yusuke1997/dblp-id-title huggingface dataset:
A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model
Pfp-fm: an accelerated FM-index
Consistency of the Neighbor-Net Algorithm
Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces
TINNiK: inference of the tree of blobs of a species network under the coalescent model
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series
On the protein folding problem in 2D-triangular lattices
Global exact optimisations for chloroplast structural haplotype scaffolding
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer
Tree-average distances on certain phylogenetic networks have their weights uniquely determined
Biologically feasible gene trees, reconciliation maps and informative triples
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Scoring function to predict solubility mutagenesis
Constructing founder sets under allelic and non-allelic homologous recombination
The solution surface of the Li-Stephens haplotype copying model
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set
Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data
A general framework for genome rearrangement with biological constraints
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
Data Mining in Bioinformatics (BIOKDD)
Data compression for sequencing data
Jaccard index based similarity measure to compare transcription factor binding site models
A sub-cubic time algorithm for computing the quartet distance between two general trees
The path-label reconciliation (PLR) dissimilarity measure for gene trees
Enumerating all maximal frequent subtrees in collections of phylogenetic trees
Computing the skewness of the phylogenetic mean pairwise distance in linear time
QTL/microarray approach using pathway information
Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations
Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming
MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics
On avoided words, absent words, and their application to biological sequence analysis
A basic analysis toolkit for biological sequences
Approximate search for known gene clusters in new genomes using PQ-trees
A branching process for homology distribution-based inference of polyploidy, speciation and loss
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
A cubic algorithm for the generalized rank median of three genomes
Quantifying steric hindrance and topological obstruction to protein structure superposition
Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability
Sorting signed circular permutations by super short operations
Learning from positive examples when the negative class is undetermined- microRNA gene identification
Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation
Efficient privacy-preserving variable-length substring match for genome sequence
Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials
Probability-based model of protein-protein interactions on biological timescales
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
Erratum to: Circular sequence comparison: algorithms and applications
Mining, compressing and classifying with extensible motifs
Bitpacking techniques for indexing genomes: I. Hash tables
Efficient algorithms for the discovery of gapped factors
RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs
Complexity and algorithms for copy-number evolution problems
Erratum to: Inferring interaction type in gene regulatory networks using co-expression data
ReCoil - an algorithm for compression of extremely large datasets of dna data
RNA folding with hard and soft constraints
"Hook"-calibration of GeneChip-microarrays: Theory and algorithm
NANUQ: a method for inferring species networks from gene trees under the coalescent model
Swiftly identifying strongly unique k-mers
Fast half-sibling population reconstruction: theory and algorithms
A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data
Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis
Multi-membership gene regulation in pathway based microarray analysis
The space of phylogenetic mixtures for equivariant models
Jane: a new tool for the cophylogeny reconstruction problem
Algorithms for detecting and analysing autocatalytic sets
Differentially mutated subnetworks discovery
MRL and SuperFine+MRL: new supertree methods
Automated design of dynamic programming schemes for RNA folding with pseudoknots
The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies
On the combinatorics of sparsification
MoDock: A multi-objective strategy improves the accuracy for molecular docking
On the optimality of the neighbor-joining algorithm
A normalization strategy for comparing tag count data
HuMiTar: A sequence-based method for prediction of human microRNA targets
Analysis of Metabolic Subnetworks by Flux Cone Projection
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
Generalized enhanced suffix array construction in external memory
Protein docking with predicted constraints
Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms
The Bourque distances for mutation trees of cancers
Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison
Towards a practical O(n log n) phylogeny algorithm
An asymmetric approach to preserve common intervals while sorting by reversals
Characteristics of predictor sets found using differential prioritization
Disk compression of k-mer sets
A safe and complete algorithm for metagenomic assembly
Double and multiple knockout simulations for genome-scale metabolic network reconstructions
An algorithm to parse segment packing in predicted protein contact maps
gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections
NANUQ + : A divide-and-conquer approach to network estimation
Space-efficient computation of k-mer dictionaries for large values of k
Models and algorithms for genome rearrangement with positional constraints
An online peak extraction algorithm for ion mobility spectrometry data
Shape decomposition algorithms for laser capture microdissection
Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs
Challenges in experimental data integration within genome-scale metabolic models
Listing all sorting reversals in quadratic time
Refining transcriptional regulatory networks using network evolutionary models and gene histories
An FPT haplotyping algorithm on pedigrees with a small number of sites
Algorithmic approaches to protein-protein interaction site prediction
New journal: Algorithms for Molecular Biology
Approximating the DCJ distance of balanced genomes in linear time
A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses
Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments
b-move: faster lossless approximate pattern matching in a run-length compressed index
Natural family-free genomic distance
A graph extension of the positional Burrows-Wheeler transform and its applications
Characterizing compatibility and agreement of unrooted trees via cuts in graphs
Reconstruction of time-consistent species trees
Identification of donor splice sites using support vector machine: a computational approach based on positional, compositional and dependency features
Compression algorithm for colored de Bruijn graphs
Binning long reads in metagenomics datasets using composition and coverage information
SMOTIF: efficient structured pattern and profile motif search
Module detection in complex networks using integer optimisation
AlfaPang: alignment free algorithm for pangenome graph construction
Parsimonious Clone Tree Integration in cancer
A simple data-adaptive probabilistic variant calling model
SNPs detection by eBWT positional clustering
TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison
Fast calculation of the quartet distance between trees of arbitrary degrees
Sparse RNA folding revisited: space-efficient minimum free energy structure prediction
Finding maximal exact matches in graphs
Designing minimal microbial strains of desired functionality using a genetic algorithm
DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?
