yusuke1997/dblp-id-title huggingface dataset:
REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance
Accurate prediction of nuclear receptors with conjoint triad feature
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
The 20 th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community
DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification
Antimicrobial peptide identification using multi-scale convolutional network
Neural network analysis of lymphoma microarray data: prognosis and diagnosis near-perfect
Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes
Gene selection algorithms for microarray data based on least squares support vector machine
SIDEKICK: Genomic data driven analysis and decision-making framework
SECIMTools: a suite of metabolomics data analysis tools
IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences
GROOLS: reactive graph reasoning for genome annotation through biological processes
CGKB: an annotation knowledge base for cowpea ( Vigna unguiculata L .) methylation filtered genomic genespace sequences
A seed expansion-based method to identify essential proteins by integrating protein-protein interaction sub-networks and multiple biological characteristics
Matrix factorization for the reconstruction of cervical cancer screening histories and prediction of future screening results
Bayesian modeling of recombination events in bacterial populations
MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants
Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines
Towards a robust out-of-the-box neural network model for genomic data
The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana
Super-delta: a new differential gene expression analysis procedure with robust data normalization
MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data
Erratum to: BicPAMS: software for biological data analysis with pattern-based biclustering
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data
A deep learning approach to predict inter-omics interactions in multi-layer networks
NormiRazor: tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies
Comparison of methods for the detection of outliers and associated biomarkers in mislabeled omics data
Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles
PIC-Me: paralogs and isoforms classifier based on machine-learning approaches
MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms
HaploPOP: a software that improves population assignment by combining markers into haplotypes
Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis
A systematic approach to identify therapeutic effects of natural products based on human metabolite information
SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects
Extracting transcription factor binding sites from unaligned gene sequences with statistical models
How to decide which are the most pertinent overly-represented features during gene set enrichment analysis
cDNA2Genome: A tool for mapping and annotating cDNAs
A simplified approach to disulfide connectivity prediction from protein sequences
The yeast kinome displays scale free topology with functional hub clusters
An analysis of entity normalization evaluation biases in specialized domains
Integrating peptides' sequence and energy of contact residues information improves prediction of peptide and HLA-I binding with unknown alleles
Identification of the sequence determinants of protein N -terminal acetylation through a decision tree approach
Interaction profile-based protein classification of death domain
A novel microbe-drug association prediction model based on graph attention networks and bilayer random forest
The role of nucleotide composition in premature termination codon recognition
Leveraging protein quaternary structure to identify oncogenic driver mutations
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa
Elucidating gene signatures that control the circadian rhythm in cyanobacteria using bioinformatics methods
A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery
Effective inter-residue contact definitions for accurate protein fold recognition
Copy Number Variation detection from 1000 Genomes project exon capture sequencing data
COVID-19 detection from chest X-ray images using CLAHE-YCrCb, LBP, and machine learning algorithms
Customised fragments libraries for protein structure prediction based on structural class annotations
PERGOLA: fast and deterministic linkage mapping of polyploids
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants
ATria: a novel centrality algorithm applied to biological networks
Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
Ensemble of rankers for efficient gene signature extraction in smoke exposure classification
An improved border detection in dermoscopy images for density based clustering
Use and mis-use of supplementary material in science publications
Combing the hairball with BioFabric: a new approach for visualization of large networks
RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU)
A new method for class prediction based on signed-rank algorithms applied to Affymetrix ® microarray experiments
The LabelHash Algorithm for Substructure Matching
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques
Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms
Reduced modeling of signal transduction - a modular approach
Graph-representation of oxidative folding pathways
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny
Virtual screening of GPCRs: An in silico chemogenomics approach
Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model
Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering
Towards bioinformatics assisted infectious disease control
Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource
MIPPIS: protein-protein interaction site prediction network with multi-information fusion
Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks
SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
In silico identification of putative promoter motifs of White Spot Syndrome Virus
An artificial intelligence-based risk prediction model of myocardial infarction
ushr: Understanding suppression of HIV in R
PrCRS: a prediction model of severe CRS in CAR-T therapy based on transfer learning
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance
libgapmis: extending short-read alignments
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions
Accurate genome-wide phasing from IBD data
Unsupervised binning of environmental genomic fragments based on an error robust selection of l -mers
Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer
miRNAminer: A tool for homologous microRNA gene search
Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion
Erratum to: PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events
Generalizing cell segmentation and quantification
GOrilla : a tool for discovery and visualization of enriched GO terms in ranked gene lists
Statistical analysis and molecular dynamics simulations of ambivalent alpha -helices
Simulation study and comparative evaluation of viral contiguous sequence identification tools
Computational identification of novel natural inhibitors of glucagon receptor for checking type II diabetes mellitus
multiMarker: software for modelling and prediction of continuous food intake using multiple biomarkers measurements
Benchmarking machine learning models for late-onset alzheimer's disease prediction from genomic data
NN-align . An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction
Automated craniofacial landmarks detection on 3D image using geometry characteristics information
Haploid to diploid alignment for variation calling assessment
Quality determination and the repair of poor quality spots in array experiments
The autophagy interaction network of the aging model Podospora anserina
Greedy feature selection for glycan chromatography data with the generalized Dirichlet distribution
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
Big data dimensionality reduction-based supervised machine learning algorithms for NASH diagnosis
Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid
DMR2+: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
Feature selection for high-dimensional temporal data
Metabolite coupling in genome-scale metabolic networks
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins
Neural representations of cryo-EM maps and a graph-based interpretation
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity
Intelligent diagnosis with Chinese electronic medical records based on convolutional neural networks
Identifying differential correlation in gene/pathway combinations
QNetDiff: a quantitative measurement of network rewiring
Genome-wide algorithm for detecting CNV associations with diseases
Satellog: A database for the identification and prioritization of satellite repeats in disease association studies
MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics
Improved functional prediction of proteins by learning kernel combinations in multilabel settings
TRAVeLer: a tool for template-based RNA secondary structure visualization
JAMI: a Java library for molecular interactions and data interoperability
LPMX: a pure rootless composable container system
The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain
FLIR vs SEEK thermal cameras in biomedicine: comparative diagnosis through infrared thermography
Hidden Markov model speed heuristic and iterative HMM search procedure
The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases
scDC: single cell differential composition analysis
Estimation of CpG coverage in whole methylome next-generation sequencing studies
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords
Clustering biological sequences with dynamic sequence similarity threshold
A SNP-centric database for the investigation of the human genome
trumpet: transcriptome-guided quality assessment of m6A-seq data
An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome
Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure
Low degree metabolites explain essential reactions and enhance modularity in biological networks
MetaDiff: differential isoform expression analysis using random-effects meta-regression
A balanced iterative random forest for gene selection from microarray data
Pattern matching for high precision detection of LINE-1s in human genomes
Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach
IntLIM: integration using linear models of metabolomics and gene expression data
Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution
Improving missing value imputation of microarray data by using spot quality weights
A new parallel pipeline for DNA methylation analysis of long reads datasets
A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation
GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments
CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets
Choosing negative examples for the prediction of protein-protein interactions
Five crucial prognostic-related autophagy genes stratified female breast cancer patients aged 40-60 years
Detecting recombination in evolving nucleotide sequences
Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques
EnsCat: clustering of categorical data via ensembling
Biomedical document triage using a hierarchical attention-based capsule network
An auditory display tool for DNA sequence analysis
MultiScale-CNN-4mCPred: a multi-scale CNN and adaptive embedding-based method for mouse genome DNA N4-methylcytosine prediction
The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules
Tissue enrichment analysis for C. elegans genomics
An improved ontological representation of dendritic cells as a paradigm for all cell types
RuleMonkey: software for stochastic simulation of rule-based models
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome
Bioactive Conformational Generation of Small Molecules: A Comparative Analysis between Force-Field and Multiple Empirical Criteria Based Methods
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
Identification of pre-microRNAs by characterizing their sequence order evolution information and secondary structure graphs
AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures
Ranking cancer drivers via betweenness-based outlier detection and random walks
Structured feature selection using coordinate descent optimization
Analysis of probe level patterns in Affymetrix microarray data
Odefy -- From discrete to continuous models
Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer
Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse
Computational analyses of eukaryotic promoters
Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering
The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards
SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides
MetaboMiner - semi-automated identification of metabolites from 2D NMR spectra of complex biofluids
The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)
A structural interpretation of the effect of GC-content on efficiency of RNA interference
Identifying structural domains of proteins using clustering
Acorn: an R package for de novo variant analysis
CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs
Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures
Clotho: addressing the scalability of forward time population genetic simulation
A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters
Conditional similarity triplets enable covariate-informed representations of single-cell data
SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics
Twiner: correlation-based regularization for identifying common cancer gene signatures
ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications
ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach
tRNA-derived fragments as novel potential biomarkers for relapsed/refractory multiple myeloma
FRASS: the web-server for RNA structural comparison
Turbocharging protein binding site prediction with geometric attention, inter-resolution transfer learning, and homology-based augmentation
Automated alignment-based curation of gene models in filamentous fungi
Quantifying robustness of biochemical network models
MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
Exploring cavity dynamics in biomolecular systems
Hybrid generative adversarial network based on frequency and spatial domain for histopathological image synthesis
Hybrid natural language processing tool for semantic annotation of medical texts in Spanish
Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture
Integrative modeling of transcriptional regulation in response to antirheumatic therapy
NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors
SAT, a flexible and optimized Web application for SSR marker development
NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae
miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark
A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D
Positive-unlabelled learning of glycosylation sites in the human proteome
Effects of scanning sensitivity and multiple scan algorithms on microarray data quality
RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers
Prediction of polyreactive and nonspecific single-chain fragment variables through structural biochemical features and protein language-based descriptors
eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains
Flux sampling in genome-scale metabolic modeling of microbial communities
openBEB: open biological experiment browser for correlative measurements
Sampling issues in quantitative analysis of dendritic spines morphology
An eScience-Bayes strategy for analyzing omics data
PASTA: splice junction identification from RNA-Sequencing data
AMDA: an R package for the automated microarray data analysis
Evaluation of O2PLS in Omics data integration
3D time series analysis of cell shape using Laplacian approaches
Recommending plant taxa for supporting on-site species identification
Fast algorithms and heuristics for phylogenomics under ILS and hybridization
SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences
Deep learning architectures for multi-label classification of intelligent health risk prediction
A decision analysis model for KEGG pathway analysis
Sparse regressions for predicting and interpreting subcellular localization of multi-label proteins
An ontology for representing hematologic malignancies: the cancer cell ontology
Tissue-associated microbial detection in cancer using human sequencing data
Logical Development of the Cell Ontology
GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis
A relation based measure of semantic similarity for Gene Ontology annotations
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees
PhenoExam: gene set analyses through integration of different phenotype databases
Regression applied to protein binding site prediction and comparison with classification
A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets
MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package
Overlapping group screening for detection of gene-gene interactions: application to gene expression profiles with survival trait
Identify Huntington's disease associated genes based on restricted Boltzmann machine with RNA-seq data
A model of the spatial tumour heterogeneity in colorectal adenocarcinoma tissue
Constructing patch-based ligand-binding pocket database for predicting function of proteins
Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs
Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival
AWclust: point-and-click software for non-parametric population structure analysis