yusuke1997/dblp-id-title huggingface dataset:
Biomedical event extraction with a novel combination strategy based on hybrid deep neural networks
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Bayesian models for pooling microarray studies with multiple sources of replications
Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system
VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery
Amino acid encoding for deep learning applications
EpiViewer: an epidemiological application for exploring time series data
Combining classifiers for improved classification of proteins from sequence or structure
Unsupervised inference of implicit biomedical events using context triggers
FeatureSelect: a software for feature selection based on machine learning approaches
An integrative modular approach to systematically predict gene-phenotype associations
Structural assembly of two-domain proteins by rigid-body docking
A novel method for predicting cell abundance based on single-cell RNA-seq data
Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases
Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models
Correction to: Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters
DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization
HGGA: hierarchical guided genome assembler
Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)
RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information
adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies
Restricted DCJ-indel model: sorting linear genomes with DCJ and indels
Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
GapCoder automates the use of indel characters in phylogenetic analysis
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes
KNN-MDR: a learning approach for improving interactions mapping performances in genome wide association studies
SPiCE: a web-based tool for sequence-based protein classification and exploration
Drug-target interactions prediction using marginalized denoising model on heterogeneous networks
Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network
Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data
A genetic ensemble approach for gene-gene interaction identification
Overview of the BioCreative III Workshop
PupDB: a database of pupylated proteins
GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models
Improving the specificity of high-throughput ortholog prediction
Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics
MEPHAS: an interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny
Empirical Bayesian selection of hypothesis testing procedures for analysis of digital gene expression data
Multiple structure alignment with msTALI
Using controls to limit false discovery in the era of big data
Determination of the differentially expressed genes in microarray experiments using local FDR
Validation and characterization of DNA microarray gene expression data distribution and associated moments
Enabling personalised disease diagnosis by combining a patient's time-specific gene expression profile with a biomedical knowledge base
Correlation analysis of the side-chains conformational distribution in bound and unbound proteins
Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species
Pushing the accuracy limit of shape complementarity for protein-protein docking
Random forest-based imputation outperforms other methods for imputing LC-MS metabolomics data: a comparative study
COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data
Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development
NOREC4DNA: using near-optimal rateless erasure codes for DNA storage
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models
Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis
Subtyping irritable bowel syndrome using cluster analysis: a systematic review
An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping
Integrating microRNA target predictions for the discovery of gene regulatory networks: a semi-supervised ensemble learning approach
Sparse reduced-rank regression for integrating omics data
Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays
Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
NEAT: a framework for building fully automated NGS pipelines and analyses
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation
Computational methods to identify novel methyltransferases
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation
Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers
Artificial Intelligence based wrapper for high dimensional feature selection
Predicting tumor cell line response to drug pairs with deep learning
Predicting drug side effects by multi-label learning and ensemble learning
Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies
FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral
Predicting drug target interactions using meta-path-based semantic network analysis
Systematic exploration of guide-tree topology effects for small protein alignments
Feature engineering for MEDLINE citation categorization with MeSH
CYCLONE: recycle contrastive learning for integrating single-cell gene expression data
Multipolar representation of protein structure
groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data
QTLTableMiner++: semantic mining of QTL tables in scientific articles
Quantized correlation coefficient for measuring reproducibility of ChIP-chip data
Testing statistical significance scores of sequence comparison methods with structure similarity
Directionality in protein fold prediction
ecpc: an R-package for generic co-data models for high-dimensional prediction
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
Universal seeds for cDNA-to-genome comparison
PMTED: a plant microRNA target expression database
Literature based discovery of alternative TCM medicine for adverse reactions to depression drugs
Reuse of imputed data in microarray analysis increases imputation efficiency
Identification and characterization of plastid-type proteins from sequence-attributed features using machine learning
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides
Graph rigidity reveals well-constrained regions of chromosome conformation embeddings
Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation
ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data
Deriving enzymatic and taxonomic signatures of metagenomes from short read data
Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides
Optimizing amino acid substitution matrices with a local alignment kernel
SciDBMaker: new software for computer-aided design of specialized biological databases
nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data
Species identification for gene name normalization
MIC_Locator: a novel image-based protein subcellular location multi-label prediction model based on multi-scale monogenic signal representation and intensity encoding strategy
Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient
Predicting protein-protein interactions using high-quality non-interacting pairs
C3: connect separate connected components to form a succinct disease module
Improving gene set analysis of microarray data by SAM-GS
Novel genetic matching methods for handling population stratification in genome-wide association studies
Improving biomarker list stability by integration of biological knowledge in the learning process
CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments
A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons
ORFer - retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files
EnsembleSplice: ensemble deep learning model for splice site prediction
Discovering patterns in drug-protein interactions based on their fingerprints
Anchor Clustering for million-scale immune repertoire sequencing data
The choice of null distributions for detecting gene-gene interactions in genome-wide association studies
Does the choice of nucleotide substitution models matter topologically?
Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
Status quo of annotation of human disease variants
Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria
Gene Expression-Based Cross Species Tissue Mapping
SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models
'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools
Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists
Learning self-supervised molecular representations for drug-drug interaction prediction
Causal discovery approach with reinforcement learning for risk factors of type II diabetes mellitus
Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots
Protein structure prediction with local adjust tabu search algorithm
Improving data interpretability with new differential sample variance gene set tests
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites
AMYCO: evaluation of mutational impact on prion-like proteins aggregation propensity
PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes
A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study
FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
SMILES alignment: a dynamic programming approach for the alignment of metabolites and other small organic molecules
Analyzing the similarity of samples and genes by MG-PCC algorithm, t-SNE-SS and t-SNE-SG maps
NeuroimaGene: an R package for assessing the neurological correlates of genetically regulated gene expression
Fuzzy rule based unsupervised approach for gene saliency
In silico drug repositioning using deep learning and comprehensive similarity measures
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking
Predicting active site residue annotations in the Pfam database
RepSeq - A database of amino acid repeats present in lower eukaryotic pathogens
Decontaminating eukaryotic genome assemblies with machine learning
Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
Prediction of beta-barrel membrane proteins by searching for restricted domains
OrthoClusterDB: an online platform for synteny blocks
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
A method for validation for clustering of phenotypic gene knockdown profiles using protein-protein interactions information
Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)
Ranking metrics in gene set enrichment analysis: do they matter?
