yusuke1997/dblp-id-title huggingface dataset:
Gene Team Tree: A Compact Representation of All Gene Teams
Obtaining highly accurate topology estimates of evolutionary trees from very short sequences
Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer
Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure
Finding Maximum Colorful Subtrees in Practice
Probabilistic Paths for Protein Complex Inference
Pseudo Boolean Programming for Partially Ordered Genomes
Probabilistic hierarchical clustering for biological data
Human genome analysis and medicine in the 21st century (abstract only)
A Regulatory Network Controlling Drosophila Development
Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology
Beyond islands (extended abstract): runs in clone-probe matrices
The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB)
Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, San Diego, CA, USA, May 22-25, 2022, Proceedings
A formally exact method to numerically analyze local denaturation in superhelical DNA
Flexible Modelling of Genetic Effects on Function-Valued Traits
On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation
Topology-Free Querying of Protein Interaction Networks
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny
MoGUL: Detecting Common Insertions and Deletions in a Population
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l -Tuples
A random graph approach to NMR sequential assignment
MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods
Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis
Aligning alignments exactly
Systems biology and malaria
Assembly-Free and Alignment-Free Sample Identification Using Genome Skims
Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks
Reconstructing an Inversion History in the Anopheles Gambiae Complex
Optimizing combinatorial library construction via split synthesis
Estimation of the True Evolutionary Distance Under the INFER Model
DCJ Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions
Devider: Long-Read Reconstruction of Many Diverse Haplotypes
Fabricating arrays of strings
OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
A High-Throughput Approach for Associating microRNAs with Their Activity Conditions
Identifying conserved gene clusters in the presence of orthologous groups
Genetics and genemoics: impact on drug discovery and development
A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information
Learning Interpretable SVMs for Biological Sequence Classification
Aligning a DNA sequence with a protein sequence
Hurdles Hardly Have to Be Heeded
Inferring Local Genealogies on Closely Related Genomes
Motif Yggdrasil: Sampling from a Tree Mixture Model
Functional Alignment of Metabolic Networks
Fragmentation Trees Reloaded
On Sorting Genomes with DCJ and Indels
Learning multiple evolutionary pathways from cross-sectional data
Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information
New Algorithms for the Genomic Duplication Problem
Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana
Haplotype-Aware Sequence Alignment to Pangenome Graphs
Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information
Human and mouse gene structure: comparative analysis and application to exon prediction
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes
Optimal sequencing by hybridization in rounds
RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints
An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data
Fast and numerically stable parametric alignment of biosequences
A simple iterative approach to parameter optimization
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads
stance-Based Protein Folding Powered by Deep Learning
Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model
Parameter Landscape Analysis for Common Motif Discovery Programs
MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies
A Fast and Exact Algorithm for the Exemplar Breakpoint Distance
Supervised learning of hidden Markov models for sequence discrimination
Fast, Flexible, and Exact Minimum Flow Decompositions via ILP
Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models
Increased Methylation Variation in Epigenetic Domains across Cancer Types
De novo repeat classification and fragment assembly
CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping
Reconstructing Domain Compositions of Ancestral Multi-domain Proteins
Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes
Extracting structured motifs using a suffix tree - algorithms and application to promoter consensus identification
Efficient database screening for rational drug design using pharmacophore-constrained conformational search
How Many Bootstrap Replicates Are Necessary?
Reversals of Fortune
Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave
A dictionary based approach for gene annotation
TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq
Approximate matching of secondary structures
The Factor Graph Network Model for Biological Systems
Invited: Prediction of protein function
Phase-independent rhythmic analysis of genome-wide expression patterns
TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates
Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion
Parametric Bootstrap for Assessment of Goodness of Fit of Models for Block Haplotype Structure
Large scale sequencing by hybridization
Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract
Accurate Assembly of Circular RNAs with TERRACE
Using Bayesian networks to analyze expression data
New Methods for Detecting Lineage-Specific Selection
Tree fitting: an algebraic approach using profile distances
Sequencing-by-hybridization at the information-theory bound: an optimal algorithm
Bridging the gap between sequence and structure (abstract)
Sorting by Translocations Via Reversals Theory
PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract)
Maxwell demon and topology simplification by type II topoisomerases
CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer
GTED: Graph Traversal Edit Distance
Algorithms for whole genome shotgun sequencing
Rearrangement Models and Single-Cut Operations
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes
SOPHIE: Viral Outbreak Investigation and Transmission History Reconstruction in a Joint Phylogenetic and Network Theory Framework
Alignment Statistics for Long-Range Correlated Genomic Sequences
101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem
Unsupervised Cell Functional Annotation for Single-Cell RNA-Seq
Regulatory element detection using correlation with expression (abstract only)
A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits
The evolutionary capacity of protein structures
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework
A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals
Accurate detection of very sparse sequence motifs
Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data
DeST-OT: Alignment of Spatiotemporal Transcriptomics Data
Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry
A Simulation Tool for the Study of Symmetric Inversions in Bacterial Genomes
Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning
Evolution of Tandemly Arrayed Genes in Multiple Species
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
Graph Theoretical Insights into Evolution of Multidomain Proteins
Safe and Complete Contig Assembly Via Omnitigs
Improved splice site detection in Genie
eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data
How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories
Efficiently Identifying Significant Associations in Genome-Wide Association Studies
Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach
Systematic and automated discovery of patterns in PROSITE families
Dynamic programming alignment accuracy
Faster reliable phylogenetic analysis
Simple and Fast Inverse Alignment
Optimizing PCR Assays for DNA Based Cancer Diagnostics
Handling long targets and errors in sequencing by hybridization
Probabilities for having a new fold on the basis of a map of all protein sequences
Safety and Completeness in Flow Decompositions for RNA Assembly
Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries
Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia
Protein Loop Closure Using Orientational Restraints from NMR Data
Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-Offs
Searching gene transfers on Bacillus subtilis using hidden Markov models
An Important Connection Between Network Motifs and Parsimony Models
A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry
Finding short DNA motifs using permuted markov models
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences
Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts
PASTA: Ultra-Large Multiple Sequence Alignment
Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs
A polyhedral approach to RNA sequence structure alignment
Computational analysis of molecular diversity for drug discovery
Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers
An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats
Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency
Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction
Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution
A new approach to analyzing gene expression time series data
Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising
Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes
Using motion planning to study protein folding pathways
ProTranslator: Zero-Shot Protein Function Prediction Using Textual Description
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets
On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem
Multi-modal Genotype and Phenotype Mutual Learning to Enhance Single-Modal Input Based Longitudinal Outcome Prediction
Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts
Interface surfaces for protein-protein complexes
Significance Of inter-species matches when evolutionary rate varies
Learning a CoNCISE Language for Small-Molecule Binding
Enabling Privacy Preserving GWAS in Heterogeneous Human Populations
Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra
Generalizable Visualization of Mega-Scale Single-Cell Data
A Symmetric Length-Aware Enrichment Test
Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels
Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency
Reconstructing Histories of Complex Gene Clusters on a Phylogeny
On the Genealogy of Asexual Diploids
Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles
Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes
A structural perspective on genome evolution
A Bayesian Active Learning Experimental Design for Inferring Signaling Networks
Modeling Dependence in Evolutionary Inference for Proteins
SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics
Predicting Nucleosome Positioning Using Multiple Evidence Tracks
Protein Function Prediction Based on Patterns in Biological Networks
A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data
Haplotypes and informative SNP selection algorithms: don't block out information
EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning
Efficient exact value computation and applications to biosequence analysis
GEM-Finder: Dissecting GWAS Variants via Long-Range Interacting Cis-Regulatory Elements with Differentiationspecific Genes
Structured motifs search
On the Sample Complexity of Cancer Pathways Identification
Sorting Cancer Karyotypes by Elementary Operations
Experiment Specific Expression Patterns
Inferring Gene Orders from Gene Maps Using the Breakpoint Distance
Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes
Towards Recovering Allele-Specific Cancer Genome Graphs
Disease Risk Predictions with Differentiable Mendelian Randomization
Internal loops in RNA secondary structure prediction
Meta-colored Compacted de Bruijn Graphs
Reconstruction of Reticulate Networks from Gene Trees
Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis
Lymphocyte turnover in HIV-1 infection and the role of the thymus in SIV infection
From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data
Detecting the Dependent Evolution of Biosequences
Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors
Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis
A PQ Framework for Reconstructions of Common Ancestors and Phylogeny
Computational Protein Design Using AND/OR Branch-and-Bound Search
Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut
A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs
SpaCeNet: Spatial Cellular Networks from Omics Data
Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance
Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species
Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis
Comparison of Protein-Protein Interaction Confidence Assignment Schemes
An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes
Genome Aliquoting Revisited
Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2
Automatic Parameter Learning for Multiple Network Alignment
The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree
Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure
Improved Ranking Functions for Protein and Modification-Site Identifications
A unified approach to word statistics
Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs
CRISPR Detection from Short Reads Using Partial Overlap Graphs
Comparative Genomics - International Workshop, RECOMB-CG 2010, Ottawa, Canada, October 9-11, 2010. Proceedings
Distributed Gradient Descent in Bacterial Food Search
Invited presentation: introns and modules in ancient conserved genes (abstract only)
On the Variance of Internode Distance Under the Multispecies Coalescent
Spectral Jaccard Similarity: A New Approach to Estimating Pairwise Sequence Alignments
Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification
Efficient extraction of mapping rules of atoms from enzymatic reaction data
De Novo peptide sequencing via tandem mass spectrometry: a graph-theoretical approach
Fast and Accurate Alignment of Multiple Protein Networks
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation
Rearrangement Scenarios Guided by Chromatin Structure
Constructing Treatment Portfolios Using Affinity Propagation
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks
Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction
Predicting Transcription Factor Binding Sites Using Structural Knowledge
Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings
Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo
Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology
Multi-track Modeling for Genome-Scale Reconstruction of 3D Chromatin Structure from Hi-C Data
A method for optimal design of a threading scoring function
HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time
The Rooted SCJ Median with Single Gene Duplications
A comparative analysis method for detecting binding sites in coding regions
Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data
Resistor: An Algorithm for Predicting Resistance Mutations Using Pareto Optimization over Multistate Protein Design and Mutational Signatures
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly
GATTACA: Lightweight Metagenomic Binning Using Kmer Counting
Perfect DCJ Rearrangement
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding
The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways
A Novel Probabilistic Methodology for eQTL Analysis of Signaling Networks
A compression algorithm for DNA sequences and its applications in genome comparison
Pedigree Reconstruction Using Identity by Descent
Tests for gene clustering
Whole genome association studies in humans (abstract)
Distinguishing Biological from Technical Sources of Variation Using a Combination of Methylation Datasets
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods
Tissue classification with gene expression profiles
Baculovirus Phylogeny Based on Genome Rearrangements
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching
Active Learning for Protein Structure Prediction
Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response
Evolution of Genome Organization by Duplication and Loss: An Alignment Approach
Application of Kernel Method to Reveal Subtypes of TF Binding Motifs
An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes
10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB)
A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics
A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes
Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction
Fast recovery of evolutionary trees with thousands of nodes
Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies
Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure
Genome analysis using clusters of orthologous groups (COGs)
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF
Building human genome maps with radiation hybrids
Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs
Multiplex De Novo Sequencing of Peptide Antibiotics
On the computational complexity of sequence design problems
Overlapping Pools for High Throughput Targeted Resequencing
A Three-Dimensional Model of the Yeast Genome
Computing the Rearrangement Distance of Natural Genomes
mClass: Cancer Type Classification with Somatic Point Mutation Data
Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution
Spatial Clustering of Multivariate Genomic and Epigenomic Information
More Efficient Algorithms for Closest String and Substring Problems
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection
Optimal detection of sequence similarity by local alignment
A solvation potential with improved contact definitions and optimized by extensive threading
OMGS: Optical Map-Based Genome Scaffolding
Designing seeds for similarity search in genomic DNA
Contribution of Structural Variation to Genome Structure: TAD Fusion Discovery and Ranking
Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models
Chromosomal breakpoint re-use in the inference of genome sequence rearrangement
Research in Computational Molecular Biology - 29th International Conference, RECOMB 2025, Seoul, South Korea, April 26-29, 2025, Proceedings
A Partial Solution to the C-Value Paradox
Geometric algorithms for the analysis of 2D-electrophoresis gels
Alignment-Free Phylogenetic Reconstruction
Classifying proteins by family using the product of correlated p -values
A Feature-Based Approach to Modeling Protein-DNA Interactions
Combining phylogenetic and hidden Markov models in biosequence analysis
The Complexity of Approximate Pattern Matching on de Bruijn Graphs
Structural Alignment of Pseudoknotted RNA
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data
Consensus Folding of Unaligned RNA Sequences Revisited
A Robust Method for Transcript Quantification with RNA-seq Data
Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
Trilogy: discovery of sequence-structure patterns across diverse proteins
Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information
Genovo: De Novo Assembly for Metagenomes
Mapping Molecular Landscapes Inside Cells
UniNovo: A Universal Tool for de Novo Peptide Sequencing
Coupled optimization in protein docking