yusuke1997/dblp-id-title huggingface dataset:
Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs
Recognition and Classification of Histones Using Support Vector Machine
A Nonhomogeneous Hidden Markov Model for Gene Mapping Based on Next-Generation Sequencing Data
The scINSIGHT Package for Integrating Single-Cell RNA-Seq Data from Different Biological Conditions
Coordinated DNA Methylation and Gene Expression Data for Identification of the Critical Genes Associated with Childhood Atopic Asthma
Predict Collagen Hydroxyproline Sites Using Support Vector Machines
GS-TCGA: Gene Set-Based Analysis of The Cancer Genome Atlas
Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs
Visual Recalibration and Gating Enhancement Network for Radiology Report Generation
Boolean Network Models of Human Preimplantation Development
Nearly Instantaneous Time-Varying Reproduction Number for Contagious Diseases - a Direct Approach Based on Nonlinear Regression
A Multiresolution Graphical Representation for Similarity Relationship and Multiresolution Clustering for Biological Sequences
Accurate Stochastic Simulation via the Step Anticipation τ -Leaping (SAL) Algorithm
Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network
Effect of Protein Repetitiveness on Protein-Protein Interaction Prediction Results Using Support Vector Machines
GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics
ComB: SNP Calling and Mapping Analysis for Color and Nucleotide Space Platforms
Methylation Signature Genes Identification of the Lung Squamous Cell Carcinoma Occurrence and Recognition Research
An Ultrafast Tool for Minimum Reticulate Networks
Anti-Cooperative and Cooperative Protein-Protein Interactions between TetR Isoforms on Synthetic Enhancers
Sequence Alignment as Hypothesis Testing
Decoy Database Improvement for Protein Folding
Efficient Simulation and Likelihood Methods for Non-Neutral Multi-Allele Models
Compound Poisson Approximation and Testing for Gene Clusters with Multigene Families
Bifurcations and Homoclinic Orbits of a Model Consisting of Vegetation-Prey-Predator Populations
Towards an Integrated Protein-Protein Interaction Network: A Relational Markov Network Approach
Estimating Genetic Similarity Matrices Using Phylogenies
Simultaneous Model Selection and Model Calibration for the Proliferation of Tumor and Normal Cells During In Vitro Chemotherapy Experiments
Probabilistic Assessment of Clone Overlaps in DNA Fingerprint Mapping via a Priori Models
Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs
Method for Calculation of Probability of Matching a Bounded Regular Expression in a Random Data String
Informational Requirements for Transcriptional Regulation
DCJ Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications
QGB: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification
EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein-Ligand Docking
Special Issue, Part 2 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023)
Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides
Validation of S. Pombe Sequence Assembly by Microarray Hybridization
Estimating Haplotype Structure and Frequencies: A Bayesian Approach to Unknown Design in Pooled Genomic Data
ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer
Incremental Paradigms of Motif Discovery
Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model
Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion
Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme
FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases
An Approximation Algorithm for Haplotype Inference by Maximum Parsimony
Studying the Evolution of Promoter Sequences: A Waiting Time Problem
Efficient Algorithms for Counting and Reporting Segregating Sites in Genomic Sequences
Counterfactual Debiased Co-Embedding Model for Enhanced Drug-Drug Interaction Prediction
A Dynamic Programming Algorithm For (1, 2)-Exemplar Breakpoint Distance
PDFll: Predictors of Disorder and Function of Proteins from the Language of Life
Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach
Reducing the Computational Complexity of Information Theoretic Approaches for Reconstructing Gene Regulatory Networks
A Preprocessor for Shotgun Assembly of Large Genomes
Efficient Modeling and Simulation of Space-Dependent Biological Systems
Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data
A Novel Genome-Information Content-Based Statistic for Genome-Wide Association Analysis Designed for Next-Generation Sequencing Data
Construction of Novel DNA Methylation-Based Prognostic Model to Predict Survival in Glioblastoma
Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach
Sequencing Potential of Nested Strand Hybridization
The k -Robinson-Foulds Dissimilarity Measures for Comparison of Labeled Trees
Compound Poisson and Poisson Process Approximations for Occurrences of Multiple Words in Markov Chains
A Linearized Constraint-Based Approach for Modeling Signaling Networks
Detailed Analysis of Molecular Mechanisms in Primary and Metastatic Melanoma
Predicting Physiological Concentrations of Metabolites from Their Molecular Structure
Retraction of: Identification of Prognosis Biomarkers of Prostatic Cancer in a Cohort of 498 Patients from TCGA, by Chen Z, Hu H. (J Comput Biol Dec 2019: epub ahead of print; DOI: 10.1089/cmb.2019.0224)
Identification of New Clusters from Labeled Data Using Mixture Models
