yusuke1997/dblp-id-title huggingface dataset:
Evolution of Tandemly Repeated Sequences Through Duplication and Inversion
Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Magog-Orford, QC, Canada, October 9-12, 2018, Proceedings
Designing multiple simultaneous seeds for DNA similarity search
Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures
Detecting Antimicrobial Resistance Through MALDI-TOF Mass Spectrometry with Statistical Guarantees Using Conformal Prediction
DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins
De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis
Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm
Identifying gene regulatory networks from experimental data
ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes Using Short Read Data
ScisTree2: An Improved Method for Large-Scale Inference of Cell Lineage Trees and Genotype Calling from Noisy Single Cell Data
Protein similarity from knot theory and geometric convolution
Power Boosts for Cluster Tests
Blocked Pattern Matching Problem and Its Applications in Proteomics
Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length
Combinatorial synthesis on macroscopic solid support units
Predicting the beta-helix fold from protein sequence data
Comparative Genomics and Extensive Recombinations in Phage Communities
Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data
The human genetic variation (abstract): oligonucleotide chips and human disease
Comparative Genomics, RECOMB 2007 International Workshop, RECOMB-CG 2007, San Diego, CA, USA, September 16-18, 2007, Proceedings
Computing life and global technologies (abstract only)
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics
The Distribution of Inversion Lengths in Bacteria
Databases for Comparative Analysis of Human-Mouse Orthologous Alternative Splicing
On the predictive power of sequence similarity in yeast
Storage and Retrieval of Individual Genomes
Towards optimally multiplexed applications of universal DNA tag systems
Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer
Parking Functions, Labeled Trees and DCJ Sorting Scenarios
Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses
Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses
Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery
Unsupervised Integration of Single-Cell Multi-omics Datasets with Disproportionate Cell-Type Representation
Shared Peptides in Mass Spectrometry Based Protein Quantification
Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome
On Sufficient Statistics of Least-Squares Superposition of Vector Sets
DNA sequence variation among humans and apes (abstract only)
The Generating Function Approach for Peptide Identification in Spectral Networks
Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data
Efficient Estimation and Applications of Cross-Validated Genetic Predictions
Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes - (Extended Abstract)
Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information
Trends in computational biology
Linear-Time Algorithms for Some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance
Protein Structure by Semidefinite Facial Reduction
A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism
Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties
Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models
Contig selection in physical mapping
Log Transformation Improves Dating of Phylogenies
Determining contact energy function for continuous state models of globular protein conformations
Integrated Protein Interaction Networks for 11 Microbes
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads
Avoiding Local Optima in Single Particle Reconstruction
Pseudoknots in RNA secondary structures
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees
Very Low Power to Detect Asymmetric Divergence of Duplicated Genes
A Parameterized Algorithm for Protein Structure Alignment
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony
Identifying satellites in nucleic acid sequences
Improved Duplication Models for Proteome Network Evolution
Evolutionary drug discovery (abstract)
Information processing by cells and biologists (abstract only)
On reconstructing species trees from gene trees in term of duplications and losses
A Fast and Exact Algorithm for the Median of Three Problem-A Graph Decomposition Approach
Discriminative motifs
A Cubic Algorithm for the Generalized Rank Median of Three Genomes
Tools for Simulating and Analyzing RNA Folding Kinetics
A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements
Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses
Context-Specific Nested Effects Models
Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements
Fast Approximation of Frequent k-mers and Applications to Metagenomics
Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases
Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules
Faster and simpler algorithm for sorting signed permutations by reversals
Sorting by reversals is difficult
The String Barcoding Problem is NP-Hard
Computational Methods for SNPs and Haplotype Inference, DIMACS/RECOMB Satellite Workshop, Piscataway, NJ, USA, November 21-22, 2002, Revised Papers
Efficient Enumeration of Phylogenetically Informative Substrings
Human Genome Sequence Variation and the Inherited Basis of Common Disease
How fast a protein chain can fold to its most stable structure?
The Incompatible Desiderata of Gene Cluster Properties
Identification of Ultramodified Proteins Using Top-Down Spectra
Multiple genome rearrangements
A multi-expert system for the automatic detection of protein domains from sequence information
Individual Gene Cluster Statistics in Noisy Maps
GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data
A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs
Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited
Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing
Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models
Locating Multiple Gene Duplications through Reconciled Trees
Hyper-k-mers: Efficient Streaming k-mers Representation
Increasing Power of Groupwise Association Test with Likelihood Ratio Test
A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny
Haplotype phase inference
Sequence homology detection through large scale pattern discovery
An Outsider's View of the Genome
Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics
Reconciliation with Non-binary Gene Trees Revisited
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks
Conservation of Combinatorial Structures in Evolution Scenarios
De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments
Engineering a scalable placement heuristic for DNA probe arrays
A Markov Random Field Framework for Protein Side-Chain Resonance Assignment
Protein Domain Embeddings for Fast and Accurate Similarity Search
Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs
Comparative Genomics, RECOMB 2005 International Workshop, RCG 2005, Dublin, Ireland, September 18-20, 2005, Proceedings
Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC
RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract)
A Framework for Orthology Assignment from Gene Rearrangement Data
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data
CSAX: Characterizing Systematic Anomalies in eXpression Data
Bayesian Non-parametric Clustering of Single-Cell Mutation Profiles
A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search
CIDANE: Comprehensive Isoform Discovery and Abundance Estimation
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes
Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy?
A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements
Computational Characterization and Identification of Core Promoters of MicroRNA Genes in C. elegans , H. sapiens and A. thaliana
Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Warsaw, Poland, April 12-15, 2015, Proceedings
Structural Variation Detection with Read Pair Information - An Improved Null-Hypothesis Reduces Bias
A data-analysis pipeline for large-scale gene expression analysis
Boosting Alignment Accuracy by Adaptive Local Realignment
Modeling Mutual Exclusivity of Cancer Mutations
On the Complexity of Sequence to Graph Alignment
Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals
Multiple Competition-Based FDR Control and Its Application to Peptide Detection
Co-linear Chaining with Overlaps and Gap Costs
PDB_ISL: an intermediate sequence library for protein structure assignment
A Model for Biased Fractionation after Whole Genome Duplication
CDGCN: Conditional de novo Drug Generative Model Using Graph Convolution Networks
Finding Mutated Subnetworks Associated with Survival in Cancer
Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees
Genome-Wide Survival Analysis of Somatic Mutations in Cancer
Clustering Near-Identical Sequences for Fast Homology Search
Proceedings of the Sventh Annual International Conference on Computational Biology, RECOMB 2003, Berlin, Germany, April 10-13, 2003
HAPLOFREQ - Estimating Haplotype Frequencies E.ciently
Fast and simple character classes and bounded gaps pattern matching, with application to protein searching
Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning
Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented Generation
Deciphering the Swine-Flu Pandemics of 1918 and 2009
Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model
Statistical Consistency of Coalescent-Based Species Tree Methods Under Models of Missing Data
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended
Orientation of Ordered Scaffolds
Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification
BBK * (Branch and Bound over K * ): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces
Semi-supervised Single-Cell Cross-modality Translation Using Polarbear
Rich Parameterization Improves RNA Structure Prediction
Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples
Multiple organism gene finding by collapsed gibbs sampling
On the Structure of Reconciliations
Leveraging Sequence Classification by Taxonomy-Based Multitask Learning
Comparative Genomics, RECOMB 2006 International Workshop, RCG 2006, Montreal, Canada, September 24-26, 2006, Proceedings
Orchestration of DNA Methylation
AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application
Trisomic Phase Inference
Reconciliation problems for duplication, loss and horizontal gene transfer
Revealing protein structures: a new method for mapping antibody epitopes
Inferring Common Origins from mtDNA
Generation and Comparative Genomics of Synthetic Dengue Viruses
Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis
Selecting Genomes for Reconstruction of Ancestral Genomes
Reconstructing reticulate evolution in species: theory and practice
APPLES: Fast Distance-Based Phylogenetic Placement
Synthetic Sequence Design for Signal Location Search
Towards an Integrated Protein-Protein Interaction Network
Detecting Protein Conformational Changes in Interactions via Scaling Known Structures
Inferring Positional Homologs with Common Intervals of Sequences
Mining protein family specific residue packing patterns from protein structure graphs
Physical network models and multi-source data integration
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History
Haplotype reconstruction from SNP alignment
An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees
At the Origin of Life: How Did Folded Proteins Evolve?
Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction
DIISCO: A Bayesian Framework for Inferring Dynamic Intercellular Interactions from Time-Series Single-Cell Data
A NMR-spectra-based scoring function for protein docking
Algorithms for MDC-Based Multi-locus Phylogeny Inference
Class prediction and discovery using gene expression data
GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling
Algorithms for phylogenetic footprinting
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination
Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM Algorithm
Modeling and Analysis of Heterogeneous Regulation in Biological Networks
A unified sequence-structure classification of protein sequences: combining sequence and structure in a map of the protein space
Dissecting Cancer Heterogeneity with a Probabilistic Genotype-Phenotype Model
Reconstructing the Phylogeny of Mobile Elements
A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference
Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies
RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy
Modeling the Combinatorial Functions of Multiple Transcription Factors
Aligning Two Genomic Sequences That Contain Duplications
Maximum Likelihood of Evolutionary Trees Is Hard
A Note on Computing Interval Overlap Statistics
Identifying Systematic Variation at the Single-Cell Level by Leveraging Low-Resolution Population-Level Data
An algorithm for finding tandem repeats of unspecified pattern size
Molecular diversity: strategies and concerns (abstract only)
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes
Haplotype Inference in Complex Pedigrees
Lattice and off-lattice side chain models of protein folding (extended abstract): linear time structure prediction better than 86% of optimal
Constrained De Novo Sequencing of Peptides with Application to Conotoxins
Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data
Bayesian Multiple Protein Structure Alignment
Assembly of Long Error-Prone Reads Using Repeat Graphs
Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks
Detecting Introgression in Anopheles Mosquito Genomes Using a Reconciliation-Based Approach
Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering
Statistical Inference of Peroxisome Dynamics
Class discovery in gene expression data
A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction
Structural alignment of large-size proteins via lagrangian relaxation
Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model
Protein Conformational Flexibility Analysis with Noisy Data
Analysis of the position dependent amino acid probabilities and its application to the search for remote homologues
An Evolutionary Study of the Human Papillomavirus Genomes
Decoding Coalescent Hidden Markov Models in Linear Time
A New Algorithm for Improving the Resolution of Cryo-EM Density Maps
Derivation of sensitive discrimination potential for virtual ligand screening
Alignment of Optical Maps
On the Inference of Ancestries in Admixed Populations
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
On Exploring Genome Rearrangement Phylogenetic Patterns
Biology as Information
Computing Robust Optimal Factories in Metabolic Reaction Networks
SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data
Lifting Prediction to Alignment of RNA Pseudoknots
Support Vector Training of Protein Alignment Models
Scalable Summary Statistics-Based Heritability Estimation Method with Individual Genotype Level Accuracy
Inferring domain-domain interactions from protein-protein interactions
String barcoding: uncovering optimal virus signatures
aBayesQR: A Bayesian Method for Reconstruction of Viral Populations Characterized by Low Diversity
Revealing the Genetic Basis of Immune Traits in the Absence of Experimental Immunophenotyping
Systems Metabolic Engineering
Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome
Folding Membrane Proteins by Deep Transfer Learning
Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures
Recent advances on the manipulation of single biomolecules
Alignment of Mass Spectrometry Data by Clique Finding and Optimization
Minimizing and Learning Energy Functions for Side-Chain Prediction
MONN: A Multi-objective Neural Network for Predicting Pairwise Non-covalent Interactions and Binding Affinities Between Compounds and Proteins
Sparse Binary Relation Representations for Genome Graph Annotation
On constructing radiation hybrid maps (extended abstract)
Efficient algorithms for lateral gene transfer problems
TissueMosaic Enables Cross-Sample Differential Analysis of Spatial Transcriptomics Datasets Through Self-supervised Representation Learning
Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract)
Advances on Genome Duplication Distances
Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape
Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking
Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to the Inference of Functional Regulatory Targets
Searching Protein 3-D Structures in Linear Time
A Statistical Framework for the Functional Analysis of Metagenomes
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates
Proteome Coverage Prediction for Integrated Proteomics Datasets
Ultra-Large Alignments Using Ensembles of Hidden Markov Models
LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins
A Geometric Clustering Algorithm and Its Applications to Structural Data
The Zero Exemplar Distance Problem
Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection
Reconstructing the History of Syntenies Through Super-Reconciliation
Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Barcelona, Spain, April 21-24, 2012. Proceedings
Biology and bioinformatics of halophilism
Algorithms for choosing differential gene expression experiments
Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance
Automatic Recognition of Cells (ARC) for 3D Images of C. elegans
A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer
Finding anchors for genomic sequence comparison
Applied computational genomics: polymorphism prediction, data mining and genomic analysis
HLA Type Inference via Haplotypes Identical by Descent
A discriminative model for identifying spatial cis-regulatory modules
High-Resolution Modeling of Cellular Signaling Networks
A bayesian approach to transcript estimation from gene array data: the BEAM technique
Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual Inference
A Tractable Variant of the Single Cut or Join Distance with Duplicated Genes
NetREX: Network Rewiring Using EXpression - Towards Context Specific Regulatory Networks
Alignment-Free Estimation of Read to Genome Distances and Its Applications
Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count Data
Linear-Time Tree Containment in Phylogenetic Networks
Perfect phylogeny and haplotype assignment
Evaluating Between-Pathway Models with Expression Data
Finding approximate tandem repeats in genomic sequences
Efficient Algorithms to Discover Alterations with Complementary Functional Association in Cancer
Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships
Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs
Large scale reconstruction of haplotypes from genotype data
Maximizing Synteny Blocks to Identify Ancestral Homologs
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer
Fast Phylogenetic Biodiversity Computations Under a Non-uniform Random Distribution
Real-Valued Group Testing for Quantitative Molecular Assays
Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding
The Similarity Distribution of Paralogous Gene Pairs Created by Recurrent Alternation of Polyploidization and Fractionation
NAP: Programming Data Planes with Approximate Data Structures
Cryptographic Path Validation for SCION in P4
P4EAD: Securing the In-band Control Channels on Commodity Programmable Switches
Introducing P4TC - A P4 implementation on Linux Kernel using Traffic Control
LANTERN: Layered Adaptive Network Telemetry Collection for Programmable Dataplanes
Poster: High-Speed Per-Packet Checksums on the Intel Tofino
Per Priority Data Rate Measurement in Data Plane
Proceedings of the 6th on European P4 Workshop, EuroP4 2023, Paris, France, 8 December 2023
Poster: Maintaining Sets With Deletions in the Data Plane
Poster: Adaptive In-Network Inference using Early-Exits
Demo: Enabling DNN Inference in the Network Data Plane
Poster: P4DME: DNS Threat Mitigation with P4 In-Network Machine Learning Offload
The Lambda Delta -calculus
A Decidable Intersection Type System based on Relevance
A Computer-Checked Verification of Milner's Scheduler
Unison: A File Synchronizer and Its Specification
Nontraditional Applications of Automata Theory
Types and Models for Higher-Order Action Calculi
A Theory of Primitive Objects - Untyped and First-Order Systems
Boxed Ambients