yusuke1997/dblp-id-title huggingface dataset:
A new synonym-substitution method to enrich the human phenotype ontology
Deconvolution of tumor composition using partially available DNA methylation data
MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals
Talk2Biomodels: AI agent-based open-source LLM initiative for kinetic biological models
Prioritization, clustering and functional annotation of MicroRNAs using latent semantic indexing of MEDLINE abstracts
Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data
FunFEA: an R package for fungal functional enrichment analysis
Learning virulent proteins from integrated query networks
Construction and use of gene expression covariation matrix
Discrimination of Approved Drugs from Experimental Drugs by Learning Methods
Machine learning techniques on homological persistence features for prostate cancer diagnosis
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification
Scaling bioinformatics applications on HPC
NITPICK: peak identification for mass spectrometry data
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
Identification of a novel miRNA-based recurrence and prognosis prediction biomarker for hepatocellular carcinoma
Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach
EasyCluster2: an improved tool for clustering and assembling long transcriptome reads
A hierarchical spike-and-slab model for pan-cancer survival using pan-omic data
DTA-SiST: de novo transcriptome assembly by using simplified suffix trees
Stratification of co-evolving genomic groups using ranked phylogenetic profiles
Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies
Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline
Protein structural class prediction based on an improved statistical strategy
SRAssembler: Selective Recursive local Assembly of homologous genomic regions
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies
HKPocket: human kinase pocket database for drug design
BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server
Motif-All: discovering all phosphorylation motifs
A distribution-guided Mapper algorithm
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers
StAR: a simple tool for the statistical comparison of ROC curves
Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index
IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods
The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line
A continuous analog of run length distributions reflecting accumulated fractionation events
SAMSA2: a standalone metatranscriptome analysis pipeline
A biomedical event extraction method based on fine-grained and attention mechanism
Feature selection for fMRI-based deception detection
Full-length title: NRPPUR database search and in vitro analysis identify an NRPS-PKS biosynthetic gene cluster with a potential antibiotic effect
AGORA: Assembly Guided by Optical Restriction Alignment
Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks
The number of reduced alignments between two DNA sequences
Effect of the sequence data deluge on the performance of methods for detecting protein functional residues
DrGA: cancer driver gene analysis in a simpler manner
Comparison of concept recognizers for building the Open Biomedical Annotator
Transposable element finder (TEF): finding active transposable elements from next generation sequencing data
A densely connected framework for cancer subtype classification
Multiple-input multiple-output causal strategies for gene selection
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data
Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS)
Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier
Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion
PGD: a machine learning-based photosynthetic-related gene detection approach
Application of the common base method to regression and analysis of covariance (ANCOVA) in qPCR experiments and subsequent relative expression calculation
Knowledge-guided multi-scale independent component analysis for biomarker identification
A cross disciplinary study of link decay and the effectiveness of mitigation techniques
Better score function for peptide identification with ETD MS/MS spectra
DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology
TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
On the Contributions of Topological Features to Transcriptional Regulatory Network Robustness
On the amyloid datasets used for training PAFIG - how (not) to extend the experimental dataset of hexapeptides
scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data
Improved Chou-Fasman method for protein secondary structure prediction
Identifying biological concepts from a protein-related corpus with a probabilistic topic model
A feature selection method for classification within functional genomics experiments based on the proportional overlapping score
Identifying and quantifying metabolites by scoring peaks of GC-MS data
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception
Conceptual-level workflow modeling of scientific experiments using NMR as a case study
Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics
Drug-target affinity prediction with extended graph learning-convolutional networks
BMC Bioinformatics reviewer acknowledgement 2015
A new graph-based method for pairwise global network alignment
Improved identification of conserved cassette exons using Bayesian networks
Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring
The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case
Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
TileQC: A system for tile-based quality control of Solexa data
Gene expression anti-profiles as a basis for accurate universal cancer signatures
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets
Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling
Optimal contact definition for reconstruction of Contact Maps
Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis
SparkGC: Spark based genome compression for large collections of genomes
NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model
Development and validation of the potential biomarkers based on m6A-related lncRNAs for the predictions of overall survival in the lung adenocarcinoma and differential analysis with cuproptosis
