yusuke1997/dblp-id-title huggingface dataset:
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
Drug-target interaction prediction based on graph convolutional autoencoder with dynamic weighting residual GCN
Analysis of interactions between the epigenome and structural mutability of the genome using Genboree workbench tools
Systems biology intertwines with single cell and AI
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning
VariFAST: a variant filter by automated scoring based on tagged-signatures
BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies
K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Bioinformatics analysis of the epitope regions for norovirus capsid protein
Block Forests: random forests for blocks of clinical and omics covariate data
MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics
Differential expression analysis with global network adjustment
Novel base triples in RNA structures revealed by graph theoretical searching methods
MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
Contrastive self-supervised clustering of scRNA-seq data
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials
Genomorama: genome visualization and analysis
Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring
CNN-based two-branch multi-scale feature extraction network for retrosynthesis prediction
In silico analysis of missense mutations in exons 1-5 of the F9 gene that cause hemophilia B
Selecting dissimilar genes for multi-class classification, an application in cancer subtyping
MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity
Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors
Visually guided classification trees for analyzing chronic patients
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters
Gains of ubiquitylation sites in highly conserved proteins in the human lineage
Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data
Robust multi-group gene set analysis with few replicates
Software for the analysis and visualization of deep mutational scanning data
Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation
Chemical-induced disease relation extraction via attention-based distant supervision
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS
Information extraction from full text scientific articles: Where are the keywords?
Multiple-kernel learning for genomic data mining and prediction
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis
Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL isoelectric focussing
Sequence-based identification of recombination spots using pseudo nucleic acid representation and recursive feature extraction by linear kernel SVM
New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning
An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters
The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data
In silico design of recombinant multi-epitope vaccine against influenza A virus
SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks
On the inversion-indel distance
Prediction of protein-protein interaction sites using an ensemble method
On the inconsistency of ℓ 1-penalised sparse precision matrix estimation
MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013
Self-organizing ontology of biochemically relevant small molecules
TOMOBFLOW: feature-preserving noise filtering for electron tomography
GFS: fuzzy preprocessing for effective gene expression analysis
Microvessel prediction in H&E Stained Pathology Images using fully convolutional neural networks
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms
iMS2Flux - a high-throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis
Estimating the optimal linear combination of predictors using spherically constrained optimization
Mora: abundance aware metagenomic read re-assignment for disentangling similar strains
Identification of biomarkers from mass spectrometry data using a "common" peak approach
Multiscale modeling reveals angiogenesis-induced drug resistance in brain tumors and predicts a synergistic drug combination targeting EGFR and VEGFR pathways
Development and validation of a coagulation-related genes prognostic model for hepatocellular carcinoma
Correction to: FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning
GCphase: an SNP phasing method using a graph partition and error correction algorithm
From trash to treasure: detecting unexpected contamination in unmapped NGS data
Correction to: Identification and characterization of conserved lncRNAs in human and rat brain
Interpretation of microbiota-based diagnostics by explaining individual classifier decisions
Bias Detection and Correction in RNA-Sequencing Data
Comprehensive study of semi-supervised learning for DNA methylation-based supervised classification of central nervous system tumors
GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments
Optimal sequencing depth design for whole genome re-sequencing in pigs
ETE: a python Environment for Tree Exploration
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics
Is searching full text more effective than searching abstracts?