A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies
Location, location, location: utilizing pipelines and services to more effectively georeference the world's biodiversity data
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots
The limit fold change model: A practical approach for selecting differentially expressed genes from microarray data
how_are_we_stranded_here: quick determination of RNA-Seq strandedness
Automatic, context-specific generation of Gene Ontology slims
Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP)
Which data subset should be augmented for deep learning? a simulation study using urothelial cell carcinoma histopathology images
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
Identifying genes that contribute most to good classification in microarrays
ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data
Guidelines for managing data and processes in bone and cartilage tissue engineering
Missing genes in the annotation of prokaryotic genomes
FPD2GB2: Automating a transition from a customized genome browser to GBrowse2
airpg: automatically accessing the inverted repeats of archived plastid genomes
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains
OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
Efficient and accurate greedy search methods for mining functional modules in protein interaction networks
Detecting overlapping protein complexes in weighted PPI network based on overlay network chain in quotient space
A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics
Haplotype reconstruction using perfect phylogeny and sequence data
iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation
Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
Does adding the drug-drug similarity to drug-target interaction prediction methods make a noticeable improvement in their efficiency?
Nanopore basecalling from a perspective of instance segmentation
Microarray analysis of gene expression during auditory hair cell regeneration in zebrafish ( Danio rerio )
A novel protein descriptor for the prediction of drug binding sites
Multi-label classification with XGBoost for metabolic pathway prediction
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data
Microarray image analysis: background estimation using quantile and morphological filters
Quantifying the relationship between co-expression, co-regulation and gene function
Correction: Minimum uncertainty as Bayesian network model selection principle
WASABI: a dynamic iterative framework for gene regulatory network inference
vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments
DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins
Identifying elemental genomic track types and representing them uniformly
Kernelized multiview signed graph learning for single-cell RNA sequencing data
metaSPARSim: a 16S rRNA gene sequencing count data simulator
Exploring drug combinations in genetic interaction network
HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations
An adaptive genetic algorithm for selection of blood-based biomarkers for prediction of Alzheimer's disease progression
A method combining a random forest-based technique with the modeling of linkage disequilibrium through latent variables, to run multilocus genome-wide association studies
StackDPP: a stacking ensemble based DNA-binding protein prediction model
DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
A web services choreography scenario for interoperating bioinformatics applications
Local sequence and sequencing depth dependent accuracy of RNA-seq reads
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles
MADOKA: an ultra-fast approach for large-scale protein structure similarity searching
VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences
Deep neural networks for human microRNA precursor detection
A simple and fast heuristic for protein structure comparison
Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study
A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information
Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
Eval: A software package for analysis of genome annotations
Meta-analysis of genes within QTLs of group A streptococcal sepsis and their expression QTLs reveal pathways modulating host differential response to streptococcal sepsis
consHLA: a next generation sequencing consensus-based HLA typing workflow
Computational inference of regulator activity in a single input motif from gene expression data
edge2vec: Representation learning using edge semantics for biomedical knowledge discovery
Two-part permutation tests for DNA methylation and microarray data
An effective and robust method for tracking multiple fish in video image based on fish head detection
Genome-wide discovery of missing genes in biological pathways of prokaryotes
Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities
Better ILP models for haplotype assembly
The Poisson distribution model fits UMI-based single-cell RNA-sequencing data
Statistical power for cluster analysis
Evaluating the use of different positional strategies for sentence selection in biomedical literature summarization
Prediction of hot spots in protein-DNA binding interfaces based on discrete wavelet transform and wavelet packet transform
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes
Protein ligand-specific binding residue predictions by an ensemble classifier
Statistical significance for hierarchical clustering in genetic association and microarray expression studies
SNP and gene networks construction and analysis from classification of copy number variations data
HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data
e!DAL - a framework to store, share and publish research data
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species
Quantifying variances in comparative RNA secondary structure prediction
Analysis of drug resistance in HIV protease
An efficient algorithm to explore liquid association on a genome-wide scale
JLAN: medical code prediction via joint learning attention networks and denoising mechanism
Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks
fuseMLR: an R package for integrative prediction modeling of multi-omics data
Performance analysis of novel methods for detecting epistasis
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale
Designing of peptides with desired half-life in intestine-like environment
GATA: a graphic alignment tool for comparative sequence analysis
Free energy estimation of short DNA duplex hybridizations
HostNet: improved sequence representation in deep neural networks for virus-host prediction
Combining joint models for biomedical event extraction
Network tuned multiple rank aggregation and applications to gene ranking
Improving automatic GO annotation with semantic similarity
GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
Validating a web application's use of genetic distance to determine helminth species boundaries and aid in identification
Solr-Plant: efficient extraction of plant names from text
Network meta-analysis correlates with analysis of merged independent transcriptome expression data
Characterization of protein-interaction networks in tumors
GMDD: a database of GMO detection methods
A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests
Discovery and analysis of consistent active sub-networks in cancers
Generating samples for association studies based on HapMap data
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer
Sensorimotor control: computing the immediate future from the delayed present
A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction
A joint model for nonparametric functional mapping of longitudinal trajectory and time-to-event
Gene selection with multiple ordering criteria
Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3
Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes