yusuke1997/dblp-id-title huggingface dataset:
Capturing context-specific regulation in molecular interaction networks
Knowledge-based biomedical word sense disambiguation: comparison of approaches
Sequential Interim Analyses of Survival Data in DNA Microarray Experiments
Clustering analysis of tumor metabolic networks
Geoseq: a tool for dissecting deep-sequencing datasets
BADASS: BActeriocin-Diversity ASsessment Software
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites
Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information
WEP: a high-performance analysis pipeline for whole-exome data
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs
affy2svaffy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling
Terminologies for text-mining; an experiment in the lipoprotein metabolism domain
systemPipeR: NGS workflow and report generation environment
RiboA: a web application to identify ribosome A-site locations in ribosome profiling data
Metabopolis: scalable network layout for biological pathway diagrams in urban map style
iSeg: an efficient algorithm for segmentation of genomic and epigenomic data
ENGINES: exploring single nucleotide variation in entire human genomes
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems
Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis
Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order
Biclustering analysis on tree-shaped time-series single cell gene expression data of Caenorhabditis elegans
Inverse similarity and reliable negative samples for drug side-effect prediction
Deep gene selection method to select genes from microarray datasets for cancer classification
Weighted protein residue networks based on joint recurrences between residues
DeepTSS: multi-branch convolutional neural network for transcription start site identification from CAGE data
AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis
Visualizing phylogenetic tree landscapes
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Identification of DNA-binding proteins using support vector machines and evolutionary profiles
fREDUCE: Detection of degenerate regulatory elements using correlation with expression
A new pooling strategy for high-throughput screening: the Shifted Transversal Design
Using HPC for teaching and learning bioinformatics software: Benefits and challenges
Combining agent based-models and virtual screening techniques to predict the best citrus-derived vaccine adjuvants against human papilloma virus
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints
General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation
A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset
Analysis of feedback loops and robustness in network evolution based on Boolean models
Correction: Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data
A supervised term ranking model for diversity enhanced biomedical information retrieval
Medie and Info-pubmed: 2010 update
Identification of properties important to protein aggregation using feature selection
Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis
Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry
A quantitative analysis of monochromaticity in genetic interaction networks
Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus
Combining dissimilarity based classifiers for cancer prediction using gene expression profiles
A pipeline for RNA-seq based eQTL analysis with automated quality control procedures
Self consistency grouping: a stringent clustering method
Multi-view heterogeneous molecular network representation learning for protein-protein interaction prediction
Improved mutation tagging with gene identifiers applied to membrane protein stability prediction
PRIN, a predicted rice interactome network
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images
Risk score prediction model based on single nucleotide polymorphism for predicting malaria: a machine learning approach
Prediction of specificity-determining residues for small-molecule kinase inhibitors
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways
miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data
WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism
A novel Bayesian approach to quantify clinical variables and to determine their spectroscopic counterparts in 1 H NMR metabonomic data
ICGE: an R package for detecting relevant clusters and atypical units in gene expression
The Cluster Variation Method for Efficient Linkage Analysis on Extended Pedigrees
Subgroup detection in genotype data using invariant coordinate selection
3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape
From biophysics to evolutionary genetics: statistical aspects of gene regulation
AVC: Selecting discriminative features on basis of AUC by maximizing variable complementarity
Model-based clustering for flow and mass cytometry data with clinical information
Effect of APOE ε4 on multimodal brain connectomic traits: a persistent homology study
TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data
An automated proteomic data analysis workflow for mass spectrometry
MUMAL2: Improving sensitivity in shotgun proteomics using cost sensitive artificial neural networks and a threshold selector algorithm
goloco: a web application to create genome scale information from surprisingly small experiments
Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images
Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images
MetNetGE: interactive views of biological networks and ontologies
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions
Systematic integration of experimental data and models in systems biology
Efficient structure learning of gene regulatory networks with Bayesian active learning
ROKU: a novel method for identification of tissue-specific genes
Network topology measures for identifying disease-gene association in breast cancer
ARYANA: Aligning Reads by Yet Another Approach
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification
PeptX: Using Genetic Algorithms to optimize peptides for MHC binding
Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data
Psychoactive pharmaceuticals as environmental contaminants may disrupt highly inter-connected nodes in an Autism-associated protein-protein interaction network
Characterizing environmental and phenotypic associations using information theory and electronic health records
On the packing density of the unbound protein-protein interaction interface and its implications in dynamics
MSCTrees: a mean-shift based toolkit for cluster analysis of phylogenetic trees
LOSITAN: A workbench to detect molecular adaptation based on a F st -outlier method
A guided network estimation approach using multi-omic information
Exploiting locational and topological overlap model to identify modules in protein interaction networks
Joint analysis of histopathology image features and gene expression in breast cancer
The application of sparse estimation of covariance matrix to quadratic discriminant analysis
Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Version VI of the ESTree db: an improved tool for peach transcriptome analysis
miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases
An improved discriminative filter bank selection approach for motor imagery EEG signal classification using mutual information
Functional annotation by identification of local surface similarities: a novel tool for structural genomics
An evidence-based approach to identify aging-related genes in Caenorhabditis elegans
Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy
Practical application of a Bayesian network approach to poultry epigenetics and stress
A novel algorithm based on bi-random walks to identify disease-related lncRNAs
ADEPT: a domain independent sequence alignment strategy for gpu architectures
fcfdr: an R package to leverage continuous and binary functional genomic data in GWAS
Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm
Error margin analysis for feature gene extraction
Visualizing metabolic network dynamics through time-series metabolomic data
Enhanced CellClassifier: a multi-class classification tool for microscopy images
Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces
SheddomeDB: the ectodomain shedding database for membrane-bound shed markers
Biological interpretation of deep neural network for phenotype prediction based on gene expression
MASQOT: a method for cDNA microarray spot quality control
Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use Case
mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate
Probabilistic inference of lateral gene transfer events
Simulation of microarray data with realistic characteristics
Predicting stroke occurrences: a stacked machine learning approach with feature selection and data preprocessing
mDAG: a web-based tool for analyzing microarray data with multiple treatments
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation
Building a protein name dictionary from full text: a machine learning term extraction approach
Probabilistic base calling of Solexa sequencing data
metaGEENOME: an integrated framework for differential abundance analysis of microbiome data in cross-sectional and longitudinal studies
Bio: : Homology: : InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping
Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network
Variable-order reference-free variant discovery with the Burrows-Wheeler Transform
Validation of an arterial tortuosity measure with application to hypertension collection of clinical hypertensive patients
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson's disease subtypes
rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
A Dynamic Bayesian Network model for the simulation of Amyotrophic Lateral Sclerosis progression
Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks
Finding motif pairs in the interactions between heterogeneous proteins via bootstrapping and boosting
QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data
TreeToReads - a pipeline for simulating raw reads from phylogenies
Filtering ASVs/OTUs via mutual information-based microbiome network analysis
An integrative model of multi-organ drug-induced toxicity prediction using gene-expression data
BGFit: management and automated fitting of biological growth curves
A correlation-based network for biomarker discovery in obesity with metabolic syndrome
On the correspondence between the transcriptomic response of a compound and its effects on its targets
Partition decoupling for multi-gene analysis of gene expression profiling data
Dynamics of protofibril elongation and association involved in Aβ42 peptide aggregation in Alzheimer's disease
T-REX : software for the processing and analysis of T-RFLP data
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM
GOnet: a tool for interactive Gene Ontology analysis
Empirical study of supervised gene screening
IDconverter and IDClight: Conversion and annotation of gene and protein IDs
EMU: reconfigurable graphical user interfaces for Micro-Manager
Identification of residue pairing in interacting β-strands from a predicted residue contact map
Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond
Detection of gene orthology from gene co-expression and protein interaction networks
Evaluation of reaction gap-filling accuracy by randomization
Detecting structural variants involving repetitive elements: capturing transposition events of IS elements in the genome of Escherichia coli
STSE: Spatio-Temporal Simulation Environment Dedicated to Biology
Identifying diseases-related metabolites using random walk
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network
EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management
Marker-free image registration of electron tomography tilt-series
Selected proceedings of the First Summit on Translational Bioinformatics 2008
EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation
GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008
EvoLaps: a web interface to visualize continuous phylogeographic reconstructions
Investigation of mRNA Splicing in Saccharomyces cerevisiae using Microarrays
Determination of growth-coupling strategies and their underlying principles
MOKPE: drug-target interaction prediction via manifold optimization based kernel preserving embedding
EpiJen: a server for multistep T cell epitope prediction
Sparse kernel canonical correlation analysis for discovery of nonlinear interactions in high-dimensional data
Manhattan Harvester and Cropper: a system for GWAS peak detection
Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster
Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports
Envelope: interactive software for modeling and fitting complex isotope distributions
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods
Topology Consistency of Disease-specific Differential Co-regulatory Networks
Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions
Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing
Modified Pearson correlation coefficient for two-color imaging in spherocylindrical cells
Short read DNA fragment anchoring algorithm
RNASeq profiling of UTR expression during neuronal plasticity
Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates
Robust PCA based method for discovering differentially expressed genes
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations
Predicting disordered regions in proteins using the profiles of amino acid indices
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis
MarVis: a tool for clustering and visualization of metabolic biomarkers
AMPDeep: hemolytic activity prediction of antimicrobial peptides using transfer learning
Evaluation of methods for detecting conversion events in gene clusters
A mixture model with a reference-based automatic selection of components for disease classification from protein and/or gene expression levels
GENOMEMASKER package for designing unique genomic PCR primers
Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value
Detecting outliers when fitting data with nonlinear regression - a new method based on robust nonlinear regression and the false discovery rate
Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach
Multiset sparse partial least squares path modeling for high dimensional omics data analysis
Improving crop production using an agro-deep learning framework in precision agriculture
OntologyWidget - a reusable, embeddable widget for easily locating ontology terms
A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations
WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species
DRACP: a novel method for identification of anticancer peptides
Inferring gene regulatory networks from classified microarray data: Initial results
Comparing neural models for nested and overlapping biomedical event detection
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data
OD-seq: outlier detection in multiple sequence alignments
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Highlights from the Fourth International Society for Computational Biology Student Council Symposium at the Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology
The development of a three-frame timeline for clinical concepts extracted from discharge summaries
DISTEVAL: a web server for evaluating predicted protein distances
A classification-based framework for predicting and analyzing gene regulatory response
Evaluating statistical learning methods for cell type classification and feature selection using RNA-seq data
pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems
SAGPEK: fast and flexible approach to identify genotypes of Sanger sequencing data
Automated interpretation of 3D laserscanned point clouds for plant organ segmentation
Inferring circadian gene regulatory relationships from gene expression data with a hybrid framework
Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches
SIGI: score-based identification of genomic islands
TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data
Rare variants analysis using penalization methods for whole genome sequence data
ProFAT: a web-based tool for the functional annotation of protein sequences
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection
High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study
Pattern recognition in lymphoid malignancies using CytoGPS and Mercator
Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
Coupled Mutation Finder: A new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations
MEvoLib v1.0: the first molecular evolution library for Python
Metabolic Network Prediction Through Pairwise Rational Kernels
Protein complexes predictions within protein interaction networks using genetic algorithms
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
Knowledge-driven enhancements for task composition in bioinformatics
TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data
Genepi: a blackboard framework for genome annotation
GENLIB: an R package for the analysis of genealogical data
Promoting ranking diversity for genomics search with relevance-novelty combined model
Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization
Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools
A survey of orphan enzyme activities
Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis
Estimating the size of the solution space of metabolic networks
Assessing stability of gene selection in microarray data analysis
Genome-wide probabilistic reconciliation analysis across vertebrates
Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins
Pairwise visual comparison of small RNA secondary structures with base pair probabilities
NATbox: a network analysis toolbox in R
Protein-protein binding site identification by enumerating the configurations
A hybrid self-attention deep learning framework for multivariate sleep stage classification
Independent Component Analysis-motivated Approach to Classificatory Decomposition of Cortical Evoked Potentials
MS-Helios: a Circos wrapper to visualize multi-omic datasets
A latent allocation model for the analysis of microbial composition and disease
MIMOX: a web tool for phage display based epitope mapping
Accurate HLA type inference using a weighted similarity graph
A new Bayesian piecewise linear regression model for dynamic network reconstruction
Methylation data imputation performances under different representations and missingness patterns
Normalization and centering of array-based heterologous genome hybridization between species of unknown or unequal divergence
Modular co-evolution of metabolic networks
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species
MultiDCoX: Multi-factor analysis of differential co-expression
Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters
PlnTFDB: an integrative plant transcription factor database
Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data
HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data
Automatic detection of exonic splicing enhancers (ESEs) using SVMs