yusuke1997/dblp-id-title huggingface dataset:
Correction to: Eye‑color and Type‑2 diabetes phenotype prediction from genotype data using deep learning methods
ProteinVolume: calculating molecular van der Waals and void volumes in proteins
Improving protein interaction prediction in GenPPi: a novel interaction sampling approach preserving network topology
From POS tagging to dependency parsing for biomedical event extraction
iEnhancer-DCLA: using the original sequence to identify enhancers and their strength based on a deep learning framework
Toolboxes for a standardised and systematic study of glycans
Characterizing Genetic Interactions in Human Disease Association Studies Using Statistical Epistasis Networks
Prediction of piRNAs using transposon interaction and a support vector machine
Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model
iProL: identifying DNA promoters from sequence information based on Longformer pre-trained model
Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks
Active learning for human protein-protein interaction prediction
'apparent': a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information
Identification of highly related references about gene-disease association
Limblab: pipeline for 3D analysis and visualisation of limb bud gene expression
Profiling networks of distinct immune-cells in tumors
A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL
Mapping biological entities using the Longest Approximately Common Prefix method
Functional characterization and topological modularity of molecular interaction networks
JLIN: A java based linkage disequilibrium plotter
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec
HoCoRT: host contamination removal tool
Enhancing drug property prediction with dual-channel transfer learning based on molecular fragment
A novel weighted pseudo-labeling framework based on matrix factorization for adverse drug reaction prediction
Comparative visualization of protein secondary structures
On single and multiple models of protein families for the detection of remote sequence relationships
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments
Fine-tuning a sentence transformer for DNA
GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique
Reliable scaling of position weight matrices for binding strength comparisons between transcription factors
String kernels for protein sequence comparisons: improved fold recognition
Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain
Regularized binormal ROC method in disease classificationusing microarray data
"gnparser": a powerful parser for scientific names based on Parsing Expression Grammar
Active machine learning for transmembrane helix prediction
Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold
Curation of viral genomes: challenges, applications and the way forward
C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data
T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory
Robust joint score tests in the application of DNA methylation data analysis
A statistical measure for the skewness of X chromosome inactivation based on case-control design
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network
Network-based support vector machine for classification of microarray samples
Predictive modeling of anti-malarial molecules inhibiting apicoplast formation
Improving multiple sequence alignment by using better guide trees
Evaluation of Glycine max mRNA clusters
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations
CloudMan as a platform for tool, data, and analysis distribution
OReFiL: an online resource finder for life sciences
MDFGNN-SMMA: prediction of potential small molecule-miRNA associations based on multi-source data fusion and graph neural networks
Forward-time simulation of realistic samples for genome-wide association studies
Viral DNA replication: new insights and discoveries from large scale computational analysis
Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells
Modeling human cancer-related regulatory modules by GA-RNN hybrid algorithms
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
High performance workflow implementation for protein surface characterization using grid technology
SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data
Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification
Statistical assessment and visualization of synergies for large-scale sparse drug combination datasets
Bayesian model selection for the Drosophila gap gene network
GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
AccPbFRET: An ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images
Integrating sequence and structural biology with DAS
Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach
A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants
Integrating functional genomics data using maximum likelihood based simultaneous component analysis
Predicting potential miRNA-disease associations based on more reliable negative sample selection
ProPhylo: Partial Phylogenetic Profiling to guide protein family construction and assignment of biological process
Comprehensive analysis of circadian periodic pattern in plant transcriptome
Improving a gold standard: treating human relevance judgments of MEDLINE document pairs
FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing
A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
An image classification approach to analyze the suppression of plant immunity by the human pathogen Salmonella Typhimurium
Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays
Automatic construction of rule-based ICD-9-CM coding systems
Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug-target interactions prediction
Automatic document classification of biological literature
MAID : An effect size based model for microarray data integration across laboratories and platforms
Graph-based signal integration for high-throughput phenotyping
Implementation of multiple-instance learning in drug activity prediction
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS
Scalable global alignment for multiple biological networks
Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions
The effect of noise-induced variance on parameter recovery from reaction times
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes
Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation
LDscaff: LD-based scaffolding of de novo genome assemblies
Graph embedding on mass spectrometry- and sequencing-based biomedical data
GeneSCF: a real-time based functional enrichment tool with support for multiple organisms
Improved protein surface comparison and application to low-resolution protein structure data
iCTNet: A Cytoscape plugin to produce and analyze integrative complex traits networks
ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding
Scientists' sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018)
Correction: MethylSeqLogo: DNA methylation smart sequence logos
Estimating the effect size of a hidden causal factor between SNPs and a continuous trait: a mediation model approach
A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain
Detecting intergene correlation changes in microarray analysis: a new approach to gene selection
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data
Selected abstracts of Bioinformatics: from Algorithms to Applications 2021 Conference
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM
Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer
Infection in the intensive care unit alters physiological networks
Quality assessment of protein model-structures based on structural and functional similarities
Integrating automated literature searches and text mining in biomarker discovery
nDNA-prot: identification of DNA-binding proteins based on unbalanced classification
Determining significance of pairwise co-occurrences of events in bursty sequences
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
Protein-protein interface hot spots prediction based on a hybrid feature selection strategy
A methodology for the structural and functional analysis of signaling and regulatory networks
Constrained hidden Markov models for population-based haplotyping
Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis
Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types
iVUN: interactive Visualization of Uncertain biochemical reaction Networks
Integrated web visualizations for protein-protein interaction databases
Protein function annotation based on heterogeneous biological networks
CAR: contig assembly of prokaryotic draft genomes using rearrangements
SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences
Protein family comparison using statistical models and predicted structural information
Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs
A hybrid algorithm for clinical decision support in precision medicine based on machine learning
Computational prediction of MoRFs based on protein sequences and minimax probability machine
Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences
Predicting Ca 2+ and Mg 2+ ligand binding sites by deep neural network algorithm
Structural alignment of protein descriptors - a combinatorial model
Multimodal deep representation learning for protein interaction identification and protein family classification
A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy
Revealing and avoiding bias in semantic similarity scores for protein pairs
Phenotype prediction based on genome-wide DNA methylation data
Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine
LW-FQZip 2: a parallelized reference-based compression of FASTQ files
GeneSetCluster: a tool for summarizing and integrating gene-set analysis results
A novel approach to phylogenetic tree construction using stochastic optimization and clustering
HLA-check: evaluating HLA data from SNP information
UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data
Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs
Using ESTs to improve the accuracy of de novo gene prediction
A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
Focused multidimensional scaling: interactive visualization for exploration of high-dimensional data
A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs
Fast noisy long read alignment with multi-level parallelism
ProbCD: enrichment analysis accounting for categorization uncertainty
BicSPAM: flexible biclustering using sequential patterns
Cross-study analyses of microbial abundance using generalized common factor methods
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Unsupervised fuzzy pattern discovery in gene expression data
DeltaProt: a software toolbox for comparative genomics
VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization
Mapping transcription mechanisms from multimodal genomic data
altAFplotter: a web app for reliable UPD detection in NGS diagnostics
Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
A specialized learner for inferring structured cis-regulatory modules
Computationally repurposing drugs for breast cancer subtypes using a network-based approach
Mining for class-specific motifs in protein sequence classification
SimHap GUI: An intuitive graphical user interface for genetic association analysis
Pathogenic Bacillus anthracis in the progressive gene losses and gains in adaptive evolution
On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes
Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels
Selection of informative clusters from hierarchical cluster tree with gene classes
Multiclass classification of microarray data samples with a reduced number of genes
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis
Secondary structure assignment that accurately reflects physical and evolutionary characteristics
Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis
Metabolomics data analysis and missing value issues with application to infarcted mouse hearts
123VCF: an intuitive and efficient tool for filtering VCF files
Feature selection for RNA cleavage efficiency at specific sites using the LASSO regression model in Arabidopsis thaliana
Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network
Scientific Laboratory Information Management System: Tissue Bank
Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database
A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches
TIGERi: modeling and visualizing the responses to perturbation of a transcription factor network
Towards a supervised classification of neocortical interneuron morphologies
Predicting and improving the protein sequence alignment quality by support vector regression
Brain medical image diagnosis based on corners with importance-values
A reexamination of information theory-based methods for DNA-binding site identification
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants
BIGSdb: Scalable analysis of bacterial genome variation at the population level
Biomine: predicting links between biological entities using network models of heterogeneous databases
Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate
MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts
Non-coding RNA detection methods combined to improve usability, reproducibility and precision
Predicting substitutions to modulate disorder and stability in coiled-coils
cnvCurator: an interactive visualization and editing tool for somatic copy number variations
Tensor decomposition-based and principal-component-analysis-based unsupervised feature extraction applied to the gene expression and methylation profiles in the brains of social insects with multiple castes
Characterization and simulation of cDNA microarray spots using a novel mathematical model
EasySMPC: a simple but powerful no-code tool for practical secure multiparty computation
Dimension reduction with redundant gene elimination for tumor classification
Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data
Assessment of potential human health risks in aquatic products based on the heavy metal hazard decision tree
ILRC: a hybrid biomarker discovery algorithm based on improved L1 regularization and clustering in microarray data
Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX
A nonparametric model for quality control of database search results in shotgun proteomics
Reconstructing networks of pathways via significance analysis of their intersections
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions
GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes
Cell ontology in an age of data-driven cell classification
PRAP: Pan Resistome analysis pipeline
Joining Illumina paired-end reads for classifying phylogenetic marker sequences
Crossfeat: a transformer-based cross-feature learning model for predicting drug side effect frequency
Bayesian integrated modeling of expression data: a case study on RhoG
Identification of conserved gene clusters in multiple genomes based on synteny and homology
Clustering of cancer data based on Stiefel manifold for multiple views
Cancer Computational Biology
A semi-automated genome annotation comparison and integration scheme
Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling
Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks
Improved hit criteria for DNA local alignment
Efficiency clustering for low-density microarrays and its application to QPCR
BioLake: an RNA expression analysis framework for prostate cancer biomarker powered by data lakehouse
AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities
Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification
A method for computing the overall statistical significance of a treatment effect among a group of genes
OntoGene web services for biomedical text mining
OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
Identification of hearing loss relevant genes in QTL on mouse chromosome 16
InCoB2014: bioinformatics to tackle the data to knowledge challenge
A context-based approach to identify the most likely mapping for RNA-seq experiments
Mining expression-dependent modules in the human interaction network
A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks
A framework for space-efficient read clustering in metagenomic samples
Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
Network analysis of gene fusions in human cancer
The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme
Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses
The expression landscape of JAK1 and its potential as a biomarker for prognosis and immune infiltrates in NSCLC
Detection of interaction articles and experimental methods in biomedical literature
Phylogenetic detection of conserved gene clusters in microbial genomes
BCRgt: a Bayesian cluster regression-based genotyping algorithm for the samples with copy number alterations
The PathOlogist: An Automated Tool for Pathway-Centric Analysis
Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010
Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methods
Graph-based machine learning model for weight prediction in protein-protein networks
Discovering MoRFs by trisecting intrinsically disordered protein sequence into terminals and middle regions
Orymold: ontology based gene expression data integration and analysis tool applied to rice
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
Deep active learning for classifying cancer pathology reports
NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface
An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images
Genotype calling in tetraploid species from bi-allelic marker data using mixture models
Cross-species gene normalization by species inference
Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters
ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment
Combining learning and constraints for genome-wide protein annotation
A novel approach for multi-SNP GWAS and its application in Alzheimer's disease
SpectralNET - an application for spectral graph analysis and visualization
Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes
Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty
Infrastructure for the life sciences: design and implementation of the UniProt website
Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes
In silico modeling of phosphorylation dependent and independent c-Myc degradation
Highlights from the Third European International Society for Computational Biology (ISCB) Student Council Symposium 2014
Pathway-PDT: a flexible pathway analysis tool for nuclear families
A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches