yusuke1997/dblp-id-title huggingface dataset:
DeepPrognosis: Preoperative prediction of pancreatic cancer survival and surgical margin via comprehensive understanding of dynamic contrast-enhanced CT imaging and tumor-vascular contact parsing
The development and evaluation of a three-dimensional ultrasound-guided breast biopsy apparatus
Multi-atlas segmentation with augmented features for cardiac MR images
Dual domain distribution disruption with semantics preservation: Unsupervised domain adaptation for medical image segmentation
Recent advances and clinical applications of deep learning in medical image analysis
Anatomy-guided multimodal registration by learning segmentation without ground truth: Application to intraprocedural CBCT/MR liver segmentation and registration
Automated eloquent cortex localization in brain tumor patients using multi-task graph neural networks
Computational methods to reduce uncertainty in the estimation of cardiac conduction properties from electroanatomical recordings
UAE: Universal Anatomical Embedding on multi-modality medical images
Automated identification of pulmonary arteries and veins depicted in non-contrast chest CT scans
Coordinate-based neural representation enabling zero-shot learning for fast 3D multiparametric quantitative MRI
NAS-optimized topology-preserving transfer learning for differentiating cortical folding patterns
A novel Bayesian respiratory motion model to estimate and resolve uncertainty in image-guided cardiac interventions
Uncertainty-aware report generation for chest X-rays by variational topic inference
Exudate-based diabetic macular edema detection in fundus images using publicly available datasets
Re-localisation of a biopsy site in endoscopic images and characterisation of its uncertainty
Structural alphabets derived from attractors in conformational space
A pseudo-value regression approach for differential network analysis of co-expression data
RefSelect: a reference sequence selection algorithm for planted ( l , d ) motif search
Bias correction and Bayesian analysis of aggregate counts in SAGE libraries
Synonym set extraction from the biomedical literature by lexical pattern discovery
A statistical approach to finding overlooked genetic associations
RDMAS: a web server for RNA deleterious mutation analysis
SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data
The tree alignment problem
scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
A novel ensemble learning method for de novo computational identification of DNA binding sites
Comparing transformation methods for DNA microarray data
Revealing sequence variation patterns in rice with machine learning methods
SMoLR: visualization and analysis of single-molecule localization microscopy data in R
Comparative study of classification algorithms for immunosignaturing data
Image segmentation and separation of spectrally similar dyes in fluorescence microscopy by dynamic mode decomposition of photobleaching kinetics
Propagating semantic information in biochemical network models
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli
Prediction of a time-to-event trait using genome wide SNP data
Optimizing diabetes classification with a machine learning-based framework
A deep learning framework for identifying essential proteins based on multiple biological information
Machine learning-based predictions of dietary restriction associations across ageing-related genes
AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders
The effect of radiofrequency ablation on pain score and non-steroidal painkiller use in osteoid osteoma patients
GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
Fast and accurate methods for phylogenomic analyses
An N6-methyladenosine regulation- and mRNAsi-related prognostic index reveals the distinct immune microenvironment and immunotherapy responses in lower-grade glioma
On the weight of indels in genomic distances
Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data
Biological clocks in theory and experiments
Prior knowledge guided eQTL mapping for identifying candidate genes
GCNCPR-ACPs: a novel graph convolution network method for ACPs prediction
A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data
ComHub: Community predictions of hubs in gene regulatory networks
Large-scale combining signals from both biomedical literature and the FDA Adverse Event Reporting System (FAERS) to improve post-marketing drug safety signal detection
SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1
LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism
Automated identification of cell-type-specific genes in the mouse brain by image computing of expression patterns
Consistency, comprehensiveness, and compatibility of pathway databases
Phylogenomic inference of functional divergence
Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers
A machine learning approach on multiscale texture analysis for breast microcalcification diagnosis
Supporting the search for cross-context links by outlier detection methods
Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment
A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases
An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data
Flexible boosting of accelerated failure time models
New challenges for text mining: mapping between text and manually curated pathways
cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data
An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease
Computation of elementary modes: a unifying framework and the new binary approach
Deep ensemble approach for pathogen classification in large-scale images using patch-based training and hyper-parameter optimization
libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny
Interactive metagenomic visualization in a Web browser
WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets
A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models
A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits
Densest subgraph-based methods for protein-protein interaction hot spot prediction
Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics
dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation
Steady state analysis of Boolean molecular network models via model reduction and computational algebra
DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data
Neutral network sizes of biological RNA molecules can be computed and are not atypically small
