yusuke1997/dblp-id-title huggingface dataset:
Alignment-free analysis of barcode sequences by means of compression-based methods
SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data
Three-dimensional tumor growth in time-varying chemical fields: a modeling framework and theoretical study
CNV-WebStore: Online CNV Analysis, Storage and Interpretation
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process
Enhanced construction of gene regulatory networks using hub gene information
NeMo: Network Module identification in Cytoscape
Including probe-level uncertainty in model-based gene expression clustering
iHMS: a database integrating human histone modification data across developmental stages and tissues
Vermont: a multi-perspective visual interactive platform for mutational analysis
Estimating causal effects with a non-paranormal method for the design of efficient intervention experiments
Taking U out, with two nucleases?
Predicting gene ontology functions from protein's regional surface structures
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma
GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes
Detecting protein complexes with multiple properties by an adaptive harmony search algorithm
State of the art: refinement of multiple sequence alignments
svapls: an R package to correct for hidden factors of variability in gene expression studies
Analysis of common targets for circular RNAs
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity
Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer
outbreaker2: a modular platform for outbreak reconstruction
Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions
High-throughput sequencing of the DBA/2J mouse genome
LocText: relation extraction of protein localizations to assist database curation
BioProspecting: novel marker discovery obtained by mining the bibleome
Extending digital PCR analysis by modelling quantification cycle data
PPAI: a web server for predicting protein-aptamer interactions
Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society
Gene network modular-based classification of microarray samples
Comparative evaluation of gene set analysis approaches for RNA-Seq data
ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization
Physicochemical property distributions for accurate and rapid pairwise protein homology detection
Evaluation of variant detection software for pooled next-generation sequence data
A comparison study on algorithms of detecting long forms for short forms in biomedical text
Quality assessment of tandem mass spectra using support vector machine (SVM)
Semi-supervised prediction of protein interaction sites from unlabeled sample information
Generalized shrinkage F-like statistics for testing an interaction term in gene expression analysis in the presence of heteroscedasticity
AMEND: active module identification using experimental data and network diffusion
A sentence sliding window approach to extract protein annotations from biomedical articles
Assessment of protein set coherence using functional annotations
A multifactorial analysis of obesity as CVD risk factor: Use of neural network based methods in a nutrigenetics context
PARPST: a PARallel algorithm to find peptide sequence tags
Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
Family-based association analysis: a fast and efficient method of multivariate association analysis with multiple variants
MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics
GOModeler- A tool for hypothesis-testing of functional genomics datasets
mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics
PIGS: improved estimates of identity-by-descent probabilities by probabilistic IBD graph sampling
Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach
SynBlast: Assisting the analysis of conserved synteny information
A novel hybrid framework for metabolic pathways prediction based on the graph attention network
GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors
Overlapping group screening for detection of gene-environment interactions with application to TCGA high-dimensional survival genomic data
EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
Reconstructing cancer karyotypes from short read data: the half empty and half full glass
A stochastic differential equation model for transcriptional regulatory networks
iHAP - integrated haplotype analysis pipeline for characterizing the haplotype structure of genes
Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method
Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering
BIRCH: A user-oriented, locally-customizable, bioinformatics system
ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry
BARCRAWL and BARTAB : software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
Statistical and visual differentiation of subcellular imaging
Classification of microarray data using gene networks
Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat
Gene expression profile of peripheral blood mononuclear cells in response to HIV-VLPs stimulation
TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs
Structural similarity assessment for drug sensitivity prediction in cancer
PlantSimLab - a modeling and simulation web tool for plant biologists
Mutual information estimation reveals global associations between stimuli and biological processes
Software for rapid time dependent ChIP-sequencing analysis (TDCA)
Assessing constancy of substitution rates in viruses over evolutionary time
A hybrid metaheuristic-deep learning technique for the pan-classification of cancer based on DNA methylation
MoAGL-SA: a multi-omics adaptive integration method with graph learning and self attention for cancer subtype classification
Genomic prediction using subsampling
Benchmarking short sequence mapping tools
Heritable clustering and pathway discovery in breast cancer integrating epigenetic and phenotypic data
CUFID-query: accurate network querying through random walk based network flow estimation
Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics
Informative gene selection and the direct classification of tumors based on relative simplicity
Improving protein coreference resolution by simple semantic classification
SimplySmart_v1, a new tool for the analysis of DNA damage optimized in primary neuronal cultures
An innovative electronic health record system for rare and complex diseases
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification
Statistical evidence for the presence of trajectory in single-cell data
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees
On the robustness of generalization of drug-drug interaction models
Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study
Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape
Multiple-level biomedical event trigger recognition with transfer learning
A unifying model of genome evolution under parsimony
TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis
Probe set algorithms: is there a rational best bet?
Reconstruction of gene co-expression network from microarray data using local expression patterns
Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server
A greedy alignment-free distance estimator for phylogenetic inference
Minimus: a fast, lightweight genome assembler
Drug repurposing with network reinforcement
Dimension Reduction with Gene Expression Data Using Targeted Variable Importance Measurement
Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling
openBIS: a flexible framework for managing and analyzing complex data in biology research
A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data
BEXCIS: Bayesian methods for estimating the degree of the skewness of X chromosome inactivation
Amplitude spectrum distance: measuring the global shape divergence of protein fragments
Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
Mining phenotypes for gene function prediction
A topological data analysis based classification method for multiple measurements
DriverRWH: discovering cancer driver genes by random walk on a gene mutation hypergraph
RMaNI: Regulatory Module Network Inference framework
DNdisorder: predicting protein disorder using boosting and deep networks
Automated web-based typing of Clostridioides difficile ribotypes via MALDI-TOF MS
Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization
NEMPD: a network embedding-based method for predicting miRNA-disease associations by preserving behavior and attribute information
A novel approach for protein subcellular location prediction using amino acid exposure
STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow
A novel machine learning architecture to improve classification of intermediate cases in health: workflow and case study for public health
Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints
Semi-supervised protein subcellular localization
Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data
Island method for estimating the statistical significance of profile-profile alignment scores
GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures
Quality control of imbalanced mass spectra from isotopic labeling experiments
GoldPolish-target: targeted long-read genome assembly polishing
svm PRAT: SVM-based Protein Residue Annotation Toolkit
Recognition of interferon-inducible sites, promoters, and enhancers
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data
Comparison of data-merging methods with SVM attribute selection and classification in breast cancer gene expression
Reconstruction of phyletic trees by global alignment of multiple metabolic networks
Ryūtō: network-flow based transcriptome reconstruction
Automated modelling of signal transduction networks
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted with domain 4 of pneumolysin against Streptococcus pneumoniae strains
Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers
Bioinformatic analysis of gene regulation in the metal-reducing bacterial family Geobacteraceae
SC3s: efficient scaling of single cell consensus clustering to millions of cells
ElasticBLAST: accelerating sequence search via cloud computing
Hierarchical decomposition of dynamically evolving regulatory networks
Amino acid classification based spectrum kernel fusion for protein subnuclear localization
GATSol, an enhanced predictor of protein solubility through the synergy of 3D structure graph and large language modeling
The COG database: an updated version includes eukaryotes
Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective
CancerNet: a unified deep learning network for pan-cancer diagnostics
PSSM-Sumo: deep learning based intelligent model for prediction of sumoylation sites using discriminative features
A web-based protein interaction network visualizer
Assessing the druggability of protein-protein interactions by a supervised machine-learning method
PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data
cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
Detecting contaminated birthdates using generalized additive models
CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
BLISS: biding site level identification of shared signal-modules in DNA regulatory sequences
SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics
Dependence of paracentric inversion rate on tract length
Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli
Using diffusion distances for flexible molecular shape comparison
Correction to: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2017: bioinformatics
CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays
Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections
BioSAVE: Display of scored annotation within a sequence context
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries
SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase
Prediction of potential drug targets based on simple sequence properties
Reconstructing the virulome of the human pathogen Streptococcus pyogenes using NMPDR subsystems-based annotation
Identification of reproducible gene expression signatures in lung adenocarcinoma
Correction: CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny
Prediction of microRNA-disease associations based on distance correlation set
LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models
Mixture density networks for the indirect estimation of reference intervals
BOND: Basic OligoNucleotide Design
The Empirical Codon Mutation Matrix as a Communication Channel
Development of an unbiased statistical method for the analysis of unigenic evolution
MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs
Addressing inaccuracies in BLOSUM computation improves homology search performance
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator
A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications
Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
TopoDoE: a design of experiment strategy for selection and refinement in ensembles of executable gene regulatory networks
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment
DDI-PULearn: a positive-unlabeled learning method for large-scale prediction of drug-drug interactions
i-SEGOPubmed: a web interface for semantic enabled browsing of PubMed using Gene Ontology
TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets
Automatic classification of protein structures relying on similarities between alignments
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs
Loqusdb: added value of an observations database of local genomic variation
Exploring matrix factorization techniques for significant genes identification of Alzheimer's disease microarray gene expression data
Subtype prediction in pediatric acute myeloid leukemia: classification using differential network rank conservation revisited
A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs
Bio: : Phylo - phyloinformatic analysis using Perl
Deafness gene screening based on a multilevel cascaded BPNN model
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins
Utilizing protein structure to identify non-random somatic mutations
GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants
NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model
ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements
A database for G proteins and their interaction with GPCRs
THINK Back: KNowledge-based Interpretation of High Throughput data
Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition
Prediction of compound-target interactions of natural products using large-scale drug and protein information
Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs
Algorithms designed for compressed-gene-data transformation among gene banks with different references
GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses
KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes
PhySIC_IST: cleaning source trees to infer more informative supertrees
inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis
Classifying chest CT images as COVID-19 positive/negative using a convolutional neural network ensemble model and uniform experimental design method
biomapp::chip: large-scale motif analysis
HIVGenoPipe: a nextflow pipeline for the detection of HIV-1 drug resistance using a real-time sample-specific reference sequence
Regional registration of whole slide image stacks containing major histological artifacts
Walk-weighted subsequence kernels for protein-protein interaction extraction
An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis
Consistency of biological networks inferred from microarray and sequencing data
In silico approach to designing rational metagenomic libraries for functional studies
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions
gcMECM: graph clustering of mutual exclusivity of cancer mutations
Primique: automatic design of specific PCR primers for each sequence in a family
Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling
Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery
A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein
Automating document classification for the Immune Epitope Database
GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database
Multi-view manifold regularized compact low-rank representation for cancer samples clustering on multi-omics data
Predicting probable Alzheimer's disease using linguistic deficits and biomarkers
U-Compare bio-event meta-service: compatible BioNLP event extraction services
Tilting the lasso by knowledge-based post-processing
LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length
YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data
Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics
QualComp: a new lossy compressor for quality scores based on rate distortion theory
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
Classification of protein sequences by means of irredundant patterns
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies
An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Multiomics data analyses to identify SLC25A17 as a novel biomarker to predict the prognosis and immune microenvironment in head and neck squamous cell carcinoma
Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm
Revisiting motif finding: do bi-objective metaheuristics surpass single-objective metaheuristics?
M-BISON: Microarray-based integration of data sources using networks
Spatiotemporal segmentation of contraction waves in the extra-embryonic membranes of the red flour beetle
ProbeMaker: an extensible framework for design of sets of oligonucleotide probes
Local functional descriptors for surface comparison based binding prediction
Defining functional distances over Gene Ontology
Introduction to semantic e-Science in biomedicine
libFLASM: a software library for fixed-length approximate string matching
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses
VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
Denoising large-scale biological data using network filters
Using dual-network-analyser for communities detecting in dual networks
Investigating reproducibility and tracking provenance - A genomic workflow case study
Comparative analysis of metagenomic classifiers for long-read sequencing datasets