From pairs of most similar sequences to phylogenetic best matches
Finding the region of pseudo-periodic tandem repeats in biological sequences
A weighted average difference method for detecting differentially expressed genes from microarray data
Gravitation field algorithm and its application in gene cluster
Enumeration of minimal stoichiometric precursor sets in metabolic networks
Evolving DNA motifs to predict GeneChip probe performance
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
A new 1.375-approximation algorithm for sorting by transpositions
Isometric gene tree reconciliation revisited
Mem-based pangenome indexing for k-mer queries
Infrared: a declarative tree decomposition-powered framework for bioinformatics
DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach
Semi-nonparametric modeling of topological domain formation from epigenetic data
Embedding gene trees into phylogenetic networks by conflict resolution algorithms
A simulation study comparing supertree and combined analysis methods using SMIDGen
INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis
Linear time minimum segmentation enables scalable founder reconstruction
On the use of cartographic projections in visualizing phylo-genetic tree space
LazyB: fast and cheap genome assembly
Finding maximum common contractions between phylogenetic networks
Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations
Finding all maximal perfect haplotype blocks in linear time
Faster algorithms for RNA-folding using the Four-Russians method
OCTAL: Optimal Completion of gene trees in polynomial time
Kohdista: an efficient method to index and query possible Rmap alignments
Improving metagenomic binning results with overlapped bins using assembly graphs
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains
A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
Invariant based quartet puzzling
Co-linear chaining on pangenome graphs
Incompatible quartets, triplets, and characters
Protein sequence and structure alignments within one framework
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph
Unifying duplication episode clustering and gene-species mapping inference
Fast lightweight accurate xenograft sorting
Prefix-free parsing for building big BWTs
A graph modification approach for finding core-periphery structures in protein interaction networks
Probabilistic approaches to alignment with tandem repeats
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures
Constructing perfect phylogenies and proper triangulations for three-state characters
Analysis of gene copy number changes in tumor phylogenetics
Core column prediction for protein multiple sequence alignments
Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance
Gerbil: a fast and memory-efficient k-mer counter with GPU-support
Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12
Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes
Clustering of reads with alignment-free measures and quality values
Efficient unfolding pattern recognition in single molecule force spectroscopy data
Pangenomic genotyping with the marker array
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model
iTriplet, a rule-based nucleic acid sequence motif finder
Alignment-free phylogeny of whole genomes using underlying subwords
An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem
ANMM4CBR: a case-based reasoning method for gene expression data classification
On the group theoretical background of assigning stepwise mutations onto phylogenies
New generalized metric based on branch length distance to compare B cell lineage trees
Efficient and accurate P-value computation for Position Weight Matrices
The gene family-free median of three
Fractional hitting sets for efficient multiset sketching
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies
Simplified sequence-based method for ATP-binding prediction using contextual local evolutionary conservation
Accelerating calculations of RNA secondary structure partition functions using GPUs
Lossless filter for multiple repeats with bounded edit distance
Fast, parallel, and cache-friendly suffix array construction
On the family-free DCJ distance and similarity
An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding
Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics
Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
Review of "Reconstructing Evolution: New mathematical and computational advances" edited by Olivier Gascuel and Mike Steel
A minimum-labeling approach for reconstructing protein networks across multiple conditions
Pareto optimization in algebraic dynamic programming
Using the longest run subsequence problem within homology-based scaffolding
Using cascading Bloom filters to improve the memory usage for de Brujin graphs
P-value based visualization of codon usage data
TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column
Estimating similarity and distance using FracMinHash
Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem
Bi-alignments with affine gaps costs
Adding hydrogen atoms to molecular models via fragment superimposition
Heuristic algorithms for best match graph editing
Non-parametric correction of estimated gene trees using TRACTION
ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networks
GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors
Assessing the efficiency of multiple sequence alignment programs
Repairing Boolean logical models from time-series data using Answer Set Programming
Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell
Split-inducing indels in phylogenomic analysis
A multiobjective approach for identifying protein complexes and studying their association in multiple disorders
Atom mapping with constraint programming
WildSpan: mining structured motifs from protein sequences
Gene tree correction for reconciliation and species tree inference
A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics
Inverse folding of RNA pseudoknot structures
Survey on Simulation for Mobile Ad-Hoc Communication for Disaster Scenarios
A Robust and Power-Efficient SoC Implementation in 65 nm
Decoupled Vector Processing Unit: Past, Present, and Future
Bidirectional Optimization Coupled Lightweight Networks for Efficient and Robust Multi-Person 2D Pose Estimation
PVSS: A Progressive Vehicle Search System for Video Surveillance Networks
A Coarse-to-Fine Method for Shape Recognition
A Multi-Agent Spatial Logic for Scenario-Based Decision Modeling and Verification in Platoon Systems
Efficient k -Nearest-Neighbor Search Algorithms for Historical Moving Object Trajectories
Adaptive Execution of Jobs in Computational Grid Environment
Jupiter Made Abstract, and Then Refined
An Algorithm Based on Tabu Search for Satisfiability Problem
Dynamic Shortest Path Monitoring in Spatial Networks
Toward High-Performance Delta-Based Iterative Processing with a Group-Based Approach
HEDC++: An Extended Histogram Estimator for Data in the Cloud
Extending STL with efficient data structures
A New Mesh Simplification Algorithm Based on Triangle Collapses
An Aided Tool for Enterprise Network Design
TagCombine: Recommending Tags to Contents in Software Information Sites
Hierarchical Approximate Matching for Retrieval of Chinese Historical Calligraphy Character
BIST Design for Detecting Multiple Stuck-Open Faults in CMOS Circuits Using Transition Count
An operational approach to belief revision
Online Feature Selection of Class Imbalance via PA Algorithm
Weakly- and Semi-Supervised Fast Region-Based CNN for Object Detection
A Game-Based Approach for PCTL* Stochastic Model Checking with Evidence
On/Off-Line Prediction Applied to Job Scheduling on Non-Dedicated NOWs
A Comprehensive and Adaptive Trust Model for Large-Scale P2P Networks
Chinese Question-Answering System
L-Tree Match: A New Data Extraction Model and Algorithm for Huge Text Stream with Noises
Orientation Field Guided Texture Synthesis
CIMS network protocol and its net models
Global-to-Local Approach to Rigorously Developing Distributed System with Exception Handling
The modelling of temporal data in the relational database environment
Approximating Geographical Queries
Playing games and proving properties of concurrent systems
Outline of Initial Design of the Structured Hypertext Transfer Protocol
Secure Two-Party Computational Geometry
A Protocol for a Private Set-Operation
Mix-Lingual Relation Extraction: Dataset and a Training Approach
CR-Morph: Controllable Rigid Morphing for 2D Animation
Hybrid Parallel Bundle Adjustment for 3D Scene Reconstruction with Massive Points
Exploiting Pre-Trained Network Embeddings for Recommendations in Social Networks
Privacy-Preserving Task Assignment in Spatial Crowdsourcing
HBIR: Hypercube-Based Image Retrieval
New Constructions for Identity-Based Unidirectional Proxy Re-Encryption
Improving the Syllable-Synchronous Network Search Algorithm for Word Decoding in Continuous Chinese Speech Recognition
