yusuke1997/dblp-id-title huggingface dataset:
Haplotype association analyses in resources of mixed structure using Monte Carlo testing
Improving peptide-MHC class I binding prediction for unbalanced datasets
KidneyGPS: a user-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies
NCACO-score: An effective main-chain dependent scoring function for structure modeling
Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics
An automatic method for identifying surface proteins in bacteria: SLEP
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer
FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data
Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view
Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation
DeepEP: a deep learning framework for identifying essential proteins
ATMAD: robust image analysis for Automatic Tissue MicroArray De-arraying
Multi-scale RNA comparison based on RNA triple vector curve representation
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer
Cluster analysis of protein array results via similarity of Gene Ontology annotation
SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics
Ontology driven integration platform for clinical and translational research
DCE@urLAB: a dynamic contrast-enhanced MRI pharmacokinetic analysis tool for preclinical data
miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer
Using discriminative vector machine model with 2DPCA to predict interactions among proteins
An algorithm for automated closure during assembly
Cross platform microarray analysis for robust identification of differentially expressed genes
Classification across gene expression microarray studies
Ontology-based instance data validation for high-quality curated biological pathways
LCS-TA to identify similar fragments in RNA 3D structures
Automated Alphabet Reduction for Protein Datasets
CAMSA: a tool for comparative analysis and merging of scaffold assemblies
Sparse PLS Discriminant Analysis: biologically relevant feature selection and graphical displays for multiclass problems
A Semi-Local Neighborhood-based Framework for Probabilistic Cell Lineage Tracing
ClusCo: clustering and comparison of protein models
On triangle inequalities of correlation-based distances for gene expression profiles
Proceedings of the Second International Symposium for Semantic Mining in Biomedicine
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform
Deciphering the connectivity structure of biological networks using MixNet
Using cited references to improve the retrieval of related biomedical documents
Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming
A machine learning pipeline for quantitative phenotype prediction from genotype data
Using structural motif descriptors for sequence-based binding site prediction
easyClock: a user-friendly desktop application for circadian rhythm analysis and visualization
Detecting large deletions at base pair level by combining split read and paired read data
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs
Occurrence prediction of pests and diseases in cotton on the basis of weather factors by long short term memory network
An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene Interactions on risk of myocardial infarction: The importance of model validation
Evolutionary chemical binding similarity approach integrated with 3D-QSAR method for effective virtual screening
Integrative missing value estimation for microarray data
A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values
RNAstructure: software for RNA secondary structure prediction and analysis
SeqVISTA: a graphical tool for sequence feature visualization and comparison
Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans
Ontology-driven indexing of public datasets for translational bioinformatics
ShatterProof: operational detection and quantification of chromothripsis
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results
HMM-FRAME: accurate protein domain classification for metagenomic sequences in the presence of frameshift errors
Juxtapose: a gene-embedding approach for comparing co-expression networks
RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms
Bacterial cell identification in differential interference contrast microscopy images
TOPS: a versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data
Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome
Pre-processing Agilent microarray data
RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources
EDLm 6 APred: ensemble deep learning approach for mRNA m 6 A site prediction
CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search
Rapid bacterial identification through volatile organic compound analysis and deep learning
iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis
SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms
PangeBlocks: customized construction of pangenome graphs via maximal blocks
Implementation of Force Distribution Analysis for Molecular Dynamics simulations
Partition-based optimization model for generative anatomy modeling language (POM-GAML)
Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis
AnEnPi: identification and annotation of analogous enzymes
Copy number variation detection using next generation sequencing read counts
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network
FreeContact: fast and free software for protein contact prediction from residue co-evolution
Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers
MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy
Novel drug-target interactions via link prediction and network embedding
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks
The complexity of gene expression dynamics revealed by permutation entropy
Identification of hot-spot residues in protein-protein interactions by computational docking
Evaluation of pooled allelotyping versus individual genotyping for genome-wide association analysis of complex disease
Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features
Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes
Statistical method on nonrandom clustering with application to somatic mutations in cancer