DCGR: feature extractions from protein sequences based on CGR via remodeling multiple information
Stability SCAD: a powerful approach to detect interactions in large-scale genomic study
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
Algorithm for DNA sequence assembly by quantum annealing
Predicted mouse peroxisome-targeted proteins and their actual subcellular locations
Beyond the state of the art of reverse vaccinology: predicting vaccine efficacy with the universal immune system simulator for influenza
Time varying causal network reconstruction of a mouse cell cycle
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
The Lair: a resource for exploratory analysis of published RNA-Seq data
Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower
MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters
POInT browse : orthology prediction and synteny exploration for paleopolyploid genomes
TPMS: a set of utilities for querying collections of gene trees
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling
MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation
Identifying cell types from single-cell data based on similarities and dissimilarities between cells
Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray
PCM-SABRE: a platform for benchmarking and comparing outcome prediction methods in precision cancer medicine
Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data
Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data
CoaSim: A flexible environment for simulating genetic data under coalescent models
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set
Erratum to: MINE: Module Identification in Networks
SAMSA: a comprehensive metatranscriptome analysis pipeline
A statistical approach to quantification of genetically modified organisms (GMO) using frequency distributions
ARG-based genome-wide analysis of cacao cultivars
Evaluation of a gene information summarization system by users during the analysis process of microarray datasets
Subfamily logos: visualization of sequence deviations at alignment positions with high information content
Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses
scHiCSRS: a self-representation smoothing method with Gaussian mixture model for imputing single cell Hi-C data
REEF: searching REgionally Enriched Features in genomes
Highlights of the 1st IEEE Symposium on Biological Data Visualization
Alternate virtual populations elucidate the type I interferon signature predictive of the response to rituximab in rheumatoid arthritis
High throughput automatic muscle image segmentation using parallel framework
Mining clinical relationships from patient narratives
Using protein language models for protein interaction hot spot prediction with limited data
Flexible analysis of spatial transcriptomics data (FAST): a deconvolution approach
Phylogenetic search through partial tree mixing
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species
Comparison of smartphone-based retinal imaging systems for diabetic retinopathy detection using deep learning
BiGAN: LncRNA-disease association prediction based on bidirectional generative adversarial network
An unsupervised learning approach for tracking mice in an enclosed area
Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases
A Taxonomic Search Engine: Federating taxonomic databases using web services
Integrated functional visualization of eukaryotic genomes
Filter bank temporally local multivariate synchronization index for SSVEP-based BCI
Predicting lncRNA-disease associations using multiple metapaths in hierarchical graph attention networks
Influence of batch effect correction methods on drug induced differential gene expression profiles
GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization
The research on gene-disease association based on text-mining of PubMed
Hamiltonian Monte Carlo methods for efficient parameter estimation in steady state dynamical systems
Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data
Selecting a single model or combining multiple models for microarray-based classifier development? - A comparative analysis based on large and diverse datasets generated from the MAQC-II project
metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states
Iterative class discovery and feature selection using Minimal Spanning Trees
Combination of scoring schemes for protein docking
FitEllipsoid: a fast supervised ellipsoid segmentation plugin
ksRepo: a generalized platform for computational drug repositioning
Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06)
ILP-based maximum likelihood genome scaffolding
QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform
Denoising single-cell RNA-seq data with a deep learning-embedded statistical framework
kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
Quantitative characterization and analysis of the dynamic NF-kappaB response in microglia
Comprehensive comparison of graph based multiple protein sequence alignment strategies
Efficient randomization of biological networks while preserving functional characterization of individual nodes
A statistical approach for array CGH data analysis
Erratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm
Group-wise normalization in differential abundance analysis of microbiome samples
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators
PWN: enhanced random walk on a warped network for disease target prioritization
M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology
Web-TCGA: an online platform for integrated analysis of molecular cancer data sets
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays
CGINet: graph convolutional network-based model for identifying chemical-gene interaction in an integrated multi-relational graph
MoMI-G: modular multi-scale integrated genome graph browser
Local Renyi entropic profiles of DNA sequences
Precise protein quantification based on peptide quantification using iTRAQ TM
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
Computational methods for ubiquitination site prediction using physicochemical properties of protein sequences
Optimization based automated curation of metabolic reconstructions
Semi-automated screening of biomedical citations for systematic reviews
Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes
MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data
Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores
Selecting single cell clustering parameter values using subsampling-based robustness metrics
Graph ranking for exploratory gene data analysis
SED, a normalization free method for DNA microarray data analysis
Minimum uncertainty as Bayesian network model selection principle
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Prediction of conformational B-cell epitopes from 3D structures by random forest with a distance-based feature
QTLminer: identifying genes regulating quantitative traits
GraphKM: machine and deep learning for K M prediction of wildtype and mutant enzymes
A metric and its derived protein network for evaluation of ortholog database inconsistency
Identifying differentially methylated genes using mixed effect and generalized least square models
Refactoring and performance analysis of the main CNN architectures: using false negative rate minimization to solve the clinical images melanoma detection problem
AnovArray: a set of SAS macros for the analysis of variance of gene expression data
Benchmark for multi-cellular segmentation of bright field microscopy images
EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments
Identifying biomarkers for breast cancer by gene regulatory network rewiring
SCITUNA: single-cell data integration tool using network alignment
MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes
Web tools for large-scale 3D biological images and atlases
Unsupervised automated high throughput phenotyping of RNAi time-lapse movies
Extract interaction detection methods from the biological literature
Minimizing recombinations in consensus networks for phylogeographic studies
Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis
Network hub-node prioritization of gene regulation with intra-network association
Color call improvement in next generation sequencing using multi-class support vector machines
PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms
A hybrid computational strategy to address WGS variant analysis in >5000 samples
High-throughput PCR assay design for targeted resequencing using primerXL
Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments
Adjusting protein graphs based on graph entropy
Context dependent substitution biases vary within the human genome
A case study in pathway knowledgebase verification
A lightweight single-view contrastive learning hypergraph neural network for food-microbe-disease association prediction
The taxonomic name resolution service: an online tool for automated standardization of plant names
Sorting by reversals, block interchanges, tandem duplications, and deletions
An empirical analysis of training protocols for probabilistic gene finders
In silico microdissection of microarray data from heterogeneous cell populations
ProtRepeatsDB: a database of amino acid repeats in genomes
InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
Iterative refinement of structure-based sequence alignments by Seed Extension
Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression
Pytrf: a python package for finding tandem repeats from genomic sequences
Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation
Support Vector Machine Implementations for Classification & Clustering
PyMulSim: a method for computing node similarities between multilayer networks via graph isomorphism networks
Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis
Correction to: CompNet: a GUI based tool for comparison of multiple biological interaction networks
Statistical tests to compare motif count exceptionalities
Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks
Unboxing cluster heatmaps
Feature selection and prediction with a Markov blanket structure learning algorithm
Classification of Suncus murinus species complex (Soricidae: Crocidurinae) in Peninsular Malaysia using image analysis and machine learning approaches
In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells
Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization
Seq2Ref: a web server to facilitate functional interpretation
MiningABs: mining associated biomarkers across multi-connected gene expression datasets
Utilization of a natural language processing-based approach to determine the composition of artifact residues
CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events
T3DB: an integrated database for bacterial type III secretion system
Transcriptional regulation prediction of antiestrogen resistance in breast cancer based on RNA polymerase II binding data
Ultra-Structure database design methodology for managing systems biology data and analyses
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data
Classification and assessment tools for structural motif discovery algorithms
A visual analytics approach for understanding biclustering results from microarray data
Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information
Addressing the unmet need for visualizing conditional random fields in biological data
Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction
caOmicsV: an R package for visualizing multidimensional cancer genomic data
Clustering analysis of proteins from microbial genomes at multiple levels of resolution
Furby: fuzzy force-directed bicluster visualization
NoLogo: a new statistical model highlights the diversity and suggests new classes of Crm1-dependent nuclear export signals
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
Automated NMR relaxation dispersion data analysis using NESSY
Acceleration of sequence clustering using longest common subsequence filtering
Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison
Developing a powerful In Silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome
Clustering with position-specific constraints on variance: Applying redescending M-estimators to label-free LC-MS data analysis
PrognosiT: Pathway/gene set-based tumour volume prediction using multiple kernel learning
Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs
Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations
Pathway-based analysis using reduced gene subsets in genome-wide association studies
A fast indexing approach for protein structure comparison
Reply: Correspondence on NanoVar's performance outlined by Jiang T. et al. in 'Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation'
ESTclean: A Cleaning Tool for Next-Gen Transcriptome Shotgun Sequencing
Improved ChIP-chip analysis by a mixture model approach
Reconstruction of 3D genome architecture via a two-stage algorithm
Helium: visualization of large scale plant pedigrees