The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees
Computing the Stochastic Dynamics of Phosphorylation Networks
Sequence Alignment with an Appropriate Substitution Matrix
Encoding and Decoding DNA Sequences by Integer Chaos Game Representation
A Comparative Study of Single-Trait and Multi-Trait Genomic Selection
The Application of 3D Zernike Moments for the Description of "Model-Free" Molecular Structure, Functional Motion, and Structural Reliability
Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW)
Identification of Differentially Expressed Genes Associated with Lymph Node Tuberculosis by the Bioinformatic Analysis Based on a Microarray
Identifying Contributors of DNA Mixtures by Means of Quantitative Information of STR Typing
MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets
Reducing Alignment Time Complexity of Ultra-Large Sets of Sequences
EMINIM: An Adaptive and Memory-Efficient Algorithm for Genotype Imputation
In Silico Characterization of B Cell and T Cell Epitopes for Subunit Vaccine Design of Salmonella typhi PgtE: A Molecular Dynamics Simulation Approach
Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment
The Distribution of Genomic Distance between Random Genomes
Interaction Relation Ontology Learning
Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads
The Average Common Substring Approach to Phylogenomic Reconstruction
DeepPPThermo: A Deep Learning Framework for Predicting Protein Thermostability Combining Protein-Level and Amino Acid-Level Features
Identification of Selective Inhibitors of LdDHFR Enzyme Using Pharmacoinformatic Methods
Multiplex Sequencing by Hybridization
Principal Component Analysis of Binding Energies for Single-Point Mutants of hT2R16 Bound to an Agonist Correlate with Experimental Mutant Cell Response
Identification of Key Biomarkers and Potential Molecular Mechanisms in Renal Cell Carcinoma by Bioinformatics Analysis
The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy
Flexible Modeling of Genetic Effects on Function-Valued Traits
Pooling Strategies for Establishing Physical Genome Maps Using FISH
Scaled Alternating Steepest Descent Algorithm Applied for Protein Structure Determination from Nuclear Magnetic Resonance Data
Generative Adversarial Networks for Neuroimage Translation
Better ILP-Based Approaches to Haplotype Assembly
Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution
Computational Quantification of Peptides from LC-MS Data
LB3D: A Protein Three-Dimensional Substructure Search Program Based on the Lower Bound of a Root Mean Square Deviation Value
Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique DNA Methylation and Gene Expression Profiles
Finding Nearly Optimal GDT Scores
Evolutionary Switches Structural Transitions via Coarse-Grained Models
MASTtreedist: Visualization of Tree Space Based on Maximum Agreement Subtree
Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement
Editorial: Whither Computational Biology
Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models
Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications
Maximum Likelihood Molecular Clock Comb: Analytic Solutions
How Homologs Can Help to Predict Protein Folds Even Though They Cannot Be Predicted for Individual Sequences
Rank-Similarity Measures for Comparing Gene Prioritizations: A Case Study in Autism
Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference
Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models
Closed-Loop Learning Control of Bio-Networks
The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences
A Spatial Haplotype Copying Model with Applications to Genotype Imputation
The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins
iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees
Balancing the Robustness and Predictive Performance of Biomarkers
Computing the Probability of RNA Hairpin and Multiloop Formation
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
Energy Consumption and Entropy Production in a Stochastic Formulation of BCM Learning
Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands
Gene Regulatory Networks Governing the Generation and Regeneration of Blood
DNA Library Design for Molecular Computation
Gene Team Tree: A Hierarchical Representation of Gene Teams for All Gap Lengths
Ligand-Receptor Pairing Via Tree Comparison
Fast Geometric Consensus Approach for Protein Model Quality Assessment
Prediction of Microbe-Disease Associations by Graph Regularized Non-Negative Matrix Factorization
MoCha: Molecular Characterization of Unknown Pathways
Deactivation of Src Family Kinases: Hypothesis Testing Using a Monte Carlo Sensitivity Analysis of Systems-Level Properties
The Importance of Age and High Degree, in Protein-Protein Interaction Networks
Elucidating Influenza Inhibition Pathways via Network Reconstruction
The Poisson Margin Test for Normalization-Free Significance Analysis of NGS Data
Rapid Significance Estimation in Local Sequence Alignment with Gaps
New Probabilistic Network Models and Algorithms for Oncogenesis
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: I. Theory
Generating Programs for Predicting the Activity of Functional Sites
Correlation Imputation for Single-Cell RNA-seq
Approximate P-Values for Local Sequence Alignments: Numerical Studies
A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility
Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue
DBCAT: Database of CpG Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells
Using Traditional and Deep Machine Learning to Predict Emergency Room Triage Levels
Prioritize and Select SNPs for Association Studies with Multi-Stage Designs
SATrans: New Free Available Software for Annotation of Transcriptome and Functional Analysis of Differentially Expressed Genes
A Bayesian Nonparametric Approach for Comparing Clustering Structures in EST Libraries
RN + : A Novel Biclustering Algorithm for Analysis of Gene Expression Data Using Protein-Protein Interaction Network
Variant-Kudu: An Efficient Tool kit Leveraging Distributed Bitmap Index for Analysis of Massive Genetic Variation Datasets
Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination
A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses
A Generalized Linear Model for Peak Calling in ChIP-Seq Data
Conjugate Gibbs Sampling for Bayesian Phylogenetic Models
Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments
Topological Signatures of Species Interactions in Metabolic Networks
On the Reduction of Errors in DNA Computation
Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes
Mutation-Replication Statistics of Polymerase Chain Reactions
A Sharp Error Probability Estimate for the Reconstruction of Phylogenetic Quartets by the Four-Point Method
Topology of RNA-RNA Interaction Structures
Algorithms for Optical Mapping
A Portable Search Engine and Browser for the Entrez DataBase
Small-World Networks and RNA Secondary Structures
Correcting BLAST e-Values for Low-Complexity Segments
Haplotype Inferring via Galled-Tree Networks Is NP-Complete
Thiamine Pyrophosphate Riboswitch in Some Representative Plant Species: A Bioinformatics Study
Bayesian Models and Markov Chain Monte Carlo Methods for Protein Motifs with the Secondary Characteristics
Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes
Code Optimization of the Subroutine to Remove Near Identical Matches in the Sequence Database Homology Search Tool PSI-BLAST
Learned Random-Walk Kernels and Empirical-Map Kernels for Protein Sequence Classification
flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning
Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data
Predicting CNS Permeability of Drug Molecules: Comparison of Neural Network and Support Vector Machine Algorithms
Statistical Methods for Microbiome Compositional Data Network Inference: A Survey
A Uniform Framework for Ordered Restriction Map Problems
Computational Performance Assessment of k-mer Counting Algorithms
Pairwide and Multiple Identification of Three-Dimensional Common Substructures in Proteins
Fast Algorithms for the Simplified Partial Digest Problem
A New Heuristic Algorithm for Protein Folding in the HP Model
REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results
Boolean Network Approach to Negative Feedback Loops of the p53 Pathways: Synchronized Dynamics and Stochastic Limit Cycles
A Multiple-Instance Learning-Based Convolutional Neural Network Model to Detect the IDH1 Mutation in the Histopathology Images of Glioma Tissues
Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018)
Probability of Autocrine Ligand Capture by Cell-Surface Receptors: Implications for Ligand Secretion Measurements
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem
XVir: A Transformer-Based Architecture for Identifying Viral Reads from Cancer Samples
A Space-Efficient Construction of the Burrows-Wheeler Transform for Genomic Data
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples
From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering
Analyzing Protein Lists with Large Networks: Edge-Count Probabilities in Random Graphs with Given Expected Degrees
Revealing Biological Modules via Graph Summarization
Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method
Mining the Biomedical Literature in the Genomic Era: An Overview
Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline
RECOMB-Comparative Genomics Special Issue
Target Specificity of the CRISPR-Cas9 System in Arabidopsis thaliana, Oryza sativa, and Glycine max Genomes
A Bayesian Network-Based Approach to Selection of Intervention Points in the Mitogen-Activated Protein Kinase Plant Defense Response Pathway
Grammatical Representations of Macromolecular Structure
Sequencing by Hybridization by Cooperating Direct and Reverse Spectra
Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs
A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification
Conditional Graphical Models for Protein Structural Motif Recognition
Preface to the Special Issue: Parallel Computing in Computational Biology: A Technological Point of View
NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins
Torsional Relaxation for Biopolymers
Identification of Biomarkers Related to Systemic Sclerosis With or Without Pulmonary Hypertension Using Co-expression Analysis
Multimodal Genotype and Phenotype Data Integration to Improve Partial Data-Based Longitudinal Prediction
Constructing Double Cyclic Codes over F2+uF2 for DNA Codes
Toward the Quantitative Prediction of T-Cell Epitopes: QSAR Studies on Peptides Having Affinity with the Class I MHC Molecular HLA-A * 0201
Subset Quantile Normalization Using Negative Control Features
Smoothing 3D Protein Structure Motifs Through Graph Mining and Amino Acid Similarities
EPTool: A New Enhancing PSSM Tool for Protein Secondary Structure Prediction
Protein Folding in the Hydrophobic-Hydrophilic(HP) Model is NP-Complete
Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes
kmer2vec: A Novel Method for Comparing DNA Sequences by word2vec Embedding
Non-Random Mating Involving Inheritance of Social Status
Disambiguating a Soft Metagenomic Clustering
A Dictionary-Based Approach for Gene Annotation
Multi-View Enhanced Tensor Nuclear Norm and Local Constraint Model for Cancer Clustering and Feature Gene Selection
An Efficient Voting Algorithm for Finding Additive Biclusters with Random Background
Probabilistic Approach for Determining the Material Properties of Meniscal Attachments In Vivo Using Magnetic Resonance Imaging and a Finite Element Model
Universal DNA Tag Systems: A Combinatorial Design Scheme
Bayesian Estimation of the Number of Inversions in the History of Two Chromosomes
Locality and Gaps in RNA Comparison
Extracting Genes Involved in Disease from a Connected Network of Perturbed Biological Processes
GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data
Joker de Bruijn: Covering k -Mers Using Joker Characters
All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State
Sorting by Reciprocal Translocations via Reversals Theory
Modeling DNA Shuffling
Stochastic Telomere Shortening and the Route to Limitless Replicative Potential
In Silico Identification of Potential Inhibitors of the Wnt Signaling Pathway in Human Breast Cancer
Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes
Over- and Underrepresentation of Short DNA Words in Herpesvirus Genomes
Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction
Alignment with Context Dependent Scoring Function
A Canonical Correlation Analysis-Based Dynamic Bayesian Network Prior to Infer Gene Regulatory Networks from Multiple Types of Biological Data
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data
Significance of Interspecies Matches when Evolutionary Rate Varies
Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices
An Algorithm for Detecting High Frequency Copy Number Polymorphisms Using SNP Arrays
Designing Sensitive and Specific Spaced Seeds for Cross-Species mRNA-to-Genome Alignment
Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time
From a Phylogenetic Tree to a Reticulated Network
Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters
Four Strikes Against Physical Mapping of DNA
Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants
Parameter Identifiability for a Profile Mixture Model of Protein Evolution
Growing Directed Acyclic Graphs: Optimization Functions for Pathway Reconstruction Algorithms
An Integration Framework of Secure Multiparty Computation and Deep Neural Network for Improving Drug-Drug Interaction Predictions
GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants
PaTre: A Method for Paralogy Trees Construction
Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals
Phylogenetic Invariants for Genome Rearrangements
Space of Gene/Species Trees Reconciliations and Parsimonious Models
Detecting and Classifying Nuclei Using Multi-Scale Fully Convolutional Network
Identification of Genes Involved in Breast Cancer Metastasis by Integrating Protein-Protein Interaction Information with Expression Data
A New Method for Quantitative Real-Time Polymerase Chain Reaction Data Analysis
A New Method Based on Coding Sequence Density to Cluster Bacteria
RECOMB Satellite Conference on Comparative Genomics(RECOMB-CG 2023)
Robustness Assessment of Whole Bacterial Genome Segmentations
Estimation of Dynamic Systems for Gene Regulatory Networks from Dependent Time-Course Data
Finding Highly Similar Regions of Genomic Sequences Through Homomorphic Encryption
Determining the Transcription Rates Yielding Steady-State Production of mRNA in the Lac Genetic Switch of Escherichia coli
Improved Denoising of Cryo-Electron Microscopy Micrographs with Simulation-Aware Pretraining
EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments
Toward Simplifying and Accurately Formulating Fragment Assembly
A New Software Package for Predictive Gene Regulatory Network Modeling and Redesign
Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data
Narratives in the Network: Interactive Methods for Mining Cell Signaling Networks
Graph Data Augmentation for Graph Convolutional Networks Learning in Robust Mental Disorder Prediction with Limited and Noisy Labels
Multi-Node Graphs: A Framework for Multiplexed Biological Assays
Local Decoding of Sequences and Alignment-Free Comparison
Substitution Matrices of Residue Triplets Derived from Protein Blocks
A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space
HAPLOFREQ-Estimating Haplotype Frequencies Efficiently
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape
Genome Phylogeny Based on Short-Range Correlations in DNA Sequences
Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure
Fast and Accurate Calculation of a Computationally Intensive Statistic for Mapping Disease Genes
Analyzing Tumor Heterogeneity by Incorporating Long-Range Mutational Influences and Multiple Sample Data into Heterogeneity Factorial Hidden Markov Model
Special Issue Preface: The 9th Computational Structural Bioinformatics Workshop
Special Issue, Part I 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022)