yusuke1997/dblp-id-title huggingface dataset:
Dynamically characterizing individual clinical change by the steady state of disease-associated pathway
Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search
Screening synteny blocks in pairwise genome comparisons through integer programming
Missing value imputation for microRNA expression data by using a GO-based similarity measure
TnseqDiff: identification of conditionally essential genes in transposon sequencing studies
rnaSeqMap: a Bioconductor package for RNA sequencing data exploration
Distilling structure in Taverna scientific workflows: a refactoring approach
ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species
EFICAz 2 : enzyme function inference by a combined approach enhanced by machine learning
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
Construction and optimization of gene expression signatures for prediction of survival in two-arm clinical trials
RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases
Predicting functional sites with an automated algorithm suitable for heterogeneous datasets
Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data
Data-driven human transcriptomic modules determined by independent component analysis
Constructing the boundary between potent and ineffective siRNAs by MG-algorithm with C-features
EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
Occlusion enhanced pan-cancer classification via deep learning
PWHATSHAP: efficient haplotyping for future generation sequencing
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships
DLAD4U: deriving and prioritizing disease lists from PubMed literature
Evolutionary models for insertions and deletions in a probabilistic modeling framework
Progressive search in tandem mass spectrometry
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database
The unifrac significance test is sensitive to tree topology
Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition
An application of convolutional neural networks with salient features for relation classification
SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
Identification of drug-target interaction by a random walk with restart method on an interactome network
False discovery rates in spectral identification
Robust volcano plot: identification of differential metabolites in the presence of outliers
SubPatCNV: approximate subspace pattern mining for mapping copy-number variations
SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies
Explorative visual analytics on interval-based genomic data and their metadata
Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
UMARS: Un-MAppable Reads Solution
MetaFIND: A feature analysis tool for metabolomics data
An efficient algorithm for improving structure-based prediction of transcription factor binding sites
Probabilistic annotation of protein sequences based on functional classifications
Identification of RNA silencing components in soybean and sorghum
Biomedical relation extraction method based on ensemble learning and attention mechanism
permGPU: Using graphics processing units in RNA microarray association studies
SCNVSim: somatic copy number variation and structure variation simulator
Method to represent the distribution of QTL additive and dominance effects associated with quantitative traits in computer simulation
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins
Analysis of multiplex gene expression maps obtained by voxelation
Study of cell differentiation by phylogenetic analysis using histone modification data
From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification
snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing
BiologicalNetworks 2.0 - an integrative view of genome biology data
A systematic framework to derive N -glycan biosynthesis process and the automated construction of glycosylation networks
DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations
An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments
Phenotypic and genotypic data integration and exploration through a web-service architecture
On how to generalize species-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome
Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy
SuRankCo: supervised ranking of contigs in de novo assemblies
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
Detection of identity by descent using next-generation whole genome sequencing data
Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols
DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing
Local alignment of generalized k-base encoded DNA sequence
Multi-labelled proteins recognition for high-throughput microscopy images using deep convolutional neural networks
SegMine workflows for semantic microarray data analysis in Orange4WS
Automatic identification of angiogenesis in double stained images of liver tissue
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package
A comparison of three programming languages for a full-fledged next-generation sequencing tool
Characterization of an inducible promoter in different DNA copy number conditions
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets
Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer
Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae
Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations
A unified framework for managing provenance information in translational research
Simultaneous learning of individual microRNA-gene interactions and regulatory comodules
A comparative study of discriminating human heart failure etiology using gene expression profiles
Interactively Illustrating Polymerization using Three-level Model Fusion
SQUAT: A web tool to mine human, murine and avian SAGE data
Detection and visualization of complex structural variants from long reads
CBDB: The codon bias database
Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands
Learning to predict expression efficacy of vectors in recombinant protein production
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases
Data integration by fuzzy similarity-based hierarchical clustering
