yusuke1997/dblp-id-title huggingface dataset:
Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo
Stronger findings from mass spectral data through multi-peak modeling
MutScan: fast detection and visualization of target mutations by scanning FASTQ data
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals
Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements
Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection
A flexible ChIP-sequencing simulation toolkit
Additional Neural Matrix Factorization model for computational drug repositioning
TiGER: A database for tissue-specific gene expression and regulation
MSCA: a spectral comparison algorithm between time series to identify protein-protein interactions
Identification of prostate cancer specific methylation biomarkers from a multi-cancer analysis
QCScreen: a software tool for data quality control in LC-HRMS based metabolomics
Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method
Tableau-based protein substructure search using quadratic programming
Orthology-driven mapping of bidirectional promoters in human and mouse genomes
Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012
An improved method to detect correct protein folds using partial clustering
A study on multi-omic oscillations in Escherichia coli metabolic networks
VESNA: an open-source tool for automated 3D vessel segmentation and network analysis
FFP: joint Fast Fourier transform and fractal dimension in amino acid property-aware phylogenetic analysis
Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service
PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing
FC_analysis: a tool for investigating atomic force microscopy maps of force curves
Predicting protein-protein binding sites in membrane proteins
Detecting clusters of transcription factors based on a nonhomogeneous poisson process model
Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state
A Bayesian variable selection procedure to rank overlapping gene sets
Detection for melanoma skin cancer through ACCF, BPPF, and CLF techniques with machine learning approach
Extracting biologically significant patterns from short time series gene expression data
A coherent mathematical characterization of isotope trace extraction, isotopic envelope extraction, and LC-MS correspondence
Discover protein sequence signatures from protein-protein interaction data
FlatProt: 2D visualization eases protein structure comparison
Computational prediction of novel non-coding RNAs in Arabidopsis thaliana
Development and tuning of an original search engine for patent libraries in medicinal chemistry
Drug voyager: a computational platform for exploring unintended drug action
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method
Incremental and unifying modelling formalism for biological interaction networks
ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data
A randomized approach to speed up the analysis of large-scale read-count data in the application of CNV detection
Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles
Rapid forward-in-time simulation at the chromosome and genome level
XperimentR: painless annotation of a biological experiment for the laboratory scientist
High-throughput bioinformatics with the Cyrille2 pipeline system
Efficient counting of k-mers in DNA sequences using a Bloom Filter
Application of machine learning in SNP discovery
DeepMPM: a mortality risk prediction model using longitudinal EHR data
Network-based group variable selection for detecting expression quantitative trait loci (eQTL)
Prediction of peptides observable by mass spectrometry applied at the experimental set level
HEPAD: enhancing hemolytic peptide prediction with adaptive feature engineering and diverse sequence descriptors
Improved high-dimensional prediction with Random Forests by the use of co-data
OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature
Detection and quantification of mitochondrial DNA deletions from next-generation sequence data
Enrichment of homologs in insignificant BLAST hits by co-complex network alignment
Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture
Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data
anamiR: integrated analysis of MicroRNA and gene expression profiling
Differences in gene expression profiles between individual islets from case #6213
A method for supporting retrieval of articles on protein structure analysis considering users' intention
NeuronBridge: an intuitive web application for neuronal morphology search across large data sets
MeSH indexing based on automatically generated summaries
Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA
Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions
An integrative methodology based on protein-protein interaction networks for identification and functional annotation of disease-relevant genes applied to channelopathies
Shape based indexing for faster search of RNA family databases
Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights
Empirical comparison of cross-platform normalization methods for gene expression data
Multi-class segmentation of neuronal structures in electron microscopy images
Identification of germ cell-specific genes in mammalian meiotic prophase
Goulphar: rapid access and expertise for standard two-color microarray normalization methods
METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets
Using deep reinforcement learning to speed up collective cell migration
IILLS: predicting virus-receptor interactions based on similarity and semi-supervised learning
Improving clustering with metabolic pathway data
AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip TM expression arrays with respect to SNPs
A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis
Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development
FALCON2: a web server for high-quality prediction of protein tertiary structures
Comparison of discriminative motif optimization using matrix and DNA shape-based models
GenomeMatcher: A graphical user interface for DNA sequence comparison
Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments
Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks
Improving protein function prediction methods with integrated literature data
Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine
Epi-letters - how to describe epigenetic signatures
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
RABiTPy: an open-source Python software for rapid, AI-powered bacterial tracking and analysis
Methods for estimating human endogenous retrovirus activities from EST databases
Fold change and p-value cutoffs significantly alter microarray interpretations
Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay
Application of unsupervised deep learning algorithms for identification of specific clusters of chronic cough patients from EMR data
CHEXVIS: a tool for molecular channel extraction and visualization
Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base
Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks
A global gene evolution analysis on Vibrionaceae family using phylogenetic profile
Favoring the hierarchical constraint in penalized survival models for randomized trials in precision medicine
A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa
An Atlas of annotations of Hydra vulgaris transcriptome
BioCreAtIvE Task1A: entity identification with a stochastic tagger
BigQ: a NoSQL based framework to handle genomic variants in i2b2
Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate
Jalview: Visualization and Analysis of Molecular Sequences, Alignments, and Structures
M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling
Crowdsourcing the nodulation gene network discovery environment
Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm
DMAP: a connectivity map database to enable identification of novel drug repositioning candidates
Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces
Matrix factorization with neural network for predicting circRNA-RBP interactions
GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations
Blast sampling for structural and functional analyses
Accurate microRNA target prediction correlates with protein repression levels
EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
A Lattice-Boltzmann scheme for the simulation of diffusion in intracellular crowded systems
A graph-based algorithm for detecting rigid domains in protein structures
A hidden Markov model approach for determining expression from genomic tiling micro arrays
Cell cycle phase classification in 3D in vivo microscopy of Drosophila embryogenesis
A method to improve protein subcellular localization prediction by integrating various biological data sources
Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models
pmTM-align: scalable pairwise and multiple structure alignment with Apache Spark and OpenMP
Preservation affinity in consensus modules among stages of HIV-1 progression
TNER: a novel background error suppression method for mutation detection in circulating tumor DNA
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
Comparative analysis of aneurysm subtypes associated genes based on protein-protein interaction network
Classifying protein-protein interaction articles using word and syntactic features
A fast exact sequential algorithm for the partial digest problem
ROCS: A reproducibility index and confidence score for interaction proteomics
A novel essential protein identification method based on PPI networks and gene expression data
Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning
A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations
GSA: an independent development algorithm for calling copy number and detecting homologous recombination deficiency (HRD) from target capture sequencing
Scmaskgan: masked multi-scale CNN and attention-enhanced GAN for scRNA-seq dropout imputation
Filtering for increased power for microarray data analysis
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar
Correction to: SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters
eccCL: parallelized GPU implementation of Ensemble Classifier Chains
Reference-agnostic representation and visualization of pan-genomes
Deciding when to stop: efficient experimentation to learn to predict drug-target interactions
Bayesian DNA copy number analysis
Impact of residue accessible surface area on the prediction of protein secondary structures
A genetic approach for building different alphabets for peptide and protein classification
BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data
misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D
Atlas - a data warehouse for integrative bioinformatics
MMGAT: a graph attention network framework for ATAC-seq motifs finding
Principal component analysis for designed experiments
Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides
A framework for feature extraction from hospital medical data with applications in risk prediction
Characterizing building blocks of resource constrained biological networks
Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs
Sequence signature analysis of chromosome identity in three Drosophila species
mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis
A systematic comparative evaluation of biclustering techniques
CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning
Generalizations of Markov model to characterize biological sequences
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features
Transductive learning as an alternative to translation initiation site identification
Drug-target interaction prediction using unifying of graph regularized nuclear norm with bilinear factorization
Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
Multi-view feature selection for identifying gene markers: a diversified biological data driven approach
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
Probe signal correction for differential methylation hybridization experiments
Large scale tissue histopathology image classification, segmentation, and visualization via deep convolutional activation features
Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth
Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms
Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia
BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference
A MATLAB tool for pathway enrichment using a topology-based pathway regulation score
Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-censored data
Protein disulfide topology determination through the fusion of mass spectrometric analysis and sequence-based prediction using Dempster-Shafer theory
Non-negative matrix factorization by maximizing correntropy for cancer clustering
Applications of the Pipeline Environment for Visual Informatics and Genomics Computations
bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests
A Non-parametric Bayesian Model for Joint Cell Clustering and Cluster Matching: Identification of Anomalous Sample Phenotypes with Random Effects
BioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA
Homology Induction: the use of machine learning to improve sequence similarity searches
KNODWAT: A scientific framework application for testing knowledge discovery methods for the biomedical domain
Drug repositioning using drug-disease vectors based on an integrated network
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions
Parallelized pairwise sequence alignment using CUDA on multiple GPUs
Mass spectrometry-based protein identification by integrating de novo sequencing with database searching
Optimizing Transformations for Automated, High Throughput Analysis of Flow Cytometry Data
ELIMINATOR: essentiality analysis using multisystem networks and integer programming
A novel phenotypic dissimilarity method for image-based high-throughput screens
fastphylo: Fast tools for phylogenetics
Multiblock variable influence on orthogonal projections (MB-VIOP) for enhanced interpretation of total, global, local and unique variations in OnPLS models
Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature
Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins
Gimli: open source and high-performance biomedical name recognition
GeneRiskCalc: a web-based tool for genetic risk association analysis in case-control studies
Proceedings of the Twelfth Annual UT-ORNL-KBRIN Bioinformatics Summit 2013
Application of multiple statistical tests to enhance mass spectrometry-based biomarker discovery
Evaluating eukaryotic secreted protein prediction
Multiple Testing for Gene Sets from Microarray Experiments
MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis
Sensbio: an online server for biosensor design
Function prediction from networks of local evolutionary similarity in protein structure
ProTaxoVis - protein taxonomic visualisation of presence
Large scale statistical inference of signaling pathways from RNAi and microarray data
AMMO-Prot: amine system project 3D-model finder
OMD Curation Toolkit: a workflow for in-house curation of public omics datasets
KATZNCP: a miRNA-disease association prediction model integrating KATZ algorithm and network consistency projection
Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data
Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms
Classification and biomarker identification using gene network modules and support vector machines
A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines
Can Zipf's law be adapted to normalize microarrays?
DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network
Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models
DHOEM: a statistical simulation software for simulating new markers in real SNP marker data
mu-CS: An extension of the TM4 platform to manage Affymetrix binary data
SyNDI: synchronous network data integration framework
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data
iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes
CELDA - an ontology for the comprehensive representation of cells in complex systems
eCOMPAGT - efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology
A fast SCOP fold classification system using content-based E-Predict algorithm
GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes
Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance
Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks
Tailored graphical lasso for data integration in gene network reconstruction
PyTMs: a useful PyMOL plugin for modeling common post-translational modifications
MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments
Ranking insertion, deletion and nonsense mutations based on their effect on genetic information
CicArMiSatDB: the chickpea microsatellite database
Development of an image classification pipeline for atherosclerotic plaques assessment using supervised machine learning
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent
Exploiting heterogeneous features to improve in silico prediction of peptide status - amyloidogenic or non-amyloidogenic
Linear fuzzy gene network models obtained from microarray data by exhaustive search
SPOC: A widely distributed domain associated with cancer, apoptosis and transcription
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
Identifying cancer driver genes based on multi-view heterogeneous graph convolutional network and self-attention mechanism
MAVEN: compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny
Pathway level analysis of gene expression using singular value decomposition
The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli
R3D-BLAST2: an improved search tool for similar RNA 3D substructures
A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
The Important Role of Calcium in Regulation of Adhesion Disassembly and Cell Migration: Mathematical Modelling
Analysis of the transcriptome of CD4 T-Lymphocytes from young Non-Obese Diabetic (NOD) mice suggests a key role for cytokines and apoptosis
Identifying risk factors for Alzheimer's disease from multivariate longitudinal clinical data using temporal pattern mining
Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility
Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification
Towards breaking the curse of dimensionality in computational methods for the conformational analysis of molecules