Identification of infectious disease-associated host genes using machine learning techniques
Supervised inference of gene-regulatory networks
Bridging the gaps: atomic simulation of macromolecular environment brings together protein docking, interaction kinetics and the crowding effects
Exploring Parasite Gene Space
Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement
The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison
Extracting predictors for lung adenocarcinoma based on Granger causality test and stepwise character selection
Inferring viral quasispecies spectra from 454 pyrosequencing reads
Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking
L2, 1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions
Storing, linking, and mining microarray databases using SRS
Bayesian mixture regression analysis for regulation of Pluripotency in ES cells
Rapid analysis of metagenomic data using signature-based clustering
CSA: a web service for the complete process of ChIP-Seq analysis
BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models
Linking entities through an ontology using word embeddings and syntactic re-ranking
ChemEx: information extraction system for chemical data curation
Evaluating the Effect of Disturbed Ensemble Distributions on SCFG Based Statistical Sampling of RNA Secondary Structures
A multivariate prediction model for microarray cross-hybridization
Automation of gene assignments to metabolic pathways using high-throughput expression data
Two-way learning with one-way supervision for gene expression data
M-CGH: Analysing microarray-based CGH experiments
Prediction of liquid-liquid phase separating proteins using machine learning
Using passenger mutations to estimate the timing of driver mutations and identify mutator alterations
Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network
Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data
Improving somatic exome sequencing performance by biological replicates
TMbed: transmembrane proteins predicted through language model embeddings
MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features
Systematic identification of yeast cell cycle transcription factors using multiple data sources
Analysis of miRNA expression profiles in breast cancer using biclustering
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
CWRML: representing crop wild relative conservation and use data in XML
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
AdmixPipe: population analyses in Admixture for non-model organisms
Predicting weighted unobserved nodes in a regulatory network using answer set programming
MUREN: a robust and multi-reference approach of RNA-seq transcript normalization
Regularized gene selection in cancer microarray meta-analysis
Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom
Inferring synteny between genome assemblies: a systematic evaluation
Statistical significance approximation for local similarity analysis of dependent time series data
GRiNS: a python library for simulating gene regulatory network dynamics
Gene-gene interaction filtering with ensemble of filters
Feature weight estimation for gene selection: a local hyperlinear learning approach
Improving biomedical information retrieval by linear combinations of different query expansion techniques
Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments
Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge
Multi-resolution independent component analysis for high-performance tumor classification and biomarker discovery
Semi-supervised contrastive learning variational autoencoder Integrating single-cell multimodal mosaic datasets
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks
StackEPI: identification of cell line-specific enhancer-promoter interactions based on stacking ensemble learning
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results
An integrative imputation method based on multi-omics datasets
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2
Rapid and precise alignment of raw reads against redundant databases with KMA
3DMMS: robust 3D Membrane Morphological Segmentation of C. elegans embryo
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
Nonlinear ridge regression improves cell-type-specific differential expression analysis
Erratum to: eSTGt: a programming and simulation environment for population dynamics
Heatmap3: an improved heatmap package with more powerful and convenient features
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins
e-Science and biological pathway semantics
CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels
GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure
Towards pixel-to-pixel deep nucleus detection in microscopy images
Benchmarking robustness of deep neural networks in semantic segmentation of fluorescence microscopy images
SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations
Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases
What we can see from very small size sample of metagenomic sequences
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences
Shape-aware stochastic neighbor embedding for robust data visualisations
Conditional clustering of temporal expression profiles
Internal and external normalization of nascent RNA sequencing run-on experiments
Protein-protein interaction site prediction by model ensembling with hybrid feature and self-attention
Gene Ontology annotations: what they mean and where they come from
The XBabelPhish MAGE-ML and XML Translator
DTL reconciliation repair
DNA sequences alignment in multi-GPUs: acceleration and energy payoff
A constrained polynomial regression procedure for estimating the local False Discovery Rate
Detailed prediction of protein sub-nuclear localization
An improved independent component analysis model for 3D chromatogram separation and its solution by multi-areas genetic algorithm
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
Leveraging permutation testing to assess confidence in positive-unlabeled learning applied to high-dimensional biological datasets
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy
HPOseq: a deep ensemble model for predicting the protein-phenotype relationships based on protein sequences
NBLDA: negative binomial linear discriminant analysis for RNA-Seq data
An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters
Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli : constraint-based simulation approach
Predict multi-type drug-drug interactions in cold start scenario
Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
An empirical Bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
PollenCALC: Software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species
Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome
ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics
DNASimCLR: a contrastive learning-based deep learning approach for gene sequence data classification
Ebbie : automated analysis and storage of small RNA cloning data using a dynamic web server
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways
Large-scale directional relationship extraction and resolution
Knowledge-based extraction of adverse drug events from biomedical text
Predicting functions of maize proteins using graph convolutional network
Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion
High-precision high-coverage functional inference from integrated data sources
Infinite mixture-of-experts model for sparse survival regression with application to breast cancer
A novel approach to simulate gene-environment interactions in complex diseases
A probabilistic model for the evolution of RNA structure
DNAism: exploring genomic datasets on the web with Horizon Charts
Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models
GPDminer: a tool for extracting named entities and analyzing relations in biological literature
Topological and functional comparison of community detection algorithms in biological networks
PathMe: merging and exploring mechanistic pathway knowledge
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
PASSIM - an open source software system for managing information in biomedical studies
Rank-based edge reconstruction for scale-free genetic regulatory networks
Differences in codon bias cannot explain differences in translational power among microbes
Gauging triple stores with actual biological data
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data
A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data
Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae
Ensemble learning for predicting ex vivo human placental barrier permeability
Computational neuroanatomy: ontology-based representation of neural components and connectivity
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization
Drug repositioning based on residual attention network and free multiscale adversarial training
Computation of significance scores of unweighted Gene Set Enrichment Analyses
Gene regulatory network inference using PLS-based methods
Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays
Next generation tools for genomic data generation, distribution, and visualization
The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics
Finding optimal threshold for correction error reads in DNA assembling
Development of revised ResNet-50 for diabetic retinopathy detection
Hierarchical representation for PPI sites prediction
Articles selected from posters presented at the Tenth Annual International Conference on Research in Computational Biology - Preface
Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences
Joint between-sample normalization and differential expression detection through ℓ 0-regularized regression
Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast
Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd
LC-N2G: a local consistency approach for nutrigenomics data analysis
AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies
Exploratory analysis of transposable elements expression in the C. elegans early embryo
An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs
Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters
Phylotree - a toolkit for computing experiments with distance-based methods for genome coevolution
DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Variance component analysis to assess protein quantification in biomarker validation: application to selected reaction monitoring-mass spectrometry
ScreenGarden: a shinyR application for fast and easy analysis of plate-based high-throughput screens
Selecting additional tag SNPs for tolerating missing data in genotyping
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease
Automatic consistency assurance for literature-based gene ontology annotation
TreeDyn: towards dynamic graphics and annotations for analyses of trees
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach
Enhanced protein fold recognition through a novel data integration approach
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions
interPopula: a Python API to access the HapMap Project dataset
Batch optimization for balanced binary sequences and DNA sequences
FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry
A novel, fast, HMM-with-Duration implementation - for application with a new, pattern recognition informed, nanopore detector
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces
Search for SINE repeats in the rice genome using correlation-based position weight matrices
MiRNA therapeutics based on logic circuits of biological pathways
Correcting the impact of docking pose generation error on binding affinity prediction
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan
DG-Affinity: predicting antigen-antibody affinity with language models from sequences
MoTeX-II: structured MoTif eXtraction from large-scale datasets
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks
AUD-DSS: a decision support system for early detection of patients with alcohol use disorder
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks
M 3 -S: a genotype calling method incorporating information from samples with known genotypes
A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies
Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Quantitative comparison of microarray experiments with published leukemia related gene expression signatures
Profiling transcription initiation in human aged brain using deep-CAGE
A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs
A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics
Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii
Exploiting physical properties in protein structure alignment
BayGO: Bayesian analysis of ontology term enrichment in microarray data
Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences
The cell line ontology-based representation, integration and analysis of cell lines used in China
Assessing the reliability of point mutation as data augmentation for deep learning with genomic data