yusuke1997/dblp-id-title huggingface dataset:
Information Theoretic Approaches to Whole Genome Phylogenies
AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization
ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules
Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002, Washington, DC, USA, April 18-21, 2002
A new method for modeling and solving the protein fold recognition problem (extended abstract)
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
Quantifying the Dynamics of Coupled Networks of Switches and Oscillators
New approaches to genomic analysis using single molecules
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets
Multivariate Segmentation in the Analysis of Transcription Tiling Array Data
Ultra-Perfect Sorting Scenarios
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles
Towards Automated Structure-Based NMR Resonance Assignment
AStarix: Fast and Optimal Sequence-to-Graph Alignment
Comparison of complete genomes: Organization and evolution (abstract)
A Coalescent-Based Approach for Complex Disease Mapping
A Simple Measure of the Dynamics of Segmented Genomes: An Application to Influenza
Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract)
Nucleosome Occupancy Information Improves de novo Motif Discovery
Ballast: A Ball-Based Algorithm for Structural Motifs
Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies
Research in Computational Molecular Biology - 27th Annual International Conference, RECOMB 2023, Istanbul, Turkey, April 16-19, 2023, Proceedings
Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data
Problems in understanding the structure and assembly of viruses (abstract)
Resolving Multicopy Duplications de novo Using Polyploid Phasing
Comparing genes and genomes (abstract): from polymorphism to phylogeny
New contact measures for the protein docking problem
A dimensionality reduction approach to modeling protein flexibility
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data
Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets
DiffDomain Enables Identification of Structurally Reorganized Topologically Associating Domains
Haplotype Blocks in Small Populations
Inference of Isoforms from Short Sequence Reads
Extracting structural information using time-frequency analysis of protein NMR data
A combinatorial approach to protein docking with flexible side-chains
Inferring the Recent Duplication History of a Gene Cluster
Representation of k-mer Sets Using Spectrum-Preserving String Sets
A Phylogenetic Approach to Genomic Language Modeling
A structural EM algorithm for phylogenetic inference
Detecting non-adjoining correlations with signals in DNA
A new approach to sequence comparison: normalized sequence alignment
Global Interaction Networks Probed by Mass Spectrometry
FastNet: Fast and Accurate Statistical Inference of Phylogenetic Networks Using Large-Scale Genomic Sequence Data
Modeling protein families using probabilistic suffix trees
A Study of Accessible Motifs and RNA Folding Complexity
Early eukaryote evolution based on mitochondrial gene order breakpoints
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory
Towards constructing physical maps by optical mapping (extended abstract): an effective, simple, combinatorial approach
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications
Analysis of gene expression profiles: class discovery and leaf ordering
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study
Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching
Hierarchical Generative Biclustering for MicroRNA Expression Analysis
Natural Parameter Values for Generalized Gene Adjacency
Optimizing for success: a new score function for distantly related protein sequence comparison
How to Achieve an Equivalent Simple Permutation in Linear Time
RNA-RNA Interaction Prediction and Antisense RNA Target Search
A Mixture Model for Signature Discovery from Sparse Mutation Data
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing
Mapping clones with a given ordering or interleaving (abstract)
Transcriptional Regulation and Cancer Genomics
Learning Regulatory Network Models that Represent Regulator States and Roles
Modeling DNA shuffling
A Unifying Framework for Summary Statistic Imputation
Sequence alignment with tandem duplication
Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes
Epistasis in Genomic and Survival Data of Cancer Patients
Simultaneous identification of duplications and lateral transfers
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, RECOMB 1999, Lyon, France, April 11-14, 1999
Deep Large-Scale Multi-task Learning Network for Gene Expression Inference
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry
IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation
Evolutionary change in developmental genetic networks
Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs
ROSE: A Deep Learning Based Framework for Predicting Ribosome Stalling
Seed Design Framework for Mapping SOLiD Reads
Heuristics for the Gene-Duplication Problem: A Theta ( n ) Speed-Up for the Local Search
A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of Transcription
A branch-and-cut approach to physical mapping with end-probes
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
Topological Signatures for Population Admixture
Using motion planning to study RNA folding kinetics
KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids
An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model
Clustering gene expression patterns
CLMB: Deep Contrastive Learning for Robust Metagenomic Binning
A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems Under DCJ
A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer
Network-Based Prediction and Analysis of HIV Dependency Factors
Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors
Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction
Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing
Multiple maxima of likelihood in phylogenetic trees: an analytic approach
Reference-based gene model prediction on DNA contigs (extended abstract)
Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning
Gene-finding via tandem mass spectrometry
Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data
A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances
An algorithmic approach to multiple complete digest mapping
Hunting for new restriction enzymes in GenBank (abstract)
Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining
Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction Models
The threading approach to the inverse protein folding problem
Microarray analysis of vertebrate embryonic neural induction
Finding Nested Common Intervals Efficiently
Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data
Inferring Cell Differentiation Maps from Lineage Tracing Data
VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction from Assembly Graphs
SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference
A Probabilistic Graphical Model for Ab Initio Folding
Ultra High Diversity Factorizable Libraries for Efficient Therapeutic Discovery
Steamboat: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues
An Overview of Combinatorial Methods for Haplotype Inference
Long Reads Enable Accurate Estimates of Complexity of Metagenomes
Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability
Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery
Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances
On the complexity and approximation of syntenic distance
An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming
ReAligner: a program for refining DNA sequence multi-alignments
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
A Practical Approach to Significance Assessment in Alignment with Gaps
On the complexity of protein folding (abstract)
UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms
Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data
A Survey of Computational Methods for Determining Haplotypes
An analytic approach to significance assessment in local sequence alignment with gaps
Using Multiple Alignments to Improve Gene Prediction
GeneCover: A Combinatorial Approach for Label-Free Marker Gene Selection
Chain growth algorithms for HP-type lattice proteins
K-mer Set Memory (KSM) Motif Representation Enables Accurate Prediction of the Impact of Regulatory Variants
BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
High Resolution Modeling of Chromatin Interactions
Modeling dependencies in protein-DNA binding sites
Comparing in situ m RNA expression patterns of drosophila embryos
The greedy path-merging algorithm for sequence assembly
Assessment of ab initio protein structure prediction
On de novo interpretation of tandem mass spectra for peptide identification
q -gram based database searching using a suffix array (QUASAR)
A Flow Procedure for the Linearization of Genome Sequence Graphs
Boosting Protein Threading Accuracy
Assessing the Robustness of Complete Bacterial Genome Segmentations
Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure
Conserved segment identification
The role of computational chemistry in translating genomic information into bioactive small molecules (abstract only)
Amino Acid Sequence Control of the Folding of the Parallel beta-Helix, the Simplest beta-Sheet Fold
Creating the backbone for the virtual cell: cell mapping projects on the run (abstract only)
An algorithm for finding novel gapped motifs in DNA sequences
Incremental Signaling Pathway Modeling by Data Integration
Charge Group Partitioning in Biomolecular Simulation
New algorithms for the duplication-loss model
Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion
CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses
Formulations and hardness of multiple sorting by reversals
DNA microarrays - the how and the why
Algorithms for inferring cis-regulatory structures and protein interaction networks
Reconstructing the pre-doubling genome
Supervised Adversarial Alignment of Single-Cell RNA-seq Data
Maximum likelihood on four taxa phylogenetic trees: analytic solutions
Topological Robustness of the Protein-Protein Interaction Networks
Improved Pangenomic Classification Accuracy with Chain Statistics
Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining
cfDecon: Accurate and Interpretable Methylation-Based Cell Type Deconvolution for Cell-Free DNA
ML-MAGES: A Machine Learning Framework for Multivariate Genetic Association Analyses with Genes and Effect Size Shrinkage
Comparative Genomics, International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings
Construction of physical maps from oligonucleotide fingerprints data
d-PBWT: Dynamic Positional Burrows-Wheeler Transform
Integer Programming Framework for Pangenome-Based Genome Inference
Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry
ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches
Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization
regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models
Inferring Tumor Evolution from Longitudinal Samples
Detecting Large Indels Using Optical Map Data
Using a mixture of probabilistic decision trees for direct prediction of protein function
ModHMM: A Modular Supra-Bayesian Genome Segmentation Method
Learning Maximally Spanning Representations Improves Protein Function Annotation
Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?
Accounting for Non-genetic Factors Improves the Power of eQTL Studies
Optimizing exact genetic linkage computations
Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation
On the power of universal bases in sequencing by hybridization
Revealing the Proteome Complexity by Mass Spectrometry
A Novel Matrix Factorization Model for Interpreting Single-Cell Gene Expression from Biologically Heterogeneous Data
An Algorithmic Framework for Predicting Side-Effects of Drugs
Sequence to Graph Alignment Using Gap-Sensitive Co-linear Chaining
Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation
Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters
CluStrat: A Structure Informed Clustering Strategy for Population Stratification
Genomic DNA k -mer Spectra: Models and Modalities
Motif discovery without alignment or enumeration (extended abstract)
DNA sequence evolution with neighbor-dependent mutation
Biological Networks: Comparison, Conservation, and Evolutionary Trees
NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees
The E-CELL project: towards integrative simulation of cellular processes
Recovering True Rearrangement Events on Phylogenetic Trees
Numerical taxonomy on data (abstract): experimental results
ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads
Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks
Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs
RNA Secondary Structure Prediction Via Energy Density Minimization
Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs
Gene selection criterion for discriminant microarray data analysis based on extreme value distributions
Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences
AutoComplete: Deep Learning-Based Phenotype Imputation for Large-Scale Biomedical Data
Fishing for Proteins in the Pacific Northwest
Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation
A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins
A complete and effective move set for simplified protein folding
netNMF-sc: A Network Regularization Algorithm for Dimensionality Reduction and Imputation of Single-Cell Expression Data
PWAS: Proteome-Wide Association Study
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants
Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Padua, Italy, May 10-13, 2020, Proceedings
Comparing sequence scaffolds
Scalable Multi-component Linear Mixed Models with Application to SNP Heritability Estimation
Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions
Enhancing Searches for Optimal Trees Using SIESTA
Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data
A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem
Genes Order and Phylogenetic Reconstruction: Application to gamma -Proteobacteria
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins
Discovering Regulatory Overlapping RNA Transcripts
Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk
Research in Computational Molecular Biology - 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings
Finding motifs in the twilight zone
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments
Pooling strategies for establishing physical genome maps using FISH
Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers
Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution
MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads
Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes
Discovering Local Patterns of Co-evolution
Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence
Set association analysis of SNP case-control and microarray data
An optimal procedure for gap closing in whole genome shotgun sequencing
Circular Networks from Distorted Metrics
lobSTR: A Short Tandem Repeat Profiler for Personal Genomes
Ultra-Accurate Complex Disorder Prediction: Case Study of Neurodevelopmental Disorders
Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks
Finding motifs using random projections
Characterizing Protein-DNA Binding Event Subtypes in ChIP-Exo Data
Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings
Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples
Designing RNA structures: natural and artificial selection
How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation
scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis
Towards predicting coiled-coil protein interactions
On the approximation of protein threading
A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells
Loss-Function Learning for Digital Tissue Deconvolution
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure
Statistical Evaluation of Genome Rearrangement
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data
The restriction scaffold problem
RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature
Automated High-Dimensional Flow Cytometric Data Analysis
Mapping Association between Long-Range Cis -Regulatory Regions and Their Target Genes Using Comparative Genomics
Context-specific Bayesian clustering for gene expression data
Read Clouds Uncover Variation in Complex Regions of the Human Genome
Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses
A structure based similarity measure for nucleic acid sequence comparison
A New Approach to Protein Identification
BCL-2: From Translocation to Therapy
Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction
Parts of the Problem of Polyploids in Rearrangement Phylogeny
Systems Biology and Regulatory Genomics, Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers
DockStar: A Novel ILP Based Integrative Method for Structural Modelling of Multimolecular Protein Complexes (Extended Abstract)
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator
Locating a Tree in a Phylogenetic Network in Quadratic Time
AptaBlocks: Accelerating the Design of RNA-Based Drug Delivery Systems
An Alignment-Free Distance Measure for Closely Related Genomes
Probabilistic discovery of overlapping cellular processes and their regulation
Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data
Dynamic Alignment-Free and Reference-Free Read Compression
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models
Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization
Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA
Inferring Piecewise Ancestral History from Haploid Sequences
TRIBAL: Tree Inference of B Cell Clonal Lineages
A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation
A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem
CELL-E: A Text-to-Image Transformer for Protein Image Prediction
Sequence comparison to graph comparison--a new generation of algorithms for network analysis of interacting molecules (abstract only)
Learning Probabilistic Protein-DNA Recognition Codes from DNA-Binding Specificities Using Structural Mappings
Dynamic Pseudo-time Warping of Complex Single-Cell Trajectories
Improving Inversion Median Computation Using Commuting Reversals and Cycle Information
Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings
Stability of Rearrangement Measures in the Comparison of Genome Sequences
Genome Rearrangement in Mitochondria and Its Computational Biology
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
Simulating Protein Motions with Rigidity Analysis
Protein folding in the hydrophobic-hydrophilic ( HP ) is NP-complete
Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings
A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data
Checking homogeneity of motifs' distribution in heterogenous sequences
Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models
Learning Microbial Interaction Networks from Metagenomic Count Data
Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors
Systems Biology and Computational Proteomics, Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers
An integrated probabilistic model for functional prediction of proteins
The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS
On Computing Breakpoint Distances for Genomes with Duplicate Genes
Universal DNA tag systems: a combinatorial design scheme