Biomedical relation extraction via knowledge-enhanced reading comprehension
Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences
LipocalinPred: a SVM-based method for prediction of lipocalins
A subgraph isomorphism algorithm and its application to biochemical data
Simulating variance heterogeneity in quantitative genome wide association studies
GPDRP: a multimodal framework for drug response prediction with graph transformer
Tiling Nussinov's RNA folding loop nest with a space-time approach
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions
Differential analysis for high density tiling microarray data
Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset
µHEM for identification of differentially expressed miRNAs using hypercuboid equivalence partition matrix
3D deep convolutional neural networks for amino acid environment similarity analysis
GOmotif: A web server for investigating the biological role of protein sequence motifs
Integrating transformers and many-objective optimization for drug design
PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data
Inverse Langmuir method for oligonucleotide microarray analysis
Parallelisation strategies for agent based simulation of immune systems
Knowledge driven decomposition of tumor expression profiles
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome
Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database - Xindice
Genetic algorithm with logistic regression for prediction of progression to Alzheimer's disease
Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering
Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia
Correction to: FastMM: an efficient toolbox for personalized constraint-based metabolic modeling
Learning protein binding affinity using privileged information
Predicting diabetic retinopathy and identifying interpretable biomedical features using machine learning algorithms
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
AllCoPol: inferring allele co-ancestry in polyploids
Novel human microbe-disease association prediction using network consistency projection
An evaluation of human protein-protein interaction data in the public domain
Exploring dynamic metabolomics data with multiway data analysis: a simulation study
TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function
Faster and more accurate pathogenic combination predictions with VarCoPP2.0
SPAligner: alignment of long diverged molecular sequences to assembly graphs
MAIRA- real-time taxonomic and functional analysis of long reads on a laptop
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
Nonlinear expression and visualization of nonmetric relationships in genetic diseases and microbiome data
Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome
Dissecting systems-wide data using mixture models: application to identify affected cellular processes
RCytoscape: tools for exploratory network analysis
Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r
mycelyso - high-throughput analysis of Streptomyces mycelium live cell imaging data
PROVAT - a versatile tool for Voronoi tessellation analysis of protein structures and complexes
ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database
ROIMCR: a powerful analysis strategy for LC-MS metabolomic datasets
qPIPSA: Relating enzymatic kinetic parameters and interaction fields
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism
Gene set analysis using sufficient dimension reduction
Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant
CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes
An improved clear cell renal cell carcinoma stage prediction model based on gene sets
Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns
Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut
RCircos: an R package for Circos 2D track plots
Visualizing and clustering high throughput sub-cellular localization imaging
Extended analysis of benchmark datasets for Agilent two-color microarrays
GeNeCK: a web server for gene network construction and visualization
Parameter estimation for stiff equations of biosystems using radial basis function networks
Balony: a software package for analysis of data generated by synthetic genetic array experiments
A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits
BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs
Correction: Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
Multivariate curve resolution of time course microarray data
A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations
Evaluation of statistical approaches for association testing in noisy drug screening data
Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma
CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes
geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research
Non parametric differential network analysis: a tool for unveiling specific molecular signatures
Predicting Bevirimat resistance of HIV-1 from genotype
Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Visual setup of logical models of signaling and regulatory networks with ProMoT
Sequence variation in ligand binding sites in proteins
Active Subnetwork Recovery with a Mechanism-Dependent Scoring Function; with application to Angiogenesis and Organogenesis studies
ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces
The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci
Assigning protein function from domain-function associations using DomFun
Using a kernel density estimation based classifier to predict species-specific microRNA precursors
isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data
Using jackknife to assess the quality of gene order phylogenies
Clinical bioinformatics for complex disorders: a schizophrenia case study
FEPI-MB: identifying SNPs-disease association using a Markov Blanket-based approach
Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
Kiwi: a tool for integration and visualization of network topology and gene-set analysis
Correction to: Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis
In silico panning for a non-competitive peptide inhibitor
miRNASNP: a database of miRNA related SNPs and their effects on miRNA function
