yusuke1997/dblp-id-title huggingface dataset:
DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction
RFMapp: ribosome flow model application
FastRemap: a tool for quickly remapping reads between genome assemblies
ALeS: adaptive-length spaced-seed design
Mapping the attractor landscape of Boolean networks with biobalm
Hybrid alignment: high-performance with universal statistics
Multipopulation harmony search algorithm for the detection of high-order SNP interactions
ISEScan: automated identification of insertion sequence elements in prokaryotic genomes
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
Align-m-a new algorithm for multiple alignment of highly divergent sequences
BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images
DSRC 2 - Industry-oriented compression of FASTQ files
A helical lock and key model of polyproline II conformation with SH3
A computer program in BASIC for estimation of LD50 of a chemical by Dixon's up and down method
ShinyCell: simple and sharable visualization of single-cell gene expression data
An interactive triple-helical collagen builder
ReadXplorer 2 - detailed read mapping analysis and visualization from one single source
R2Dtool: integration and visualization of isoform-resolved RNA features
Using substitution probabilities to improve position-specific scoring matrices
Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data
A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance
Robust accurate identification of peptides (RAId): deciphering MS 2 data using a structured library search with de novo based statistics
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
Disulfide by Design TM : a computational method for the rational design of disulfide bonds in proteins
Integrating literature-constrained and data-driven inference of signalling networks
Fast alignment-free sequence comparison using spaced-word frequencies
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition
POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins
Testing microbiome association using integrated quantile regression models
Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat
PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data
QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics
Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data
Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets
JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites
Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data
Annotation and merging of SBML models with semanticSBML
Unravelling reference bias in ancient DNA datasets
A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge
DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency
Fragmentstein - facilitating data reuse for cell-free DNA fragment analysis
A CART-based approach to discover emerging patterns in microarray data
Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways
TAPAS: tool for alternative polyadenylation site analysis
BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome
Feature selection may improve deep neural networks for the bioinformatics problems
Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny
Structural search and retrieval using a tableau representation of protein folding patterns
Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
Expanded utility of the R package, qgg, with applications within genomic medicine
Kollector: transcript-informed, targeted de novo assembly of gene loci
DeepFam: deep learning based alignment-free method for protein family modeling and prediction
Graph embedding on biomedical networks: methods, applications and evaluations
Classification with reject option in gene expression data
MedicCyc: a biochemical pathway database for Medicago truncatula
Omega: an Overlap-graph de novo Assembler for Metagenomics
PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome
DNASTAT: a Pascal unit for the statistical analysis of DNA and protein sequences
UniCarb-DB: a database resource for glycomic discovery
Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer
J-Circos: an interactive Circos plotter
diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype
GWASinspector: comprehensive quality control of genome-wide association study results
ShinyKGode: an interactive application for ODE parameter inference using gradient matching
hacksig: a unified and tidy R framework to easily compute gene expression signature scores
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis
CMEP: a database for circulating microRNA expression profiling
Classification of microarray data with factor mixture models
On the problem of confounders in modeling gene expression
Bayesian-based selection of metabolic objective functions
Dot plot sequence comparisons on Macintosh computers
Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays
GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology
NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population
JETTA: junction and exon toolkits for transcriptome analysis
Multi-scale structural analysis of proteins by deep semantic segmentation
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis
baobabLUNA : the solution space of sorting by reversals
InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes
Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq
Toward a gold standard for promoter prediction evaluation
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data
Advancing entity recognition in biomedicine via instruction tuning of large language models
4mCPred: machine learning methods for DNA N4-methylcytosine sites prediction
Bioinformatics and the theoretical foundations of molecular biology
Understanding and predicting disease relationships through similarity fusion
Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions
SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing
Protter: interactive protein feature visualization and integration with experimental proteomic data
A simple algorithm for detecting circular permutations in proteins
IE-Kb: intron exon knowledge base
Classification of mislabelled microarrays using robust sparse logistic regression
A comprehensive web tool for toehold switch design
Learning phenotype densities conditional on many interacting predictors
Connectedness of PPI network neighborhoods identifies regulatory hub proteins
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs
pyconsFold: a fast and easy tool for modeling and docking using distance predictions
GENOME: a rapid coalescent-based whole genome simulator
DiffGraph: an R package for identifying gene network rewiring using differential graphical models
Pathway analysis using random forests classification and regression
LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse
ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes
Comparison of genetic variants in matched samples using thesaurus annotation
Correction to: NeoFox: annotating neoantigen candidates with neoantigen features
TreeDom: a graphical web tool for analysing domain architecture evolution
miRe2e: a full end-to-end deep model based on transformers for prediction of pre-miRNAs
Mathematical simulation and analysis of cellular metabolism and regulation
Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data
customProDB : an R package to generate customized protein databases from RNA-Seq data for proteomics search
MANTIS: a phylogenetic framework for multi-species genome comparisons
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins
Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data
Accelerating open modification spectral library searching on tensor core in high-dimensional space
Statistical analysis of antigen receptor spectratype data
QVZ: lossy compression of quality values
Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data
PheneBank: a literature-based database of phenotypes
The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures
Identification of functional links between genes using phylogenetic profiles
Protein (multi-)location prediction: utilizing interdependencies via a generative model
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads
A network approach to exploring the functional basis of gene-gene epistatic interactions in disease susceptibility
SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy
A major component approach to presenting consensus sequences
Mapping the genetic architecture of complex traits in experimental populations
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition
Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis
Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions
Crystallographic protein model-building on the web
Application of learning to rank to protein remote homology detection
Dasty2, an Ajax protein DAS client
Restriction site mapping is in separation theory
The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens
Multi-omics enrichment analysis using the GeneTrail2 web service
pyGOMoDo: GPCRs modeling and docking with python
Defining an informativeness metric for clustering gene expression data
Upcoming challenges for multiple sequence alignment methods in the high-throughput era
Object-oriented sequence analysis: SCL - a C++ class library
STracking: a free and open-source Python library for particle tracking and analysis
iScore: a novel graph kernel-based function for scoring protein-protein docking models
Flexible empirical Bayes models for differential gene expression
Reconstruction of gene networks using Bayesian learning and manipulation experiments
An empirical study on KDIGO-defined acute kidney injury prediction in the intensive care unit
Matching amino acid and nucleotide sequences of mouse rheumatoid factor CDRH3-FRH4 segments to other mouse antibodies with known specificities
Genome-wide association analysis by lasso penalized logistic regression
The influence of missing value imputation on detection of differentially expressed genes from microarray data
mBrainAligner-Web: a web server for cross-modal coherent registration of whole mouse brains
VARAN: a web server for Variability Analysis of DNA microarray experiments
Construction and completion of flux balance models from pathway databases
DIST: direct imputation of summary statistics for unmeasured SNPs
Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle
Bayesian correlated clustering to integrate multiple datasets
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
Physical Module Networks: an integrative approach for reconstructing transcription regulation
ScType enables fast and accurate cell type identification from spatial transcriptomics data
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization
Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry
Cancer subtype classification and modeling by pathway attention and propagation
GPU accelerated biochemical network simulation
BioJava: an open-source framework for bioinformatics
Fast and interpretable genomic data analysis using multiple approximate kernel learning
Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples
QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable
A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
Network-based cancer heterogeneity analysis incorporating multi-view of prior information
eGOB: eukaryotic Gene Order Browser
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
MedPost: a part-of-speech tagger for bioMedical text
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis
DeepEventMine: end-to-end neural nested event extraction from biomedical texts
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database
State aggregation for fast likelihood computations in molecular evolution
Gene Unscrambler for detangling scrambled genes in ciliates
Identifying signaling genes in spatial single-cell expression data
3-D multi-variate data display tool as a protein design aid
Web-based network analysis and visualization using CellMaps
A Bayesian framework for de novo mutation calling in parents-offspring trios
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
Gap statistics for whole genome shotgun DNA sequencing projects
A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in
Learning context-aware structural representations to predict antigen and antibody binding interfaces
Fragment assembly with short reads
Syntactic recognition of regulatory regions in Escherichia coli
Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations
Towards region-specific propagation of protein functions
BioEditor - Simplifying Macromolecular Structure Annotation
MOMENT: software for analysis and display of amphiphilic regions in proteins
MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms
CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome
Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments
IntegratedMRF: random forest-based framework for integrating prediction from different data types
MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites
IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line
NeuroCirc: an integrative resource of circular RNA expression in the human brain
Detecting potential labeling errors in microarrays by data perturbation
Authors' response to 'Comment on: ERGC: An efficient Referential Genome Compression Algorithm'
ROCR: visualizing classifier performance in R
Stepwise inference of likely dynamic flux distributions from metabolic time series data
Model-based optimization of subgroup weights for survival analysis
A haplotype-aware de novo assembly of related individuals using pedigree sequence graph
PiHelper: an open source framework for drug-target and antibody-target data
AbFlex: designing antibody complementarity determining regions with flexible CDR definition
Why are complementary DNA strands symmetric?