Automatic extraction of informal topics from online suicidal ideation
CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies
Metabolic Network Analysis: Implication And Application
AgdbNet - antigen sequence database software for bacterial typing
An embedded gene selection method using knockoffs optimizing neural network
The Mycoplasma conjunctivae genome sequencing, annotation and analysis
Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths
Statistical method to compare massive parallel sequencing pipelines
Conceptual modelling for life sciences based on systemist foundations
BEROLECMI: a novel prediction method to infer circRNA-miRNA interaction from the role definition of molecular attributes and biological networks
Correction: Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment
MicroRNA categorization using sequence motifs and k-mers
Inferring gene coexpression networks for low dose ionizing radiation using graph theoretical algorithms and systems genetics
The textual characteristics of traditional and Open Access scientific journals are similar
rapmad: Robust Analysis of Peptide Microarray Data
ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis
Protein evolution driven by symmetric structural repeats
MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates
A unified framework for finding differentially expressed genes from microarray experiments
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
Functional assessment of time course microarray data
SIMMAP: Stochastic character mapping of discrete traits on phylogenies
Correlation AnalyzeR: functional predictions from gene co-expression correlations
TLGP: a flexible transfer learning algorithm for gene prioritization based on heterogeneous source domain
Visual parameter optimisation for biomedical image processing
A benchmark for microRNA quantification algorithms using the OpenArray platform
A comparison of RNA folding measures
Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics: Burns, TN, USA. April 21-23, 2017
Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text
Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D
A non-negative spike-and-slab lasso generalized linear stacking prediction modeling method for high-dimensional omics data
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction
SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
IPLaminator: an ImageJ plugin for automated binning and quantification of retinal lamination
The evolution of the tape measure protein: units, duplications and losses
PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval
CRISPR-GRANT: a cross-platform graphical analysis tool for high-throughput CRISPR-based genome editing evaluation
Drug repurposing and prediction of multiple interaction types via graph embedding
SNVHMM: predicting single nucleotide variants from next generation sequencing
Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission
CosinorPy: a python package for cosinor-based rhythmometry
DEvis: an R package for aggregation and visualization of differential expression data
PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD
Legofit: estimating population history from genetic data
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach
Automated genome mining for natural products
Word correlation matrices for protein sequence analysis and remote homology detection
A method of searching for related literature on protein structure analysis by considering a user's intention
Taxonomic and functional diversity of microbial community from a mining environment
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach
kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
Diversity-guided Lamarckian random drift particle swarm optimization for flexible ligand docking
MixtureTree: a program for constructing phylogeny
Predicting circRNA-drug sensitivity associations via graph attention auto-encoder
GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors
Computational Analysis of Insulin in the Ageing Fruit Fly
Projections for fast protein structure retrieval
Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies
A novel method to compare protein structures using local descriptors
Comparison of seven in silico tools for evaluating of daphnia and fish acute toxicity: case study on Chinese Priority Controlled Chemicals and new chemicals
TAGOPSIN: collating taxa-specific gene and protein functional and structural information
Measure of synonymous codon usage diversity among genes in bacteria
A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data
sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs
Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data
Speeding disease gene discovery by sequence based candidate prioritization
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes
Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis
GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing
Extracting chemical reactions from text using Snorkel
Agent based modeling of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis
Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites
The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data
USI: a fast and accurate approach for conceptual document annotation
A statistical score for assessing the quality of multiple sequence alignments
PredAOT: a computational framework for prediction of acute oral toxicity based on multiple random forest models
Comparing variant calling algorithms for target-exon sequencing in a large sample
iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation
BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization
On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation
A comparative analysis of the information content in long and short SAGE libraries
Type2 diabetes mellitus prediction using data mining algorithms based on the long-noncoding RNAs expression: a comparison of four data mining approaches
Progressive multiple sequence alignments from triplets
Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces
Sub-population analysis based on temporal features of high content images
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics
The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data
Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing
Netter: re-ranking gene network inference predictions using structural network properties
Inferring RNA sequence preferences for poorly studied RNA-binding proteins based on co-evolution
Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features
Replacing normalizations with interval assumptions enhances differential expression and differential abundance analyses
RepBox: a toolbox for the identification of repetitive elements
Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data
An improved ant colony algorithm with diversified solutions based on the immune strategy
Empirical evaluation of scoring functions for Bayesian network model selection
Coregulation of transcription factors and microRNAs in human transcriptional regulatory network
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
Word add-in for ontology recognition: semantic enrichment of scientific literature
MLGCN-Driver: a cancer driver gene identification method based on multi-layer graph convolutional neural network
Semi-supervised class discovery using quantitative phenotypes - CVD as a case study
Flexible mapping of homology onto structure with Homolmapper
Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps
Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance
Visualization of large microarray experiments with space maps
"Harshlighting" small blemishes on microarrays
A compressed large language model embedding dataset of ICD 10 CM descriptions
Enhanced prediction of hemolytic activity in antimicrobial peptides using deep learning-based sequence analysis
MetaTM - a consensus method for transmembrane protein topology prediction
Mathematical model of hypoxia and tumor signaling interplay reveals the importance of hypoxia and cell-to-cell variability in tumor growth inhibition
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
Convolutional architectures for virtual screening
A novel biomarker selection method combining graph neural network and gene relationships applied to microarray data
Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology
Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia
DNA motif alignment by evolving a population of Markov chains
Filtering, FDR and power
Advancing drug-target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining
Literature mining for context-specific molecular relations using multimodal representations (COMMODAR)
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
PanGEA: Identification of allele specific gene expression using the 454 technology
An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network
FuGEFlow: data model and markup language for flow cytometry
EnzymeDetector: an integrated enzyme function prediction tool and database
TelomereHunter - in silico estimation of telomere content and composition from cancer genomes
A power law global error model for the identification of differentially expressed genes in microarray data
cPath: open source software for collecting, storing, and querying biological pathways
Identification and analysis of methylation call differences between bisulfite microarray and bisulfite sequencing data with statistical learning techniques
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design
GDR ( G enome D atabase for R osaceae): integrated web resources for Rosaceae genomics and genetics research
Sequence-based prediction of protein-protein interactions using weighted sparse representation model combined with global encoding
Indirect two-sided relative ranking: a robust similarity measure for gene expression data
CGHPRO - A comprehensive data analysis tool for array CGH
A three-state prediction of single point mutations on protein stability changes
Sampling and counting genome rearrangement scenarios
Modelling and visualizing fine-scale linkage disequilibrium structure
Capsule-LPI: a LncRNA-protein interaction predicting tool based on a capsule network
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes
Analysis of secondary structural elements in human microRNA hairpin precursors
A new method for enhancer prediction based on deep belief network
Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models
COPLA, a taxonomic classifier of plasmids
Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
csdR, an R package for differential co-expression analysis
PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison
scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
A generic classification-based method for segmentation of nuclei in 3D images of early embryos
A procedure for identifying homologous alternative splicing events
Bioinformatics: indispensable, yet hidden in plain sight?
DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses
Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis
Sparse data embedding and prediction by tropical matrix factorization
GeneNotes - A novel information management software for biologists
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders
Large-scale identification of polymorphic microsatellites using an in silico approach
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data
Tools for loading MEDLINE into a local relational database
Network analysis of metabolic enzyme evolution in Escherichia coli
MIMO: an efficient tool for molecular interaction maps overlap
CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
RGG: A general GUI Framework for R scripts
GC-Content Normalization for RNA-Seq Data
PnpProbs: a better multiple sequence alignment tool by better handling of guide trees
Artificial intelligence classification model for macular degeneration images: a robust optimization framework for residual neural networks
Centrality of drug targets in protein networks
Sieve-based relation extraction of gene regulatory networks from biological literature
HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
Lesion detection in demoscopy images with novel density-based and active contour approaches
Comprehensive evaluation of RNA-seq quantification methods for linearity