yusuke1997/dblp-id-title huggingface dataset:
Degeneracy and genetic assimilation in RNA evolution
Repositioning drugs by targeting network modules: a Parkinson's disease case study
The regulatory pattern of target gene expression by aberrant enhancer methylation in glioblastoma
LAPIS is a fast web API for massive open virus sequencing data
Copy number variation signature to predict human ancestry
Sorting by weighted inversions considering length and symmetry
Investigation and identification of protein γ-glutamyl carboxylation sites
Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy
Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)
The challenges of explainable AI in biomedical data science
YBYRÁ facilitates comparison of large phylogenetic trees
An improved DNA-binding hot spot residues prediction method by exploring interfacial neighbor properties
Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner
CoXpress: differential co-expression in gene expression data
LiverWiki: a wiki-based database for human liver
Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels
A statistical model for the analysis of beta values in DNA methylation studies
The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool
inPHAP: Interactive visualization of genotype and phased haplotype data
Biana: a software framework for compiling biological interactions and analyzing networks
Various criteria in the evaluation of biomedical named entity recognition
Artificial and natural duplicates in pyrosequencing reads of metagenomic data
RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads
Acceptance Prediction for Answers on Online Health-care Community
Integrating gene expression and GO classification for PCA by preclustering
Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes
Clustering under the line graph transformation: application to reaction network
The Text-mining based PubChem Bioassay neighboring analysis
TOGGLE: toolbox for generic NGS analyses
A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder
Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images
The ancient history of the structure of ribonuclease P and the early origins of Archaea
eNetXplorer: an R package for the quantitative exploration of elastic net families for generalized linear models
OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data
M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy
Mixed reality simulation of rasping procedure in artificial cervical disc replacement (ACDR) surgery
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics
Mining locus tags in PubMed Central to improve microbial gene annotation
Using empirical biological knowledge to infer regulatory networks from multi-omics data
Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
Investigating drug repositioning opportunities in FDA drug labels through topic modeling
Predicting the recurrence of noncoding regulatory mutations in cancer
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily
PubMed related articles: a probabilistic topic-based model for content similarity
YOC, A new strategy for pairwise alignment of collinear genomes
NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology
Approaching the taxonomic affiliation of unidentified sequences in public databases - an example from the mycorrhizal fungi
gtrellis: an R/Bioconductor package for making genome-level Trellis graphics
A multi-network integration approach for measuring disease similarity based on ncRNA regulation and heterogeneous information
Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency
GapFiller: a de novo assembly approach to fill the gap within paired reads
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs
Population structure analysis on 2504 individuals across 26 ancestries using bioinformatics approaches
Reconstruction of cell population dynamics using CFSE
Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine
Object-based representation and analysis of light and electron microscopic volume data using Blender
Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks
Automatic landmark annotation and dense correspondence registration for 3D human facial images
Improving the accuracy of expression data analysis in time course experiments using resampling
A modular computational framework for automated peak extraction from ion mobility spectra
SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services
Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)
Navigating 3D electron microscopy maps with EM-SURFER
BIOCAT: a pattern recognition platform for customizable biological image classification and annotation
A probabilistic classifier for olfactory receptor pseudogenes
Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate
ESAE-SDA: ensemble sparse autoencoder framework for epigenomics-informed snoRNA-disease associations prediction
Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data
Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence
Big data analysis for evaluating bioinvasion risk
An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
Efficient known ncRNA search including pseudoknots
De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline
Wavelet Screening: a novel approach to analyzing GWAS data
Analysis and verification of the HMGB1 signaling pathway
Association filtering and generative adversarial networks for predicting lncRNA-associated disease
Scoring amino acid mutation to predict pandemic risk of avian influenza virus
Optimising orbit counting of arbitrary order by equation selection
Shrinkage Clustering: a fast and size-constrained clustering algorithm for biomedical applications
Evolving knowledge graph similarity for supervised learning in complex biomedical domains