Integration of probabilistic functional networks without an external Gold Standard
Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution
Is this the right normalization? A diagnostic tool for ChIP-seq normalization
Conservation of regulatory elements between two species of Drosophila
Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning
GeneDig: a web application for accessing genomic and bioinformatics knowledge
Inference of radio-responsive gene regulatory networks using the graphical lasso algorithm
EMDLP: Ensemble multiscale deep learning model for RNA methylation site prediction
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis
sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database
Bioinformatics research at SBB-2019
An unsupervised partition method based on association delineated revised mutual information
Phylo-mLogo : an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences
DCMF-PPI: a protein-protein interaction predictor based on dynamic condition and multi-feature fusion
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space
Analysis of equine protein-coding gene structure and expression by RNA-sequencing
Convolutional neural network based on SMILES representation of compounds for detecting chemical motif
MARV: a tool for genome-wide multi-phenotype analysis of rare variants
Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection
Usage of cell nomenclature in biomedical literature
ArrayIDer : automated structural re-annotation pipeline for DNA microarrays
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection
WebGIVI: a web-based gene enrichment analysis and visualization tool
ARGV: 3D genome structure exploration using augmented reality
Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm
Applying negative rule mining to improve genome annotation
A novel method for cross-species gene expression analysis
Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development
RNAmute: RNA secondary structure mutation analysis tool
AlignHUSH : Alignment of HMMs Using Structure and Hydrophobicity information
Translog, a web browser for studying the expression divergence of homologous genes
Calculating semantic relatedness for biomedical use in a knowledge-poor environment
An adaptive threshold determination method of feature screening for genomic selection
Learning smoothing models of copy number profiles using breakpoint annotations
SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
HOMER: a human organ-specific molecular electronic repository
Discovery of co-occurring driver pathways in cancer
A ratiometric-based measure of gene co-expression
Comparison of normalization methods for CodeLink Bioarray data
ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application
LSCplus: a fast solution for improving long read accuracy by short read alignment
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts
TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis
Determination of sample size for a multi-class classifier based on single-nucleotide polymorphisms: a volume under the surface approach
The SGS3 protein involved in PTGS finds a family
Drug candidate identification based on gene expression of treated cells using tensor decomposition-based unsupervised feature extraction for large-scale data
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs
Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis
JColorGrid: software for the visualization of biological measurements
The development of an open-access database for human transcriptional regulation interactions
Machine learning-based approaches for ubiquitination site prediction in human proteins
SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees
A novel glycosylation-related gene signature predicts survival in patients with lung adenocarcinoma
Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses
PANEV: an R package for a pathway-based network visualization
BMC Bioinformatics reviewer acknowledgement 2014
MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning
The implementation of e-learning tools to enhance undergraduate bioinformatics teaching and learning: a case study in the National University of Singapore
PDB-Explorer: a web-based interactive map of the protein data bank in shape space
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees
VIST - a Variant-Information Search Tool for precision oncology
Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis
4273pi: Bioinformatics education on low cost ARM hardware
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data
EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction
Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases
Improving the analysis of designed studies by combining statistical modelling with study design information
A method for aligning RNA secondary structures and its application to RNA motif detection
Comparison of data mining and allometric model in estimation of tree biomass
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types
A Bregman-proximal point algorithm for robust non-negative matrix factorization with possible missing values and outliers - application to gene expression analysis
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects
Divisive hierarchical maximum likelihood clustering
A machine learning strategy to identify candidate binding sites in human protein-coding sequence
PathNetDRP: a novel biomarker discovery framework using pathway and protein-protein interaction networks for immune checkpoint inhibitor response prediction
Tests for finding complex patterns of differential expression in cancers: towards individualized medicine
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"
A realistic assessment of methods for extracting gene/protein interactions from free text
An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example
Predicting combinations of drugs by exploiting graph embedding of heterogeneous networks
Analyzing transfer learning impact in biomedical cross-lingual named entity recognition and normalization
A robust nonlinear low-dimensional manifold for single cell RNA-seq data