yusuke1997/dblp-id-title huggingface dataset:
Distinguishing Numbers and Re-emebedding Structures of Triangulations on Closed Surfaces
Long cycles in graphs and digraphs
On Non-Rank Facets of Stable Set Polytopes of Webs with Clique Number Four-Extended Abstract-
There is a unique crossing-minimal rectilinear drawing of K 18
Some clustering algorithms in normed planes
Coupling methods to establish threshold functions in random graphs
Applications of the Erdős-Rado Canonical Ramsey Theorem to Erdős-Type Problems
On the connectedness property of service areas for the Network Facility Location Problem
An inflation algorithm and a toroidal mesh algorithm for edge-bipartite graphs
A new refinement procedure for graph isomorphism algorithms
Lines of Life for MGS Symbolic Descriptions
On Generalized Line Graphs with Crossing Number One
Discrepancy of Sums of two Arithmetic Progressions
Linear and Differential Cryptanalysis of Russian GOST
Packing, Counting and Covering Hamilton cycles in random directed graphs
Mixed colorings of hypergraphs
Intersection graphs of homothetic polygons
Lower Bound of the Covering Radius of Irreducible Goppa Codes
Feasibility Conditions on the Parameters of a Strongly Regular Graph
Higher Weights and Binary Self-Dual Codes
Maximum modulus points of meromorphic functions and Valiron's defect
On a Conjecture of Víctor Neumann-Lara
On the metrical rigidity of binary codes
Large-scale multi-period precedence constrained knapsack problem: A mining application
Parallel Contextual Array Grammars and Languages
The Structure of Linear Codes of Constant Weight
On Finding The Limit Shape Of Optimal Convex Lattice Polygons
The spectral excess theorem for distance-regular graphs having distance-d graph with fewer distinct eigenvalues
Nowhere-zero 5-flows and (1, 2)-factors
Clique-independent sets of Helly circular-arc graphs
Gaps in discrete random samples: extended abstract
An algebraic-perturbation variant of Barvinok's algorithm
On some applications of information indices in chemical graph theory
Computing and maximizing the exact reliability of wireless backhaul networks
Cubes polynomial and its derivatives
A Continuous Strategy to Solve a Class of Discrete Optimization Problems
An extremal problem on graphs
2-1 routing requests in the hypercube
Combinatorial Structures of Max-Type Functions characterizing the Optimal Solution of the Equivalence Problem
Separation of Antiweb-Wheel Inequalities Over Stable Set Polytopes
Abelian Colourings of Cubic Graphs
Self-Similar Polygonal Tiling: extended abstract
Average Longest Path and Maximum Cost Network Flows with Multiple-Criteria Weights
Invariant Kekulé structures in fullerene graphs
On diagnosability of large multiprocessor networks
Combinatorial Aspects of Interval Orders and Interval Graphs
Generating Functions and the Solutions of Full History Recurrence Equations
On the ratios and geometric boundaries of complex Horadam sequences
Social Networks Spread Rumors in Sublogarithmic Time
An application of flag algebras to a problem of Erdős and Sós
Finding a majority ball with majority answers
Robust Train Timetabling and Stop Planning with Uncertain Passenger Demand
On Rerouting Connection Requests in Networks with Shared Bandwidth
Linkages in Polytope Graphs
A Compact Linearisation of Euclidean Single Allocation Hub Location Problems
Some remarks on 3-partitions of multisets
On the aircraft conflict resolution problem: A VNS approach in a multiobjective framework
On the clique behavior of circulants with three small jumps
On Hamilton Cycles in Locally Connected Graphs with Vertex Degree Constraints
Solving the Two-Stage Robust FTTH network design Problem under Demand Uncertainty
Generalizations of a theorem of Paul Erdős with application
Automatic annotation of organellar genomes with DOGMA
multiTFA: a Python package for multi-variate thermodynamics-based flux analysis
Automatic registration of microarray images. II. Hexagonal grid
CoDNaS: a database of conformational diversity in the native state of proteins
Protein model quality assessment using 3D oriented convolutional neural networks
Design and application of PDBlib, a C++ macromolecular class library
BLAST PRINTS - alternative perspectives on sequence similarity
The Bayesian lasso for genome-wide association studies
ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes
INDRA-IPM: interactive pathway modeling using natural language with automated assembly
HiGwas: how to compute longitudinal GWAS data in population designs
OMAMO: orthology-based alternative model organism selection
Hierarchical classification of hydrolases catalytic sites
Modeling macro-molecular interfaces with Intervor
Benchmarking gene ontology function predictions using negative annotations
Quantitative performance metrics for robustness in circadian rhythms
Primer design using genetic algorithm
modSaRa: a computationally efficient R package for CNV identification
Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map
chipPCR: an R package to pre-process raw data of amplification curves
STATUS, SEQSTAT, CSTATUS and LOAD: computer programs that facilitate large DNA-sequencing projects
Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data
FAS: assessing the similarity between proteins using multi-layered feature architectures
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
BIRD: identifying cell doublets via biallelic expression from single cells
DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools
SimulaTE: simulating complex landscapes of transposable elements of populations
Metabolic network-guided binning of metagenomic sequence fragments
Intersect: identification and visualization of overlaps in database search results
CINEMA-MX: a modular multiple alignment editor
A multivariate approach for integrating genome-wide expression data and biological knowledge
A bi-dimensional regression tree approach to the modeling of gene expression regulation
Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model
A general computational method for robustness analysis with applications to synthetic gene networks
MESMER: minimal ensemble solutions to multiple experimental restraints
KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality
FusionEncoder: identification of intrinsically disordered regions based on multi-feature fusion
WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest
Fast protein fragment similarity scoring using a Binet-Cauchy kernel
Accurate self-correction of errors in long reads using de Bruijn graphs
Evaluation of annotation strategies using an entire genome sequence
Optimization strategies for fast detection of positive selection on phylogenetic trees
The effect of kinship in re-identification attacks against genomic data sharing beacons
Galaxy LIMS for next-generation sequencing
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons
Improved spliced alignment from an information theoretic approach
LOX: inferring Level Of eXpression from diverse methods of census sequencing
Developing structural profile matrices for protein secondary structure and solvent accessibility prediction
A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information
In silico gene function prediction using ontology-based pattern identification
Gene expression network analysis and applications to immunology
Multiple sequence alignment by parallel simulated annealing
Resolution improvement by modulation of analog-to-digital converters
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia
BrAPI - an application programming interface for plant breeding applications
CLIN-X : pre-trained language models and a study on cross-task transfer for concept extraction in the clinical domain
Signals in DNA sequences and their potential properties
PESTO: Parameter EStimation TOolbox
On global sequence alignment
Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types
On the feasibility of deep learning applications using raw mass spectrometry data
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures
webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration
GATHER: a systems approach to interpreting genomic signatures
AnoniMME: bringing anonymity to the Matchmaker Exchange platform for rare disease gene discovery
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity
Bayesian mixture analysis for metagenomic community profiling
FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps
Protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses
Inferring phylogeny from whole genomes
PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt
Probabilistic thermodynamic analysis of metabolic networks
Modeling and analyzing complex biological networks incooperating experimental information on both network topology and stable states
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA: I. A simulation model
Similarity of position frequency matrices for transcription factor binding sites
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles
Short algorithm to compensate for sampling-volume errors in diffusion- cell studies
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method
DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria
Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data
A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem
Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry
NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data
SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop
The need for a human gene index
RTNsurvival: an R/Bioconductor package for regulatory network survival analysis
CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure
Prediction and simulation of motion in pairs of transmembrane alpha-helices
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment
Open source platform for the execution and analysis of mechanical refolding experiments
FindNonCoding: rapid and simple detection of non-coding RNAs in genomes
hopsy - a methods marketplace for convex polytope sampling in Python
MrBait: universal identification and design of targeted-enrichment capture probes
GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data
Integrating full spectrum of sequence features into predicting functional microRNA-mRNA interactions
2D NMR metabonomic analysis: a novel method for automated peak alignment
TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data
AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs
Environment specific substitution tables improve membrane protein alignment
ChromoHub: a data hub for navigators of chromatin-mediated signalling
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE
Two effective methods for correcting experimental high-throughput screening data
E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs
Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology
PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks
CWig: compressed representation of Wiggle/BedGraph format
Tanglegrams for rooted phylogenetic trees and networks
pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies
Optimal adjustment sets for causal query estimation in partially observed biomolecular networks
Combining co-evolution and secondary structure prediction to improve fragment library generation
A two-part mixed-effects model for analyzing longitudinal microbiome compositional data
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs
PowerMarker: an integrated analysis environment for genetic marker analysis
Explainable multimodal machine learning model for classifying pregnancy drug safety
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings
GeneComber: Combining Outputs of Gene Prediction Programs for Improved Results
Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs
Modular organization of protein interaction networks
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors
CRAVAT: cancer-related analysis of variants toolkit
GeneInfoMiner - a web server for exploring biomedical literature using batch sequence ID
PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes
Cytoscape ESP: simple search of complex biological networks
C-It: a knowledge database for tissue-enriched genes
Compression of protein sequence databases
MoleMCL: a multi-level contrastive learning framework for molecular pre-training
AFLPinSilico, simulating AFLP fingerprints
Alpha-XIC: a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry
Protein function prediction and annotation in an integrated environment powered by web services (AFAWE)
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics
ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging
Towards an accurate and efficient heuristic for species/gene tree co-estimation
Figaro: a novel statistical method for vector sequence removal
Mining experimental evidence of molecular function claims from the literature
Correction to: DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
Prediction of kinase-specific phosphorylation sites using conditional random fields
Protein interaction interface region prediction by geometric deep learning
Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