Using simulated fluorescence cell micrographs for the evaluation of cell image segmentation algorithms
Multi-model inference using mixed effects from a linear regression based genetic algorithm
3D Network exploration and visualisation for lifespan data
A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping
COPASAAR - A database for proteomic analysis of single amino acid repeats
Antigenic cartography of H1N1 influenza viruses using sequence-based antigenic distance calculation
iGTP: A software package for large-scale gene tree parsimony analysis
LUD, a new protein domain associated with lactate utilization
Predicting miRNA-disease associations based on graph attention network with multi-source information
Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation
MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling
In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles
Identifying overlapping mutated driver pathways by constructing gene networks in cancer
Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S -adenosylmethionine to three crystal structures
Automated recognition and analysis of body bending behavior in C. elegans
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
The Representation of Protein Complexes in the Protein Ontology (PRO)
fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization
Multiple imputation and direct estimation for qPCR data with non-detects
Segmental HOG: new descriptor for glomerulus detection in kidney microscopy image
SequelTools: a suite of tools for working with PacBio Sequel raw sequence data
easyDAS: Automatic creation of DAS servers
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
Mining the human proteome for conserved mechanisms
Detecting multivariate differentially expressed genes
ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data
Predicting miRNA-disease associations based on PPMI and attention network
Predicting rice blast disease: machine learning versus process-based models
Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines
Fizzy: feature subset selection for metagenomics
Identification of driver genes based on gene mutational effects and network centrality
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
PyElph - a software tool for gel images analysis and phylogenetics
VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology
hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups
An environment for relation mining over richly annotated corpora: the case of GENIA
Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays
Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot
Dissecting protein architecture with communication blocks and communicating segment pairs
Erratum to: A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions
Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces
A bag-of-words approach for Drosophila gene expression pattern annotation
Protein function prediction by massive integration of evolutionary analyses and multiple data sources
A test for comparing two groups of samples when analyzing multiple omics profiles
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations
Sorting by reversals and block-interchanges with various weight assignments
Estimate hidden dynamic profiles of siRNA effect on apoptosis
Tandem mass spectrometry data quality assessment by self-convolution
GuiTope: an application for mapping random-sequence peptides to protein sequences
Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family
The challenge of managing the evolution of genomics data over time: a conceptual model-based approach
Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets
Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study
Reranking candidate gene models with cross-species comparison for improved gene prediction
CAT-DTI: cross-attention and Transformer network with domain adaptation for drug-target interaction prediction
Symptoms are known by their companies: towards association guided disease diagnosis assistant
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
HORI: a web server to compute Higher Order Residue Interactions in protein structures
Deterministic and stochastic population-level simulations of an artificial lac operon genetic network
Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data
IDSS: deformation invariant signatures for molecular shape comparison
Analysis tools for the interplay between genome layout and regulation
DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data
Quantitative measures for the management and comparison of annotated genomes
ImmunoNodes - graphical development of complex immunoinformatics workflows
SABERTOOTH: protein structural alignment based on a vectorial structure representation
Automatic construction of metabolic models with enzyme constraints
Identification of significant periodic genes in microarray gene expression data
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit
CNCA aligns small annotated genomes
Fold-specific sequence scoring improves protein sequence matching
Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression
Predicting combinative drug pairs towards realistic screening via integrating heterogeneous features
A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application
A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling
Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes
Using machine learning to detect the differential usage of novel gene isoforms
Bayesian modeling of ChIP-chip data using latent variables
Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies
Vertical and horizontal integration of multi-omics data with miodin
Do pathogenic bacteria encode more secreted proteins than their non-pathogenic relatives?
