yusuke1997/dblp-id-title huggingface dataset:
Concomitant prediction of function and fold at the domain level with GO-based profiles
PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data
A multi-view genomic data simulator
Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns
Improved general regression network for protein domain boundary prediction
Snagger: A user-friendly program for incorporating additional information for tagSNP selection
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples
Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues
Novel artificial intelligence-based identification of drug-gene-disease interaction using protein-protein interaction
Visualizing histopathologic deep learning classification and anomaly detection using nonlinear feature space dimensionality reduction
High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow
NPGREAT: assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads
Proteochemometric modeling of HIV protease susceptibility
A boosting method for maximizing the partial area under the ROC curve
Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences
Differential splicing using whole-transcript microarrays
SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing
Inference of gene regulatory subnetworks from time course gene expression data
Validation and quality assurance for genome browser database exports
LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks
AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts
AliGROOVE - visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support
Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data
Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment
Towards a theoretical understanding of false positives in DNA motif finding
BioNOT: A searchable database of biomedical negated sentences
Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy
A Scan Statistic to Extract Causal Gene Clusters from Case-Control Genome-wide Rare CNV Data
'gitana' (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures
Kismeth: Analyzer of plant methylation states through bisulfite sequencing
Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors
TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata
Impact of missing data imputation methods on gene expression clustering and classification
Ensemble analysis of adaptive compressed genome sequencing strategies
Role of environmental specificity in CASP results
An ensemble framework for identifying essential proteins
Comparison of co-expression measures: mutual information, correlation, and model based indices
OTO: Ontology Term Organizer
Disorder recognition in clinical texts using multi-label structured SVM
An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition
A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families
Simulation of gene family histories
A performant bridge between fixed-size and variable-size seeding
A discriminative method for protein remote homology detection and fold recognition combining Top- n -grams and latent semantic analysis
BitTorious: global controlled genomics data publication, research and archiving via BitTorrent extensions
Ranking the whole MEDLINE database according to a large training set using text indexing
Deep learning with language models improves named entity recognition for PharmaCoNER
Image-centric compression of protein structures improves space savings
Gebiss: An ImageJ Plugin for the Specification of Ground Truth and the Performance Evaluation of 3D Segmentation Algorithms
CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species
A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata
Pickaxe: a Python library for the prediction of novel metabolic reactions
LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures
BioGateway: a semantic systems biology tool for the life sciences
Methodology for the inference of gene function from phenotype data
Weekly ILI patient ratio change prediction using news articles with support vector machine
An individualized predictor of health and disease using paired reference and target samples
Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data
trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios
Uncovering latent biological function associations through gene set embeddings
Identification of early mild cognitive impairment using multi-modal data and graph convolutional networks
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data
Gene set analyses for interpreting microarray experiments on prokaryotic organisms
SIMAGE: simulation of DNA-microarray gene expression data
Discovering co-occurring patterns and their biological significance in protein families
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone
The Biomedical Discourse Relation Bank
eL-DASionator: an LDAS upload file generator
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers
MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)
Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes
Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization
Connectivity independent protein-structure alignment: a hierarchical approach
BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data
annot8r: GO, EC and KEGG annotation of EST datasets
IsoSVM - Distinguishing isoforms and paralogs on the protein level
Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium
A nearest-neighbors network model for sequence data reveals new insight into genotype distribution of a pathogen
iStable: off-the-shelf predictor integration for predicting protein stability changes
Assembly of non-unique insertion content using next-generation sequencing
Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants
A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history
Accommodating multiple potential normalizations in microbiome associations studies
Identifying glycan motifs using a novel subtree mining approach
SMuRF: a novel tool to identify regulatory elements enriched for somatic point mutations
Multivariate pattern analysis: a method and software to reveal, quantify, and visualize predictive association patterns in multicollinear data
Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism
A novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference
A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)
MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis
Analysis of in vivo single cell behavior by high throughput, human-in-the-loop segmentation of three-dimensional images
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods
Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage
Identifying vital nodes for yeast network by dynamic network entropy
TeraStitcher - A Tool for Fast Automatic 3D-Stitching of Teravoxel-Sized Microscopy Images
JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow
DAFS: a data-adaptive flag method for RNA-sequencing data to differentiate genes with low and high expression
Metabolic network alignment in large scale by network compression
Normalized L3-based link prediction in protein-protein interaction networks
AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction
From hybridization theory to microarray data analysis: performance evaluation
Joint reconstruction of neuron and ultrastructure via connectivity consensus in electron microscope volumes
ArrayD: A general purpose software for Microarray design
JOA: Joint Overlap Analysis of multiple genomic interval sets
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry
A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data
Accelerated search for biomolecular network models to interpret high-throughput experimental data
HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies
Dynamic evaluation of unruptured intracranial aneurysms by 4D-CT angiography: comparison with digital subtraction angiography (DSA) and surgical findings
Parameter estimation for robust HMM analysis of ChIP-chip data
CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data
Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks
MSIFinder: a python package for detecting MSI status using random forest classifier
SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances
Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains
Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model
Clustering of gene expression data: performance and similarity analysis
CGTS: a site-clustering graph based tagSNP selection algorithm in genotype data
GFF3sort: a novel tool to sort GFF3 files for tabix indexing
Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data
Improving deep learning method for biomedical named entity recognition by using entity definition information
Comparative analysis of haplotype association mapping algorithms