JSBML: a flexible Java library for working with SBML
DeeReCT-PolyA: a robust and generic deep learning method for PAS identification
A metric model of amino acid substitution
WHIDE - a web tool for visual data mining colocation patterns in multivariate bioimages
TrAGEDy - trajectory alignment of gene expression dynamics
LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification
WebGLORE: a Web service for Grid LOgistic REgression
An efficient concordant integrative analysis of multiple large-scale two-sample expression data sets
SCRIP: an accurate simulator for single-cell RNA sequencing data
Matching methods for observational microarray studies
Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities
RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis
BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data
A unifying framework for joint trait analysis under a non-infinitesimal model
The LCB Data Warehouse
Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets
MIToS.jl: mutual information tools for protein sequence analysis in the Julia language
EROS-DOCK: protein-protein docking using exhaustive branch-and-bound rotational search
Differential and trajectory methods for time course gene expression data
Fast evaluation of internal loops in RNA secondary structure prediction
MatchMixeR: a cross-platform normalization method for gene expression data integration
iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions
BioJava: an open-source framework for bioinformatics in 2012
Single-cell RNA sequencing data analysis based on non-uniformε-neighborhood network
Bayesian model selection for characterizing genomic imprinting effects and patterns
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images
Improved ancestry inference using weights from external reference panels
Analysis of whole-genome microarray replicates using mixed models
Multiclass cancer classification and biomarker discovery using GA-based algorithms
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
L-GRAAL: Lagrangian graphlet-based network aligner
ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants
PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes
GRAM and genfragII: solving and testing the single-digest, partially ordered restriction map problem
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes
Interoperable and scalable data analysis with microservices: applications in metabolomics
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
ballaxy: web services for structural bioinformatics
Comprehensive study on iterative algorithms of multiple sequence alignment
SAM: a system for iteratively building marker maps
Automatic 3D neuron tracing using all-path pruning
Intergenic sequence inspector: searching and identifying bacterial RNAs
Sequence and structural aspects of functional diversification in class I-mannosidase evolution
Multiple sequence alignment using simulated annealing
A knowledge model for analysis and simulation of regulatory networks
GENI-DB: a database of global events for epidemic intelligence
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis
Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation
Unpaired data empowers association tests
Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry
qpcR : an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis
AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures
Structure-aware protein self-supervised learning
Adplot: detection and visualization of repetitive patterns in complete genomes
Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data
Metabolite identification through multiple kernel learning on fragmentation trees
SW#-GPU-enabled exact alignments on genome scale
Prioritization of oligogenic variant combinations in whole exomes
ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation
A statistical method for the detection of variants from next-generation resequencing of DNA poolsA probabilistic method for the detection and genotyping of small indels from population-scale sequence data
Genetic algorithms applied to multi-class prediction for the analysis of gene expression data
Functional evaluation of domain-domain interactions and human protein interaction networks
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function
FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations
Improved orthology inference with Hieranoid 2