Analysis with respect to instrumental variables for the exploration of microarray data structures
Machine learning approach for pooled DNA sample calibration
Nanopore current transduction analysis of protein binding to non-terminal and terminal DNA regions: analysis of transcription factor binding, retroviral DNA terminus dynamics, and retroviral integrase-DNA binding
MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification
Improved prediction of critical residues for protein function based on network and phylogenetic analyses
Ensemble disease gene prediction by clinical sample-based networks
Detection and correction of probe-level artefacts on microarrays
Finding microRNA regulatory modules in human genome using rule induction
Ensemble approach to predict specificity determinants: benchmarking and validation
DIRECT: RNA contact predictions by integrating structural patterns
The effect of data transformation on low-dimensional integration of single-cell RNA-seq
Filling out the structural map of the NTF2-like superfamily
A Computational Framework for Proteome-Wide Pursuit and Prediction of Metalloproteins using ICP-MS and MS/MS Data
Estimation of duplication history under a stochastic model for tandem repeats
Graphical representation of ribosomal RNA probe accessibility data using ARB software package
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions
An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm
Gene analogue finder: a GRID solution for finding functionally analogous gene products
Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features
Privacy-preserving search for chemical compound databases
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets
HDN-DDI: a novel framework for predicting drug-drug interactions using hierarchical molecular graphs and enhanced dual-view representation learning
ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset
Self-training in significance space of support vectors for imbalanced biomedical event data
Distinguishing the species of biomedical named entities for term identification
Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community
SUPERFICIAL - Surface mapping of proteins via structure-based peptide library design
Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif
Tensor product algorithms for inference of contact network from epidemiological data
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement
LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation
A structural study for the optimisation of functional motifs encoded in protein sequences
acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data
How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis
Jimena: efficient computing and system state identification for genetic regulatory networks
Correction: Holomics ‑ a user‑friendly R shiny application for multi‑omics data integration and analysis
Hierarchical clustering-based coarse-to-fine classification framework for microbial protein function prediction
Algorithms for reconstruction of chromosomal structures
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays
Automatic segmentation of deep intracerebral electrodes in computed tomography scans
Fusing literature and full network data improves disease similarity computation
Extraction of human kinase mutations from literature, databases and genotyping studies
Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites
Power and sample size estimation in microarray studies
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices
Improving the Performance of SVM-RFE to Select Genes in Microarray Data
PlanktoVision - an automated analysis system for the identification of phytoplankton
Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrroly-sine containing genes
Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data
RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database
Fuzzy clustering of CPP family in plants with evolution and interaction analyses
Modeling protein-peptide interactions using protein fragments: fitting the pieces?
Principal component analysis for predicting transcription-factor binding motifs from array-derived data
Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
Multi-omics profiling reveals microRNA-mediated insulin signaling networks
Correction: Multiple imputation and direct estimation for qPCR data with non-detects
Knowledge-guided gene ranking by coordinative component analysis
A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology
A meta-data based method for DNA microarray imputation
A standard curve based method for relative real time PCR data processing
Single object profiles regression analysis (SOPRA): a novel method for analyzing high-content cell-based screens
A sequence-based multiple kernel model for identifying DNA-binding proteins
A method for computing an inventory of metazoan mitochondrial gene order rearrangements
l1kdeconv: an R package for peak calling analysis with LINCS L1000 data
Erratum to: 'CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments'
Improving protein fold recognition by random forest
A semi-supervised tensor regression model for siRNA efficacy prediction
Similarity maps and hierarchical clustering for annotating FT-IR spectral images
Tamock: simulation of habitat-specific benchmark data in metagenomics
Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction
GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Spot quantification in two dimensional gel electrophoresis image analysis: comparison of different approaches and presentation of a novel compound fitting algorithm
Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology
An automatic method to calculate heart rate from zebrafish larval cardiac videos
Multi-task learning sparse group lasso: a method for quantifying antigenicity of influenza A(H1N1) virus using mutations and variations in glycosylation of Hemagglutinin
ProCMD: a database and 3D web resource for protein C mutants
Characterizing disease states from topological properties of transcriptional regulatory networks
NETTAB 2012 on "Integrated Bio-Search"
AttentionDDI: Siamese attention-based deep learning method for drug-drug interaction predictions
Comparing methods for drug-gene interaction prediction on the biomedical literature knowledge graph: performance versus explainability
Simulated evolution applied to study the genetic code optimality using a model of codon reassignments
Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity
FunFam protein families improve residue level molecular function prediction
A linear delay algorithm for enumerating all connected induced subgraphs
Degeneracy measures in biologically plausible random Boolean networks
Portraits of breast cancer progression
New decoding algorithms for Hidden Markov Models using distance measures on labellings
An automated real-time integration and interoperability framework for bioinformatics
GelJ - a tool for analyzing DNA fingerprint gel images
Searching for bidirectional promoters in Arabidopsis thaliana
Systems biology driven software design for the research enterprise
Evaluation of tree-based statistical learning methods for constructing genetic risk scores
A multilayer dynamic perturbation analysis method for predicting ligand-protein interactions
A preliminary study on automated freshwater algae recognition and classification system
Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers
Using context-specific effect of miRNAs to identify functional associations between miRNAs and gene signatures
Interpretation of convolutional neural networks reveals crucial sequence features involving in transcription during fiber development
Beyond the one-way ANOVA for 'omics data
Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection