Problem
Identifying Satellites and Periodic Repetitions in Biological Sequences
Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for Short-Read DNA Sequences
GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks
In Memoriam: Eugene L. Lawler
Deconvolving Sequence Variation in Mixed DNA Populations
Space-Efficient Whole Genome Comparisons with BurrowsWheeler Transforms
Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties
Singular Value Decomposition-Based Penalized Multinomial Regression for Classifying Imbalanced Medulloblastoma Subgroups Using Methylation Data
Scale-Free Spanning Trees and Their Application in Genomic Epidemiology
The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution
Screening of Severe Acute Respiratory Syndrome Coronavirus 2 RNA-Dependent RNA Polymerase Inhibitors Using Computational Approach
Inference of Haplotypes from Samples of Diploid Populations: Complexity and Algorithms
A Probabilistic Model of Neutral and Selective Dynamics of Protein Network Evolution
Selected Papers from RECOMB'97 - Preface
CRDet: Improving Signet Ring Cell Detection by Reinforcing the Classification Branch
Viral Capsid Assembly: A Quantified Uncertainty Approach
Fast and Accurate Algorithms for Mapping and Aligning Long Reads
Preface: Research in Computational Molecular Biology (RECOMB 2011)
Integrated Analysis of the Gene Expression Changes During Colorectal Cancer Progression by Bioinformatic Methods
Relationship Information Contained in Gamete Identiti by Descent Data
Discovering High-Order Patterns of Gene Expression Levels
DNA Methylation Heterogeneity Induced by Collaborations Between Enhancers
Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays
Designing an A* Algorithm for Calculating Edit Distance between Rooted-Unordered Trees
Integrated Survival Analysis of mRNA and microRNA Signature of Patients with Breast Cancer Based on Cox Model
Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix
Hidden Markov Models of the G-Protein-Coupled Receptor Family
A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient
Mathematical Modeling for Functional Divergence after Gene Duplication
Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules
Biogeography-Based Multi-Objective Discrete Optimization with Constraints
A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses
Metagenomic Classification Using an Abstraction Augmented Markov Model
Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming
An Integer Linear Programming Model to Optimize Coding DNA Sequences By Joint Control of Transcript Indicators
Multiple Genome Rearrangement and Breakpoint Phylogeny
Distinguishing Features of 16S rDNA Gene for Five Dominating Bacterial Genus Observed in Bioremediation
Automatic 3D Protein Structure Classification without Structural Alignment
Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression
Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing
Prognostic Markers Identification in Glioma by Gene Expression Profile Analysis
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs
Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification (TAP) Data
Preface: 2 nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010)
Stochastic Transcriptional Regulatory Systems with Time Delays: A Mean-Field Approximation
SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport
Compressed Sensing Methods for DNA Microarrays, RNA Interference, and Metagenomics
A de Bruijn Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community
Agreement in Spiking Neural Networks
Everyone Is a Protagonist: Residue Conformational Preferences in High-Resolution Protein Structures
The 7th Computational Structural Bioinformatics Workshop
NPI-DCGNN: An Accurate Tool for Identifying ncRNA-Protein Interactions Using a Dual-Channel Graph Neural Network
Logic Integer Programming Models for Signaling Networks
Protein-Protein Interaction Prediction Model Based on ProtBert-BiGRU-Attention
Gapped Permutation Pattern Discovery for Gene Order Comparisons
On Contigs and Coverage
Analysis of the Physicochemical Properties of Acaricides Based on Lipinski's Rule of Five
Comprehensive Analysis Identifying Wnt Ligands Gene Family for Biochemical Recurrence in Prostate Adenocarcinoma and Construction of a Nomogram
Are the Duplication Cost and Robinson-Foulds Distance Equivalent?
Comparing Pedigree Graphs
A Wavelet Approach to Detect Enriched Regions and Explore Epigenomic Landscapes
Interpretation of Pooling Experiments Using the Markov Chain Monte Carlo Method
A Poisson Log-Normal Model for Constructing Gene Covariation Network Using RNA-seq Data
A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality
Epigenetic Hypothesis Tests for Methylation and Acetylation in a Triple Microarray System
Screening and Identification of Key Biomarkers in Pancreatic Cancer: Evidence from Bioinformatic Analysis
Predictive Estimates of Risks Associated with Type 2 Diabetes Mellitus on the Basis of Biochemical Biomarkers and Derived Time-Dependent Parameters
Pfeature: A Tool for Computing Wide Range of Protein Features and Building Prediction Models
A Bayesian Change Point Model for Dynamic Alternative Transcription Start Site Usage During Cellular Differentiation
The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models
A Theoretical Model for Whole Genome Alignment
Describing the Complexity of Systems: Multivariable "Set Complexity" and the Information Basis of Systems Biology
Consensus Tree Under the Ancestor-Descendant Distance is NP-Hard
An Integrated Probabilistic Model for Functional Prediction of Proteins
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads
A Robust Method for Transcript Quantification with RNA-Seq Data
The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods
Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity
An Iterative Algorithm for Correcting Sequencing Errors in DNA Coding Regions
Multigranularity Label Prediction Model for Automatic International Classification of Diseases Coding in Clinical Text
Aligning Protein Sequences with Predicted Secondary Structure
Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks
Preface: Special RECOMB 2000 Issue
ProCanBio: A Database of Manually Curated Biomarkers for Prostate Cancer
Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements
Counting Distinguishable RNA Secondary Structures
Cuckoo Search-Based Optimization for Cancer Classification: A New Hybrid Approach
Impact of Microarray Preprocessing Techniques in Unraveling Biological Pathways
On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction
FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters
Bayesian Blind Source Separation for Data with Network Structure
Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics
Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels
Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values
Efficient Exact p-Value Computation for Small Sample, Sparse, and Surprising Categorical Data
An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile
Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases
De Novo Prediction of Drug-Target Interactions Using Laplacian Regularized Schatten p-Norm Minimization
MetaMLP: A Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples
Modeling and Analysis of Protein Design under Resource Constraints
A Comprehensive Repertoire of Transfer RNA-Derived Fragments and Their Regulatory Networks in Colorectal Cancer
GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery
The Subsequence Composition of Polypeptides
Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models
DrIVeNN: Drug Interaction Vectors Neural Network
Leveraging an Image-Enhanced Cross-Modal Fusion Network for Radiology Report Generation
ISFMDA: Learning Interactions of Selected Features-Based Method for Predicting Potential MicroRNA-Disease Associations
Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements
High-Accuracy Positivity-Preserving Finite Difference Approximations of the Chemotaxis Model for Tumor Invasion
A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression
An Empirical Bayesian Significance Test of cDNA Library Data
Discriminative Motifs
HyperDiffuseNet: A Deep Hyperbolic Manifold Learning Method for Dimensionality Reduction in Spatial Transcriptomics
Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference
Special Issue: Selected Papers of the Inaugural DahShu Data Science Symposium: Computational Precision Health (CPH 2017)
Haplotype Reconstruction in Large Pedigrees with Untyped Individuals through IBD Inference
Biclustering Sparse Binary Genomic Data
Bioinformatic Analysis Suggests That Three Hub Genes May Be a Vital Prognostic Biomarker in Pancreatic Ductal Adenocarcinoma
Algorithms for Colinear Chaining with Overlaps and Gap Costs
R2KS: A Novel Measure for Comparing Gene Expression Based on Ranked Gene Lists
Reconstructing Ancestral Haplotypes with a Dictionary Model
Recovering Independent Associations in Genetics: A Comparison
The URMS-RMS Hybrid Algorithm for Fast and Sensitive Local Protein Structure Alignment
Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences
Improving Predicition of Protein Secondary Structure Using Structured Neural Networks and Multiple Sequence Alignments
Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge
Superbubbles, Ultrabubbles, and Cacti
A Mathematical Model for Peptide Inhibitor Design
A Transfer Learning-Based Classification Model for Particle Pruning in Cryo-Electron Microscopy
Computation of Repetitions and Regularities of Biologically Weighted Sequences
Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis -Regulatory Code
Sc-TUSV-Ext: Single-Cell Clonal Lineage Inference from Single Nucleotide Variants, Copy Number Alterations, and Structural Variants
Cloud-based MOTIFSIM: Detecting Similarity in Large DNA Motif Data Sets
Identifying Gene Clusters within Localized Regions in Multiple Genomes
Genomics via Optical Mapping II: Ordered Restriction Maps
A Paradigm for Class Prediction Using Gene Expression Profiles
Sequential Integration of Fuzzy Clustering and Expectation Maximization for Transcription Factor Binding Site Identification
Large-Scale Simulations of Bacterial Populations Over Complex Networks
EnsMOD: A Software Program for Omics Sample Outlier Detection
The Loss in Power When the Test of Differential Expression Is Performed under a Wrong Scale
Validation of a Mathematical Model of Gene Transcription in Aggregated Cellular Systems: Application to L1 Retrotransposition
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm
Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs
Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs
Bayesian Haplotype Inference via the Dirichlet Process
ApoE Modifier Alleles for Alzheimer's Disease Discovered by Information Theory Dependency Measures: MIST Software Package
A Innovative Strategy for Identifying Subtypes Through the Analysis of Multi-Omics Data with Adversarial Autoencoders
Progressive Multiple Alignment with Constraints
Stochastic Analysis for the Dual Virus Parallel Transmission Model with Immunity Delay
A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry
Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning
Network-Induced Classification Kernels for Gene Expression Profile Analysis
An Overview on the Distribution of Word Counts in Markov Chains
Translator: A Trans fer L earning Approach to Facilitate Single-Cell AT AC-Seq Data Analysis fr o m R eference Dataset
Finding Intron/Exon Splice Junctions Using INFO, Interruption Finder and Organizer
Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites
The MicroRNA Landscapes Profiling Reveals Potential Signatures of Necrotizing Enterocolitis in Infants
GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif
Winnowing Sequences from a Database Search
Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space
Graphlet Kernels for Prediction of Functional Residues in Protein Structures
Haplotype Reconstruction from SNP Alignment
A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes
Reconstructing Ancestral Autosomal Arrangements in the Anopheles gambiae Complex
Screening of Clinical Factors Related to Prognosis of Breast Cancer Based on the Cox Proportional Risk Model
Inverse Protein Folding in 3D Hexagonal Prism Lattice under HPC Model
Computational Methods for a Class of Network Models
Combinatorial Properties of RNA Secondary Structures
A Weighted Multipath Measurement Based on Gene Ontology for Estimating Gene Products Similarity
Exploration of the Differentially Expressed Long Noncoding RNAs and Genes of Morphine Tolerance via Bioinformatic Analysis
Robustness of Inference of Haplotype Block Structure
Towards Optimally Multiplexed Applications of Universal Arrays
Classification of Metaphase Chromosomes Using Deep Convolutional Neural Network
Parallel Computing of Physical Maps--A Comparative Study in SIMD and MIMD Parallelism
Handling Long Targets and Errors in Sequencing by Hybridization
An Earth Mover's Distance-Based Self-Supervised Framework for Cellular Dynamic Grading in Live-Cell Imaging
Identification of a Novel Scaffold for Inhibition of Dipeptidyl Peptidase-4
On the Complexity of Sequence-to-Graph Alignment
T-GOWler: Discovering Generalized Process Models Within Texts
Survival Prediction and Gene Identification with Penalized Global AUC Maximization
Integrating Biological Knowledge with Gene Expression Profiles for Survival Prediction of Cancer
17th International Symposium on Bioinformatics Research and Applications (ISBRA 2021)
Maximum Discrimination Hidden Markov Models of Sequence Consensus
Physical Mapping by STS Hybridization: Algorithmic Strategies and the Challenge of Software Evaluation
An Exact Matching Method for 16S rRNA Taxonomy Classification
Improved Practical Algorithms for Rooted Subtree Prune and Regraft (rSPR) Distance and Hybridization Number
Computing Knock-Out Strategies in Metabolic Networks
The Mitochondrial Protein Atlas: A Database of Experimentally Verified Information on the Human Mitochondrial Proteome
Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance
Optimizing Exact Genetic Linkage Computations
A Strategy for Database Interoperation
Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data
Characterization of Complex Biological Systems by Matrix Invariants
Improved Background Correction for Spotted DNA Microarrays
A Discrete-Event Approach to Transcription Control with Dynamic Event-Controllability
Retraction of: A Study of Potential SARS-CoV-2 Antiviral Drugs and Preliminary Research of Their Molecular Mechanism, Based on Anti-SARS-CoV Drug Screening and Molecular Dynamics Simulation (doi: 10.1089/cmb.2020.0112)
Large Local Analysis of the Unaligned Genome and Its Application
Pre-Processing Optimization of RNA Immunoprecipitation Microarray Data
Extracting Mutant-Affected Protein-Protein Interactions via Gaussian-Enhanced Representation and Contrastive Learning
Identifying Conserved Gene Clusters in the Presence of Homology Families
Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles
Storage and Retrieval of Highly Repetitive Sequence Collections
D3GB: An Interactive Genome Browser for R, Python, and WordPress
An Effective Method for Detecting Gene Conversion Events in Whole Genomes
Optimizing PCR Assays for DNA-Based Cancer Diagnostics
A Gene Selection Method Considering Measurement Errors
Dimensionality Reduction of Single-Cell RNA Sequencing Data by Combining Entropy and Denoising AutoEncoder
Stability of Characters and Construction of Phylogenetic Trees
A Reversible Jump Markov Chain Monte Carlo Algorithm for Bacterial Promoter Motifs Discovery
Easy Identification of Generalized Common and Conserved Nested Intervals
Correction: Journal of Computational Biology: 2014; 21/4: 303-319
Preface: Selected Papers from the Workshop Bioinformatics and Artificial Intelligence Joined with the International Joint Conference on Artificial Intelligence
Identification of Cancer Driver Modules Based on Graph Clustering from Multiomics Data
Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana : A Compound Distribution Approach
IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction
Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment
Tumor Mutation Burden Computation in Two Pan-Cancer Precision Medicine Next-Generation Sequencing Panels
On Combinatorial DNA Word Design
Essential Protein Prediction Based on node2vec and XGBoost
Using Motion Planning to Study RNA Folding Kinetics
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data
Identification of Potential Gene Signatures Related to Sleep Deprivation
The 2nd International Workshop on Pattern Recognition in Healthcare Analytics 2023 Preface
fjoin: Simple and Efficient Computation of Feature Overlaps
Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation
Biomarker Discovery Using Statistically Significant Gene Sets
Comparison of Additive Trees Using Circular Orders
Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm
Explainable Deep Learning for Augmentation of Small RNA Expression Profiles
A Protein Class Database Organized with ProSite Protein Groups and PIR Superfamilies
Is there Room for Ethics within Bioinformatics Education?
Quick, Practical Selection of Effective Seeds for Homology Search
A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment
A Novel Method to Predict Highly Expressed Genes Based on Radius Clustering and Relative Synonymous Codon Usage
Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal
How Scale-Free Are Biological Networks
On the Complexity of Multiple Sequence Alignment
A Curated Target Gene Pool Assisting Early Disease Prediction and Patient-Specific Treatment for Small Cell Lung Cancer
RIBRA - An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem
Constructing Aligned Sequence Blocks
CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships
A Bayesian Model for Detecting Past Recombination Events in DNA Multiple Alignments
Considering Unknown Unknowns: Reconstruction of Nonconfoundable Causal Relations in Biological Networks
Curcumin-Synthetic Analogs Library Screening by Docking and Quantitative Structure-Activity Relationship Studies for AXL Tyrosine Kinase Inhibition in Cancers
Symbolic Data Analysis to Defy Low Signal-to-Noise Ratio in Microarray Data for Breast Cancer Prognosis
A Computational Approach to Studying Protein Folding Problems Considering the Crucial Role of the Intracellular Environment
An Integrative Approach for Identifying Network Biomarkers of Breast Cancer Subtypes Using Genomic, Interactomic, and Transcriptomic Data
A Flow Procedure for Linearization of Genome Sequence Graphs
Scalable Species Tree Inference with External Constraints
Maximum Parsimony, Substitution Model, and Probability Phylogenetic Trees
Principal Component Analysis and Large-Scale Correlations in Non-Coding Sequences of Human DNA
Method for Identifying Cancer-Related Genes Using Gene Similarity-Based Collaborative Filtering
Probabilistic Learning in Immune Network: Weighted Tree Matching Model
A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies
A Simple Iterative Approach to Parameter Optimization
Efficient Design of Compact Unstructured RNA Libraries Covering All k -mers
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations
Sparse Inverse Covariance Estimation with L 0 Penalty for Network Construction with Omics Data
A Dynamic Scale-Free Network Particle Swarm Optimization for Extracting Features on Multi-Omics Data
Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs
Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
RECOMB 2020 Special Issue
On the Dynamics of HIV-Tuberculosis Coinfection Model with Temporal Recovery from Tuberculosis: An Analysis
Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays
Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing
GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis
Descendants of Whole Genome Duplication within Gene Order Phylogeny
The Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions
SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding
Use of DFT Distance Metrics for Classification of SARS-CoV-2 Genomes
Robust Optimal Metabolic Factories
Quantitative Model for Binary Measurements of Protein-Protein Interactions
An Exhaustive Scan Method for SNP Main Effects and SNP × SNP Interactions Over Highly Homozygous Genomes
CNB-MAC 2023 Special Issue
Maximum Likelihood Genome Assembly
Group Testing to Annihilate Pairs Applied to DNA Cross-Hybridization Elimination Using SYBR Green I