A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer's disease progression
Computable visually observed phenotype ontological framework for plants
CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure
Context-specific gene regulatory networks subdivide intrinsic subtypes of breast cancer
DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features
A perl package and an alignment tool for phylogenetic networks
kClust: fast and sensitive clustering of large protein sequence databases
Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions
Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches
Avoiding the pitfalls of gene set enrichment analysis with SetRank
Growth hormone induces proliferation in the zebrafish inner ear
A comparative study of disease genes and drug targets in the human protein interactome
Determining gene expression on a single pair of microarrays
A multi-label classification model for full slice brain computerised tomography image
Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm
Improving ontologies by automatic reasoning and evaluation of logical definitions
Modelling the bioinformatics tertiary analysis research process
Condensing Raman spectrum for single-cell phenotype analysis
Multiple instance neural networks based on sparse attention for cancer detection using T-cell receptor sequences
Positive-unlabeled learning for the prediction of conformational B-cell epitopes
AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity
RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy
Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information
Detection and visualization of communities in mass spectrometry imaging data
Evaluation of clustering algorithms for gene expression data
Techniques for analysing pattern formation in populations of stem cells and their progeny
Modeling allosteric signal propagation using protein structure networks
Fast inexact mapping using advanced tree exploration on backward search methods
DeeplyEssential: a deep neural network for predicting essential genes in microbes
MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
ShinyOmics: collaborative exploration of omics-data
Interpretable deep learning methods for multiview learning
Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses
Modelling osteomyelitis
Haystack, a web-based tool for metabolomics research
A document level neural model integrated domain knowledge for chemical-induced disease relations
MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level
Computational enhancer prediction: evaluation and improvements
Improving structural variant clustering to reduce the negative effect of the breakpoint uncertainty problem
RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks
DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data
IdentiCS - Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability
BCDForest: a boosting cascade deep forest model towards the classification of cancer subtypes based on gene expression data
Sequence and annotation of the Wizard007 mycobacterium phage genome
Molecular complex detection in protein interaction networks through reinforcement learning
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology
The influence of different types of translational inaccuracies on the genetic code structure
Automated quality control for a molecular surveillance system
Information transfer in signaling pathways: A study using coupled simulated and experimental data
Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016)
Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations
Inferring ontology graph structures using OWL reasoning
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data
RankAggreg, an R package for weighted rank aggregation
AntiBP2: improved version of antibacterial peptide prediction
Gentrepid V2.0: a web server for candidate disease gene prediction
SeQual-Stream: approaching stream processing to quality control of NGS datasets
Characterising RNA secondary structure space using information entropy
WellInverter: a web application for the analysis of fluorescent reporter gene data
Exploiting physico-chemical properties in string kernels
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana
EGNAS: an exhaustive DNA sequence design algorithm
SoftPanel: a website for grouping diseases and related disorders for generation of customized panels
ΔΔPT: a comprehensive toolbox for the analysis of protein motion
Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking
MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions
FSBC: fast string-based clustering for HT-SELEX data
quantGenius: implementation of a decision support system for qPCR-based gene quantification
miRTar: an integrated system for identifying miRNA-target interactions in Human
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
Native structure-based modeling and simulation of biomolecular systems per mouse click
Discovery of prognostic biomarkers for predicting lung cancer metastasis using microarray and survival data
Our strategy to achieve and document reproducible computing
NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences
poolMC: Smart pooling of mRNA samples in microarray experiments
Identifying peaks in *-seq data using shape information
Consequential considerations when mapping tRNA fragments
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
An algorithm of discovering signatures from DNA databases on a computer cluster
miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules
Data preparation and interannotator agreement: BioCreAtIvE Task 1B
Inferring topology from clustering coefficients in protein-protein interaction networks
TassDB2 - A comprehensive database of subtle alternative splicing events
Development of a prognostic signature of patients with esophagus adenocarcinoma by using immune-related genes
Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed)
Alternative mapping of probes to genes for Affymetrix chips
CORRIE: enzyme sequence annotation with confidence estimates
Incremental genetic K-means algorithm and its application in gene expression data analysis
Kerfuffle: a web tool for multi-species gene colocalization analysis
A protocol to evaluate RNA sequencing normalization methods
Pan-cancer analysis of systematic batch effects on somatic sequence variations
PredictEFC: a fast and efficient multi-label classifier for predicting enzyme family classes
PRPI-SC: an ensemble deep learning model for predicting plant lncRNA-protein interactions
Stack-VTP: prediction of vesicle transport proteins based on stacked ensemble classifier and evolutionary information
Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies
Computational identification of rare codons of Escherichia coli based on codon pairs preference
Impact of post-alignment processing in variant discovery from whole exome data
Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography
Full L 1 -regularized Traction Force Microscopy over whole cells
Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction
PEPOP: Computational design of immunogenic peptides
Identification of single-stranded and double-stranded dna binding proteins based on protein structure
Quail Genomics: a knowledgebase for Northern bobwhite
eGIFT: Mining Gene Information from the Literature
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs
eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings
The rise and fall of breakpoint reuse depending on genome resolution
Hybrid fragment-SMILES tokenization for ADMET prediction in drug discovery
A protein-dependent side-chain rotamer library
The relative vertex clustering value - a new criterion for the fast discovery of functional modules in protein interaction networks
Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis
RNA secondary structure factorization in prime tangles
DOSim: An R package for similarity between diseases based on Disease Ontology
MALVIRUS: an integrated application for viral variant analysis
Computational identification of strain-, species- and genus-specific proteins
CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
VANLO - Interactive visual exploration of aligned biological networks
MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes
Reliable heritability estimation using sparse regularization in ultrahigh dimensional genome-wide association studies
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation
Haplotype frequency estimation error analysis in the presence of missing genotype data
Analysis of DNA strand-specific differential expression with high density tiling microarrays
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers
In-silico prediction of blood-secretory human proteins using a ranking algorithm
POPE: post optimization posterior evaluation of likelihood free models
Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control
Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates
Exploring the information transmission properties of noise-induced dynamics: application to glioma differentiation
Breaking the computational barriers of pairwise genome comparison
The maximum entropy principle for compositional data
Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry
Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics
Masking as an effective quality control method for next-generation sequencing data analysis
Elucidating the crosstalk mechanism between IFN-gamma and IL-6 via mathematical modelling
scEvoNet: a gradient boosting-based method for prediction of cell state evolution
Bayesian compositional generalized linear mixed models for disease prediction using microbiome data
TIANA: transcription factors cooperativity inference analysis with neural attention
Improve hot region prediction by analyzing different machine learning algorithms
In Silico screening for functional candidates amongst hypothetical proteins
Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures
Integrative biclustering of heterogeneous datasets using a Bayesian nonparametric model with application to chemogenomics
Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction
Extracting consistent knowledge from highly inconsistent cancer gene data sources
A neural joint model for entity and relation extraction from biomedical text
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database
DDmap: a MATLAB package for the double digest problem using multiple genetic operators
Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate
PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data
A semi-parametric Bayesian model for unsupervised differential co-expression analysis
The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation
Abbreviation definition identification based on automatic precision estimates
Efficient classification of complete parameter regions based on semidefinite programming
Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis
Applications of a formal approach to decipher discrete genetic networks
Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana
Metabonomics evaluations of age-related changes in the urinary compositions of male Sprague Dawley rats and effects of data normalization methods on statistical and quantitative analysis
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
Exploring behaviors of stochastic differential equation models of biological systems using change of measures
Modeling measurement error in tumor characterization studies
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
Human protein-protein interaction prediction
A factor model to analyze heterogeneity in gene expression
A permutation-based method to identify loss-of-heterozygosity using paired genotype microarray data
Flanking sequence context-dependent transcription factor binding in early Drosophila development
G-DOC Plus - an integrative bioinformatics platform for precision medicine
Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana
In silico evaluation of the influence of the translocon on partitioning of membrane segments
iGepros: an integrated gene and protein annotation server for biological nature exploration
Disambiguation of biomedical text using diverse sources of information
On Bayesian modeling of censored data in JAGS
SNPxE: SNP-environment interaction pattern identifier
A base measure of precision for protein stability predictors: structural sensitivity