POAVIZ: A Partial Order Multiple Sequence Alignment Visualizer
Fast and accurate read alignment for resequencing
Prediction of subcellular localization using sequence-biased recurrent networks
LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis
NeoFox: annotating neoantigen candidates with neoantigen features
affyGG: computational protocols for genetical genomics with Affymetrix arrays
Intervention in gene regulatory networks with maximal phenotype alteration
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations
ModLink+: improving fold recognition by using protein-protein interactions
Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables
Ensembling graph attention networks for human microbe-drug association prediction
A reinforcement learning framework for pooled oligonucleotide design
LFQC: a lossless compression algorithm for FASTQ files
MISA-web: a web server for microsatellite prediction
Concept-based annotation of enzyme classes
Bioframe: operations on genomic intervals in Pandas dataframes
MDB: a database system utilizing automatic construction of modules and STAR-derived universal language
VISTA : visualizing global DNA sequence alignments of arbitrary length
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
pyNBS: a Python implementation for network-based stratification of tumor mutations
Analysis of impedance-based cellular growth assays
COPS Benchmark: interactive analysis of database search methods
Bridges: a tool for identifying local similarities in long sequences
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
A microcomputer program for comparison and alignment of DNA sequence gel readings
An interpretable alphabet for local protein structure search based on amino acid neighborhoods
graph2tab, a library to convert experimental workflow graphs into tabular formats
Mismatch string kernels for discriminative protein classification
Stability selection for regression-based models of transcription factor-DNA binding specificity
SDSE: a software package to simulate the evolution of a pair of DNA sequences
gwasurvivr: an R package for genome-wide survival analysis
Efficient comparative phylogenetics on large trees
A novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression
FastMap: Fast eQTL mapping in homozygous populations
SubCons: a new ensemble method for improved human subcellular localization predictions
sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure
integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory
Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
DASS: efficient discovery and p -value calculation of substructures in unordered data
Inference of cellular level signaling networks using single-cell gene expression data in Caenorhabditis elegans reveals mechanisms of cell fate specification
On the reliability and the limits of inference of amino acid sequence alignments
New analytical tool for analysis of splice site sequence determinants
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites
Visualizing relationships between nucleic acid sequences using correlation images
Targeted realignment of LC-MS profiles by neighbor-wise compound-specific graphical time warping with misalignment detection
Identification of key concepts in biomedical literature using a modified Markov heuristic
The Bioinformatics Open Source Conference (BOSC) 2013
MEWpy: a computational strain optimization workbench in Python
A hybrid method to cluster protein sequences based on statistics and artificial neural networks
Deciphering the complexity of human non-coding promoter-proximal transcriptome
bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens
Incremental threading optimization (TITO) to help alignment and modelling of remote homologues
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases
A Bayesian approach to accurate and robust signature detection on LINCS L1000 data
Event extraction across multiple levels of biological organization
NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis
RUCS: rapid identification of PCR primers for unique core sequences
SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data
Improving translation initiation site and stop codon recognition by using more than two classes
NOE net -Use of NOE networks for NMR resonance assignment of proteins with known 3D structure
GOAnnotator: accurate protein function annotation using automatically retrieved literature
The Los Alamos hepatitis C sequence database
Partial least squares proportional hazard regression for application to DNA microarray survival data
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model
Epigenomic k -mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning
OPAL: prediction of MoRF regions in intrinsically disordered protein sequences
Biological Random Walks: multi-omics integration for disease gene prioritization
Hexanucleotide frequency database
ADME SARfari: comparative genomics of drug metabolizing systems
MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data
veqtl-mapper: variance association mapping for molecular phenotypes
The evolution of nitrogen fixation in cyanobacteria
PRADA: pipeline for RNA sequencing data analysis
Computational prediction of eukaryotic phosphorylation sites
ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels
TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs
Variance-stabilizing transformations for two-color microarrays
Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI
κ-helix and the helical lock and key model: a pivotal way of looking at polyproline II
Identifying disease-causing mutations with privacy protection
Association mapping and fine mapping with TreeLD
ATPdock: a template-based method for ATP-specific protein-ligand docking
Overlap detection on long, error-prone sequencing reads via smooth q-gram
DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism
RelExplain - integrating data and networks to explain biological processes
iMAT: an integrative metabolic analysis tool
Deciphering the associations between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach
Identifying residues that determine palmitoylation using association rule mining
Bayesian integrative model for multi-omics data with missingness
BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
DiNGO: standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models
Missing value estimation methods for DNA microarrays
Squeakr: an exact and approximate k-mer counting system
Journaled string tree - a scalable data structure for analyzing thousands of similar genomes on your laptop