yusuke1997/dblp-id-title huggingface dataset:
Real value prediction of protein solvent accessibility using enhanced PSSM features
Efficient alpha, beta-motif Finder for Identification of Phenotype-related Functional Modules
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures
Application of sequence semantic and integrated cellular geography approach to study alternative biogenesis of exonic circular RNA
Joint genotype inference with germline and somatic mutations
Prediction of dinucleotide-specific RNA-binding sites in proteins
Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k -spaced amino acid pairs
Correction: cosinoRmixedeffects: an R package for mixed-effects cosinor models
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
RNA: (guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure
ElliPro: a new structure-based tool for the prediction of antibody epitopes
RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'
MMiRNA-Viewer 2 , a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network
Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator
PennCNV in whole-genome sequencing data
CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter
FiGS: a filter-based gene selection workbench for microarray data
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models
micropanmicropan: an R-package for microbial pan-genomics
FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information
SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures
An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices
Prioritisation of Disease Gene Candidates: A Systems Biology Approach
Automatic annotation of protein motif function with Gene Ontology terms
SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines
Conserved co-expression for candidate disease gene prioritization
Routine performance and errors of 454 HLA exon sequencing in diagnostics
In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells
Using Stochastic Causal Trees to Augment Bayesian Networks for Modeling eQTL Datasets
GlycomeDB - integration of open-access carbohydrate structure databases
Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock
QMachine: commodity supercomputing in web browsers
A study on the application of topic models to motif finding algorithms
New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data
Data mining of enzymes using specific peptides
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures
Amogel: a multi-omics classification framework using associative graph neural networks with prior knowledge for biomarker identification
Reconstructing genome mixtures from partial adjacencies
AllergenAI: a deep learning model predicting allergenicity based on protein sequence
PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity
Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition
GEVALT: An integrated software tool for genotype analysis
GAIA: a gram-based interaction analysis tool - an approach for identifying interacting domains in yeast
Content-based histopathology image retrieval using CometCloud
How to inherit statistically validated annotation within BAR+ protein clusters
An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast
Robust detection of periodic time series measured from biological systems
An automated graphics tool for comparative genomics: the Coulson plot generator
Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations
Filtering Genes for Cluster and Network Analysis
A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks
Benchmark datasets of immune receptor-epitope structural complexes
Correction: versatile and declarative dynamic programming using pair algebras
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
The assessment of efficient representation of drug features using deep learning for drug repositioning
MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data
Redundancy in electronic health record corpora: analysis, impact on text mining performance and mitigation strategies
A graph-based approach for designing extensible pipelines
BBP: Brucella genome annotation with literature mining and curation
Early response index: a statistic to discover potential early stage disease biomarkers
An ICT infrastructure to integrate clinical and molecular data in oncology research
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context
Benchmarking natural-language parsers for biological applications using dependency graphs
A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree
Extending rnaSPAdes functionality for hybrid transcriptome assembly
Skeleton optimization of neuronal morphology based on three-dimensional shape restrictions
DeepAEG: a model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies
YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters
SNPFile - A software library and file format for large scale association mapping and population genetics studies
Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets
methBLAST and methPrimerDB: web-tools for PCR based methylation analysis
The dynamics of functional classes of plant genes in rediploidized ancient polyploids
SNP-VISTA: An interactive SNP visualization tool
Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome
Detection and categorization of bacteria habitats using shallow linguistic analysis
Combining gene expression data from different generations of oligonucleotide arrays
Correction to: MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package
MotifMap: integrative genome-wide maps of regulatory motif sites for model species
Quantifying single nucleotide variant detection sensitivity in exome sequencing
BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences
TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases
OLSVis: an animated, interactive visual browser for bio-ontologies
Drug-target interaction prediction with tree-ensemble learning and output space reconstruction
FluxFix: automatic isotopologue normalization for metabolic tracer analysis
