yusuke1997/dblp-id-title huggingface dataset:
A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity
Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling
A Bayesian change-point algorithm for detecting copy number alteration
Accurate and fast methods to estimate the population mutation rate from error prone sequences
ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors
PentaPlot: A software tool for the illustration of genome mosaicism
TopoQual polishes circular consensus sequencing data and accurately predicts quality scores
CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components
Automatic structure classification of small proteins using random forest
Adaptive deep feature representation learning for cross-subject EEG decoding
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins
Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)
GCNFORMER: graph convolutional network and transformer for predicting lncRNA-disease associations
Fragment assignment in the cloud with eXpress-D
An Integrated Korean Biodiversity and Genetic Information Retrieval System
CircPrime: a web-based platform for design of specific circular RNA primers
MetaTron: advancing biomedical annotation empowering relation annotation and collaboration
Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis
Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets
A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support
RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets
SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota
MSXFGP: combining improved sparrow search algorithm with XGBoost for enhanced genomic prediction
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens
Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals
Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer
QuaDMutEx: quadratic driver mutation explorer
Comparison of sequence-dependent tiling array normalization approaches
CMPF: Class-switching minimized pathfinding in metabolic networks
Clustering approaches for visual knowledge exploration in molecular interaction networks
Tissue-based Alzheimer gene expression markers - comparison of multiple machine learning approaches and investigation of redundancy in small biomarker sets
A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions
C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search
perfectphyloR: An R package for reconstructing perfect phylogenies
RegNetB: Predicting Relevant Regulator-Gene Relationships in Localized Prostate Tumor Samples
MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles
Systematic gene function prediction from gene expression data by using a fuzzy nearest-cluster method
Development of predicitve models to distinguish metals from non-metal toxicants, and individual metal from one another
MaTSE: the gene expression time-series explorer
SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization
A network embedding-based multiple information integration method for the MiRNA-disease association prediction
Quantitative prediction of the effect of genetic variation using hidden Markov models
Digital surveillance in Latin American diseases outbreaks: information extraction from a novel Spanish corpus
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
Finding biological process modifications in cancer tissues by mining gene expression correlations
A two-step approach to qPCR experimental design and software for data analysis
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
Maptcha: an efficient parallel workflow for hybrid genome scaffolding
A fast structural multiple alignment method for long RNA sequences
A high level interface to SCOP and ASTRAL implemented in Python
Methods for the integration of multi-omics data: mathematical aspects
The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences
A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge
Semantic representation of monogenean haptoral Bar image annotation
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data
BAGEL: a computational framework for identifying essential genes from pooled library screens
Genetic algorithm learning as a robust approach to RNA editing site prediction
A fault-tolerant method for HLA typing with PacBio data
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis
Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data
BS Seeker: precise mapping for bisulfite sequencing
Elucidation of functional consequences of signalling pathway interactions
ETHNOPRED: a novel machine learning method for accurate continental and sub-continental ancestry identification and population stratification correction
Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in Breast Cancer
LINNAEUS: A species name identification system for biomedical literature
PFClust: a novel parameter free clustering algorithm
Gen Htr : a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing
Fast and robust group-wise eQTL mapping using sparse graphical models
Efficient branch-and-bound techniques for two-locus association mapping
Very Important Pool (VIP) genes - an application for microarray-based molecular signatures
Correction to: Computational approaches for cancer 2017 workshop overview
Attenuating dependence on structural data in computing protein energy landscapes
Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis
Small molecule drug and biotech drug interaction prediction based on multi-modal representation learning
A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy
WGCNA: an R package for weighted correlation network analysis
Enabling proteomics-based identification of human cancer variations
Improved compound-protein interaction site and binding affinity prediction using self-supervised protein embeddings
SALON ontology for the formal description of sequence alignments
NaviSE: superenhancer navigator integrating epigenomics signal algebra
AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization
A powerful parent-of-origin effects test for qualitative traits on X chromosome in general pedigrees
DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates
Ranking analysis of F -statistics for microarray data
Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds
A general-purpose signal processing algorithm for biological profiles using only first-order derivative information
A mutation degree model for the identification of transcriptional regulatory elements
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments
A computational diffusion model to study antibody transport within reconstructed tumor microenvironments
QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics
A reinforcement learning approach for protein-ligand binding pose prediction
Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures
CIG-P: Circular Interaction Graph for Proteomics
Comparison of kNN and k-means optimization methods of reference set selection for improved CNV callers performance
The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis
Incorporating genetic networks into case-control association studies with high-dimensional DNA methylation data
DOCKSCORE: a webserver for ranking protein-protein docked poses
Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia
gcplyr: an R package for microbial growth curve data analysis
The acquisition of novel N-glycosylation sites in conserved proteins during human evolution
Testing adequacy for DNA substitution models
Confirmation of human protein interaction data by human expression data
CAD systems for COVID-19 diagnosis and disease stage classification by segmentation of infected regions from CT images
Mining microbe-disease interactions from literature via a transfer learning model
Optimized mixed Markov models for motif identification
Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools
Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies
Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates
Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
ResynPy: a software for selecting pairs of complementary inbred lines to resynthesize valuable heterozygous genotypes
SEQOPTICS: a protein sequence clustering system
GeneLibrarian: an effective gene-information summarization and visualization system
Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking
GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest
Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme
Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
Fast automated cell phenotype image classification
EDISA: extracting biclusters from multiple time-series of gene expression profiles
Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics
Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
Haplotypes of the imprinted insulin gene are associated with size for gestational age and umbilical cord IGF-II levels
USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences
SynergyImage: image-based model for drug combinations synergy score prediction
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
Graph4Med: a web application and a graph database for visualizing and analyzing medical databases
Providing visualisation support for the analysis of anatomy ontology data
Identification of temporal association rules from time-series microarray data sets
SegCorr a statistical procedure for the detection of genomic regions of correlated expression
Identification of all-against-all protein-protein interactions based on deep hash learning
Revealing the functionality of hypothetical protein KPN00728 from Klebsiella pneumoniae MGH78578: molecular dynamics simulation approaches
Improving contig binning of metagenomic data using (d 2 S ) oligonucleotide frequency dissimilarity
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
BigTop: a three-dimensional virtual reality tool for GWAS visualization
BioCAD: an information fusion platform for bio-network inference and analysis
A web-based multi-genome synteny viewer for customized data
Correction: DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs
Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network
DBS: a fast and informative segmentation algorithm for DNA copy number analysis
HarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation
Erratum to: Genomic prediction using subsampling
VaccImm: simulating peptide vaccination in cancer therapy
CODA-ML: context-specific biological knowledge representation for systemic physiology analysis
Leveraging gene correlations in single cell transcriptomic data
PREP-Mt: predictive RNA editor for plant mitochondrial genes
Random forest versus logistic regression: a large-scale benchmark experiment
Building multiclass classifiers for remote homology detection and fold recognition
Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs
AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data
Regulatory network operations in the Pathway Tools software
QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles
Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation
A context-blocks model for identifying clinical relationships in patient records
Prider: multiplexed primer design using linearly scaling approximation of set coverage
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays
Prodigal: prokaryotic gene recognition and translation initiation site identification
An Ensemble Deep Learning based Predictor for Simultaneously Identifying Protein Ubiquitylation and SUMOylation Sites
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information
Empirical Bayes estimation of posterior probabilities of enrichment: A comparative study of five estimators of the local false discovery rate
PedGenie: meta genetic association testing in mixed family and case-control designs
Double matrix completion for circRNA-disease association prediction
A weighted q -gram method for glycan structure classification
Was the Scanner Calibration Slide Used for Its Intended Purpose?
An interpretable framework for clustering single-cell RNA-Seq datasets
BALL - biochemical algorithms library 1.3
Normalization and missing value imputation for label-free LC-MS analysis
Mapping behavioral specifications to model parameters in synthetic biology
SuperNoder: a tool to discover over-represented modular structures in networks
Identification of alcohol preference relevant genes in QTL on mouse chromosome 2
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data
Control of multilayer biological networks and applied to target identification of complex diseases
A network perspective on the topological importance of enzymes and their phylogenetic conservation
SFREEMAP - A simulation-free tool for stochastic mapping
Incorporating exon-exon junction reads enhances differential splicing detection
Evaluation and comparison of mammalian subcellular localization prediction methods
mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes
designGG: an R-package and web tool for the optimal design of genetical genomics experiments
Statistical identification of gene association by CID in application of constructing ER regulatory network
A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays
Microarray data mining using landmark gene-guided clustering
MinLinMo: a minimalist approach to variable selection and linear model prediction
Genomic scale analysis of lateral gene transfer in Apicomplexan parasites: insights into early eukaryotic evolution, host-pathogen interaction and drug target development
Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations
Novel gene sets improve set-level classification of prokaryotic gene expression data
Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2
SSELM-neg: spherical search-based extreme learning machine for drug-target interaction prediction
xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
Gene regulatory networks inference using a multi-GPU exhaustive search algorithm
topr: an R package for viewing and annotating genetic association results
Homology-based inference sets the bar high for protein function prediction
Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets
A flexible framework for sparse simultaneous component based data integration
Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates
A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis
MLW-gcForest: a multi-weighted gcForest model towards the staging of lung adenocarcinoma based on multi-modal genetic data
Learning mixed graphical models with separate sparsity parameters and stability-based model selection
Contrastive learning-based multi-mechanism disentangled assessment for drug-drug interaction
Identification and validation of a siglec-based and aging-related 9-gene signature for predicting prognosis in acute myeloid leukemia patients
A state-of-the-art technique to perform cloud-based semantic segmentation using deep learning 3D U-Net architecture
Identification of models of heterogeneous cell populations from population snapshot data
Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data
A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra
Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces
The GENIUS Grid Portal and robot certificates: a new tool for e-Science
Genome wide association study of nonsynonymous Single Nucleotide Polymorphisms for seven common diseases
GiniClust3: a fast and memory-efficient tool for rare cell type identification
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
Parallel sequence tagging for concept recognition
Enhanced identification of significant regulators of gene expression
Autoencoders with shared and specific embeddings for multi-omics data integration
Shape-based peak identification for ChIP-Seq
A simplicial complex-based approach to unmixing tumor progression data
Filtering procedures for untargeted LC-MS metabolomics data
Classification of heterogeneous microarray data by maximum entropy kernel
A system for de-identifying medical message board text
TBMap: a taxonomic perspective on the phylogenetic database TreeBASE
CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences
Content-based microarray search using differential expression profiles
HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer
PP-DDP: a privacy-preserving outsourcing framework for solving the double digest problem
Design of a combinatorial DNA microarray for protein-DNA interaction studies
Evaluation of 3D-Jury on CASP7 models
Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks
COSAP: Comparative Sequencing Analysis Platform
The Ruby UCSC API: accessing the UCSC genome database using Ruby
Building better interdisciplinary scientists: creating graduate level courses to address the communication gap in interdisciplinary research
Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression
HECTAR: A method to predict subcellular targeting in heterokonts
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations
The human "magnesome": detecting magnesium binding sites on human proteins
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins
Orthology prediction at scalable resolution by phylogenetic tree analysis
Mining influential genes based on deep learning
A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data
Dualmarker: a flexible toolset for exploratory analysis of combinatorial dual biomarkers for clinical efficacy
Computational RNA secondary structure design: empirical complexity and improved methods
EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays
Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis
Quantitative systems-level determinants of drug targets
Annot: a Django-based sample, reagent, and experiment metadata tracking system
LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB
Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application
Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory
Network-based modular latent structure analysis
Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory
A distributed framework for aligning short reads to genomes
False discovery rate control in two-stage designs
Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey ( Symphytum officinale )
Hierarchical graphs for rule-based modeling of biochemical systems
NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline
HTPheno: An Image Analysis Pipeline for High-Throughput Plant Phenotyping
Robustness of Random Forest-based gene selection methods
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns
ChainRank, a chain prioritisation method for contextualisation of biological networks
eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies
Empirical Bayes models for multiple probe type microarrays at the probe level