Closest string with outliers
SketchBio: a scientist's 3D interface for molecular modeling and animation
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
DiscovEpi: automated whole proteome MHC-I-epitope prediction and visualization
Metamotifs - a generative model for building families of nucleotide position weight matrices
A successful hybrid deep learning model aiming at promoter identification
CoExpresso: assess the quantitative behavior of protein complexes in human cells
A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis
diceR: an R package for class discovery using an ensemble driven approach
MONALISA for stochastic simulations of Petri net models of biochemical systems
Protein comparison at the domain architecture level
Methods for visual mining of genomic and proteomic data atlases
AligNet: alignment of protein-protein interaction networks
Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously
DPI_CDF: druggable protein identifier using cascade deep forest
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks
ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations
BioCreative III interactive task: an overview
Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest
SLDR: a computational technique to identify novel genetic regulatory relationships
A statistical framework to evaluate virtual screening
Functional homogeneity and specificity of topological modules in human proteome
Docking protein domains in contact space
The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
Validation of genetic variants from NGS data using deep convolutional neural networks
A journey to Semantic Web query federation in the life sciences
New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits
Sequencing error correction without a reference genome
SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
Designing multiple degenerate primers via consecutive pairwise alignments
Multi-probe attention neural network for COVID-19 semantic indexing
High throughput profile-profile based fold recognition for the entire human proteome
dbMPIKT: a database of kinetic and thermodynamic mutant protein interactions
A statistical approach for 5′ splice site prediction using short sequence motifs and without encoding sequence data
Discovering gene annotations in biomedical text databases
The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases
Variational attenuation correction in two-view confocal microscopy
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems
TRIP - T cell receptor/immunoglobulin profiler
Thermodynamic scaling behavior in genechips
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
Efficient deformation algorithm for plasmid DNA simulations
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction
Use of a structural alphabet for analysis of short loops connecting repetitive structures
Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum
A framework for publishing primary biodiversity data
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data
SV-Pop: population-based structural variant analysis and visualization
Computing expectation values for RNA motifs using discrete convolutions
Bayesian model to detect phenotype-specific genes for copy number data
MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools
SNP interaction detection with Random Forests in high-dimensional genetic data
Genomic data integration and user-defined sample-set extraction for population variant analysis
PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory
Novel software package for cross-platform transcriptome analysis (CPTRA)
Recognizing flu-like symptoms from videos
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom
Correction: MSLP: mRNA subcellular localization predictor based on machine learning techniques
SCIFIO: an extensible framework to support scientific image formats
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
Genome rearrangements with indels in intergenes restrict the scenario space
TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences
Machine learning for discovering missing or wrong protein function annotations - A comparison using updated benchmark datasets
Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)
Large scale analysis of amino acid substitutions in bacterial proteomics
MCtandem: an efficient tool for large-scale peptide identification on many integrated core (MIC) architecture
Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites
Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data
EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts
Comparative mapping of sequence-based and structure-based protein domains
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline
SSBER: removing batch effect for single-cell RNA sequencing data
Deep learning improves the ability of sgRNA off-target propensity prediction
Substitution matrix based color schemes for sequence alignment visualization
Effect of data normalization on fuzzy clustering of DNA microarray data
Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes
Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data
ContextD: an algorithm to identify contextual properties of medical terms in a Dutch clinical corpus
PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
Evolution@home: Global computing quantifies evolution due to Muller's ratchet
CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates
Representation of target-bound drugs by computed conformers: implications for conformational libraries
Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins
Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes
Identification of NAD interacting residues in proteins
A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches
SV-MeCa: an XGBoost-based meta-caller approach for structural variant calling from short-read data
Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method
Quantum Coupled Mutation Finder: Predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming
Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice
A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family
An improved random forest-based computational model for predicting novel miRNA-disease associations
Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links
Improving protein order-disorder classification using charge-hydropathy plots
Dynamic sensitivity analysis of biological systems
SeSAM: software for automatic construction of order-robust linkage maps
Inferring latent task structure for Multitask Learning by Multiple Kernel Learning
AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree
Re-alignment of the unmapped reads with base quality score
Automated prostate tissue referencing for cancer detection and diagnosis
Automatic learning of pre-miRNAs from different species
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology
Constrained distance transforms for spatial atlas registration
Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond
web cellHTS2: A web-application for the analysis of high-throughput screening data
Prediction of backbone dihedral angles and protein secondary structure using support vector machines
Transcriptomic characterization of short duration endoplasmic reticulum stress on cultured human proximal tubule cells
MRCQuant- an accurate LC/MS relative isotopic quantification algorithm on TOF instruments
Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data
Ferret: a sentence-based literature scanning system
The EnzymeTracker: an open-source laboratory information management system for sample tracking
Multi-type feature fusion based on graph neural network for drug-drug interaction prediction
Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and STRUCTURE
Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM
Washing scaling of GeneChip microarray expression
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method
Integrating protein-protein interactions and text mining for protein function prediction
Validation of protein models by a neural network approach
A flexible R package for nonnegative matrix factorization
Biowep: a workflow enactment portal for bioinformatics applications
Optimal neighborhood indexing for protein similarity search
Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization
DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks
A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli
Combining Affymetrix microarray results
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution
2-kupl: mapping-free variant detection from DNA-seq data of matched samples
CoeViz: a web-based tool for coevolution analysis of protein residues
Model verification tools: a computational framework for verification assessment of mechanistic agent-based models