Analysis of density based and fuzzy c-means clustering methods on lesion border extraction in dermoscopy images
Massive non-natural proteins structure prediction using grid technologies
Supervised group Lasso with applications to microarray data analysis
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores
Progressive multiple sequence alignment with indel evolution
MicroTar: predicting microRNA targets from RNA duplexes
Towards ontology-driven navigation of the lipid bibliosphere
Predicting residue-wise contact orders in proteins by support vector regression
G4Boost: a machine learning-based tool for quadruplex identification and stability prediction
Automated sparse feature selection in high-dimensional proteomics data via 1-bit compressed sensing and K-Medoids clustering
MSH-DTI: multi-graph convolution with self-supervised embedding and heterogeneous aggregation for drug-target interaction prediction
Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network
Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes
An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs
Workflows for microarray data processing in the Kepler environment
Automatic classification of sentences to support Evidence Based Medicine
Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2
Survey-based naming conventions for use in OBO Foundry ontology development
A comparative study of S/MAR prediction tools
Establishing bioinformatics research in the Asia Pacific
Identifying Alzheimer's disease-related proteins by LRRGD
An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets
DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
Handling multiple testing while interpreting microarrays with the Gene Ontology Database
A stepwise framework for the normalization of array CGH data
Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites
PIKE-R2P: Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction
Implementation of machine learning in the clinic: challenges and lessons in prospective deployment from the System for High Intensity EvaLuation During Radiation Therapy (SHIELD-RT) randomized controlled study
On the comparison of regulatory sequences with multiple resolution Entropic Profiles
The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes
Binning sequences using very sparse labels within a metagenome
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)
Optimal precursor ion selection for LC-MALDI MS/MS
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies
Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis
CMIC: an efficient quality score compressor with random access functionality
Compressing DNA sequence databases with coil
Modeling aspects of the language of life through transfer-learning protein sequences
Detection and tracking of overlapping cell nuclei for large scale mitosis analyses
WEScover: selection between clinical whole exome sequencing and gene panel testing
Mining gene expression data by interpreting principal components
iBarcode.org: web-based molecular biodiversity analysis
An efficient grid layout algorithm for biological networks utilizing various biological attributes
Probe computing model based on small molecular switch
cnnLSV: detecting structural variants by encoding long-read alignment information and convolutional neural network
In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites
scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data
ETISEQ - an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics
Reducing bias in RNA sequencing data: a novel approach to compute counts
GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions
Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data
Evolution of drug resistance in HIV protease
Least-squares methods for identifying biochemical regulatory networks from noisy measurements
Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets
TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data
In silico design of a multi-epitope vaccine against HPV16/18
CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides
SLMSuite: a suite of algorithms for segmenting genomic profiles
The antibiotic resistance proteome of Acinetobacter baumanii MDR isolate MMC#4
Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage
PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data
Ontological visualization of protein-protein interactions
UFFizi: a generic platform for ranking informative features
A random effect multiplicative heteroscedastic model for bacterial growth
PDA: Pooled DNA analyzer
Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes
A multiple kernel learning algorithm for drug-target interaction prediction
CINOEDV: a co-information based method for detecting and visualizing n -order epistatic interactions
MISDP: multi-task fusion visit interval for sequential diagnosis prediction
NeurphologyJ: an automatic neuronal morphology quantification method and its application in pharmacological discovery
Inter-protein residue covariation information unravels physically interacting protein dimers
Multivariate search for differentially expressed gene combinations
Identification of prognostic and predictive biomarkers in high-dimensional data with PPLasso
Multi-cancer samples clustering via graph regularized low-rank representation method under sparse and symmetric constraints
Prediction of unconventional protein secretion by exosomes
Multivariate analysis of microarray data: differential expression and differential connection
Computing the protein binding sites
Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
Efficient alignment of pyrosequencing reads for re-sequencing applications
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
CAGEfightR: analysis of 5′-end data using R/Bioconductor
Spherical: an iterative workflow for assembling metagenomic datasets
RCMF: a robust collaborative matrix factorization method to predict miRNA-disease associations
Impact of the spotted microarray preprocessing method on fold-change compression and variance stability
Statistical validation of megavariate effects in ASCA
Sparse sliced inverse regression for high dimensional data analysis
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules
A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
Efficient decoding algorithms for generalized hidden Markov model gene finders
miREE: miRNA Recognition Elements Ensemble
AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning
Structural comparison of metabolic networks in selected single cell organisms
EPEPT: A web service for enhanced P-value estimation in permutation tests
Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data
Correction: MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts
pcaReduce: hierarchical clustering of single cell transcriptional profiles
SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition
Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
Learning-guided automatic three dimensional synapse quantification for drosophila neurons
Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients
Aggregation of experts: an application in the field of "interactomics" (detection of interactions on the basis of genomic data)
A practical guideline for intracranial volume estimation in patients with Alzheimer's disease
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes
Quantitative synteny scoring improves homology inference and partitioning of gene families
Class similarity network for coding and long non-coding RNA classification
Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis
Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments
SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles
An approach for proteins and their encoding genes synonyms integration based on protein ontology
iPhy: an integrated phylogenetic workbench for supermatrix analyses
A fast and efficient gene-network reconstruction method from multiple over-expression experiments
Integration and visualization of systems biology data in context of the genome
Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets
Bacterial genotyping by 16S rRNA mass cataloging
Time warping of evolutionary distant temporal gene expression data based on noise suppression
Highlights from the tenth ISCB Student Council Symposium 2014
IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier
Hypergraph models of biological networks to identify genes critical to pathogenic viral response
Improved supervised prediction of aging-related genes via weighted dynamic network analysis
Simcryocluster: a semantic similarity clustering method of cryo-EM images by adopting contrastive learning
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison
FoldHSphere: deep hyperspherical embeddings for protein fold recognition
BioLMiner and the BioCreative II.5 challenge
Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models
HALC: High throughput algorithm for long read error correction
The causal effect of red blood cell folate on genome-wide methylation in cord blood: a Mendelian randomization approach
PanoromiX: a time-course network medicine platform integrating molecular assays and pathophenotypic data
Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity
Alignment-free methods for metagenomic profiling
Semi-supervised learning improves regulatory sequence prediction with unlabeled sequences
Using large public data repositories to discover novel genetic mutations with prospective links to melanoma
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Trends in life science grid: from computing grid to knowledge grid
Meta-eQTL: a tool set for flexible eQTL meta-analysis
rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs
Deconvolution of bulk blood eQTL effects into immune cell subpopulations
Concept recognition as a machine translation problem
CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment
Exploring and linking biomedical resources through multidimensional semantic spaces
AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa
A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks
Assessing stationary distributions derived from chromatin contact maps
Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method
Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms
Quantifying conformational changes in GPCRs: glimpse of a common functional mechanism
APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010
Tisslet tissues-based learning estimation for transcriptomics
An iteration method for identifying yeast essential proteins from heterogeneous network
Computational framework to support integration of biomolecular and clinical data within a translational approach
SDA: a semi-parametric differential abundance analysis method for metabolomics and proteomics data
Segmentation and intensity estimation for microarray images with saturated pixels
COSMOS: cloud enabled NGS analysis
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
GNNMutation: a heterogeneous graph-based framework for cancer detection
GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms
Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data
Robust edge-based biomarker discovery improves prediction of breast cancer metastasis
NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing
Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes
Conditional permutation importance revisited
Knowledge-based analysis of proteomics data
Fixed-parameter tractable sampling for RNA design with multiple target structures
A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data
Exploiting topic modeling to boost metagenomic reads binning
Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition
A comparison of common programming languages used in bioinformatics
Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence
A statistical method for the conservative adjustment of false discovery rate (q-value)
BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS
Computing power of quantitative trait locus association mapping for haploid loci
Intervention in prediction measure: a new approach to assessing variable importance for random forests