NfvInsight: A Framework for Automatically Deploying and Benchmarking VNF Chains
Efficient Incremental Maintenance for Distributive and Non-Distributive Aggregate Functions
A Transactional Asynchronous Replication Scheme for Mobile Database Systems
On dependability of computing systems
Efficient Data Access for Location-Dependent Spatial Queries
Machine Learning Aided Key-Guessing Attack Paradigm Against Logic Block Encryption
Clausal Presentation of Theories in Deduction Modulo
VEGA Infrastructure for Resource Discovery in Grids
Mining Patterns from Change Logs to Support Reuse-Driven Evolution of Software Architectures
CNLPA-MVS: Coarse-Hypotheses Guided Non-Local PatchMatch Multi-View Stereo
Temperature-Aware Electromigration Analysis with Current-Tracking in Power Grid Networks
Securing Recommender Systems Against Shilling Attacks Using Social-Based Clustering
SmartPipe: Towards Interoperability of Industrial Applications via Computational Reflection
3D Face Similarity Measure by Fréchet Distances of Geodesics
Object identity in database systems
JacUOD: A New Similarity Measurement for Collaborative Filtering
A Secure Elliptic Curve-Based RFID Protocol
Structure of Weakly Invertible Semi-Input-Memory Finite Automata with Delay 2
Some Representation Theorems for Recovering Contraction Relations
Facilitating Service Discovery with Semantic Overlay
Combining gprof and event-driven monitoring for analyzing distributed programs: a rough view of NCSA mosaic
Trends in Computing with DNA
An Uncertainty Enhanced Trust Evolution Strategy for e-Science
Modelling enterprises with object-oriented paradigm
CFP: A Coherence-Free Processor Design
Inferring Solids Composed of Linear and Quadratic Surfaces from Incomplete Three Views
Neighborhood Combination Search for Single-Machine Scheduling with Sequence-Dependent Setup Time
Multi-Instance Learning from Supervised View
Efficient Video Cutout by Paint Selection
Pseudo-Randomness of Certain Sequences of k Symbols with Length pq
A Note on the Single Genotype Resolution Problem
Incremental Alignment Manifold Learning
A Motion Compensated Lifting Wavelet Codec for 3D Video Coding
Digital Multi-Signature Scheme Based on the Elliptic Curve Cryptosystem
A Logic Filter for Tumor Detection on Mammograms
A partial evaluator for a parallel lambda language
SMART: Speedup Job Completion Time by Scheduling Reduce Tasks
FlexPDA: A Flexible Programming Framework for Deep Learning Accelerators
Hybrid Broadcast for the Video-on-Demand Service
CK-Modes Clustering Algorithm Based on Node Cohesion in Labeled Property Graph
Joint Label-Specific Features and Correlation Information for Multi-Label Learning
Genome-Wide Analysis of Epigenetic Modifications
Active Learning Query Strategies for Classification, Regression, and Clustering: A Survey
Uncertain Distance-Based Range Queries over Uncertain Moving Objects
An Energy-Efficient Instruction Scheduler Design with Two-Level Shelving and Adaptive Banking
openGauss: An Open-Source Database for the Era of Artificial Intelligence
Multimodal Biometric Score Fusion Using Gaussian Mixture Model and Monte Carlo Method
Unified Parallel Lattice Structures for Block Time-Recursive Real-Valued Discrete Gabor Transforms
A boundary element method for simulation of deformable objects
Discovering Typed Communities in Mobile Social Networks
Rigidity Constraints for Large Mesh Deformation
A New Algebraic Modelling Approach to Distributed Problem-Solving in MAS
A Survey on Clock Synchronization in the Industrial Internet
Fast ray tracing NURBS surfaces
An Empirical Comparison Between Tutorials and Crowd Documentation of Application Programming Interface
A Differential Evolution Approach for Protein Folding Using a Lattice Model
A Model of Grid Service Capacity
A Fast Algorithm for Mining Association Rules
3D Ear Shape Matching Using Joint α-Entropy
Seeing Human Weight from a Single RGB-D Image
Differential Attack on Five Rounds of the SC2000 Block Cipher *
Global Optimization for Advertisement Selection in Sponsored Search
You Are How You Behave - Spatiotemporal Representation Learning for College Student Academic Achievement
Classifying Uncertain and Evolving Data Streams with Distributed Extreme Learning Machine
A Rigorous Architectural Approach to Adaptive Software Engineering
Source Code Prioritization Using Forward Slicing for Exposing Critical Elements in a Program
Data-Driven Approaches for Spatio-Temporal Analysis: A Survey of the State-of-the-Arts