yusuke1997/dblp-id-title huggingface dataset:
Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species
Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering
Scoring functions for transcription factor binding site prediction
svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification
Erratum to: Weakly supervised learning of biomedical information extraction from curated data
Comprehensive analyses of a CD8 + T cell infiltration related gene signature with regard to the prediction of prognosis and immunotherapy response in lung squamous cell carcinoma
DeepBP: Ensemble deep learning strategy for bioactive peptide prediction
Bias in random forest variable importance measures: Illustrations, sources and a solution
Non-specific filtering of beta-distributed data
FEGS: a novel feature extraction model for protein sequences and its applications
Inferring chromosome radial organization from Hi-C data
Prediction of nuclear proteins using SVM and HMM models
Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes
HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases
MBA: a literature mining system for extracting biomedical abbreviations
Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles
Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates
Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows
DeSP: a systematic DNA storage error simulation pipeline
Loop-mediated isothermal amplification assays for the detection of antimicrobial resistance elements in Vibrio cholera
graphite - a Bioconductor package to convert pathway topology to gene network
What can we learn from noncoding regions of similarity between genomes?
Correction: Bayesian kinetic modeling for tracer-based metabolomic data
Individualized co-expression-like index (iCKI) enables gene-gene interactions as individual biomarkers for complex disease
DPDDI: a deep predictor for drug-drug interactions
WACS: improving ChIP-seq peak calling by optimally weighting controls
Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes
Amazing symmetrical clustering in chloroplast genomes
Prediction of protein-protein interactions from amino acid sequences using a novel multi-scale continuous and discontinuous feature set
A method for increasing expressivity of Gene Ontology annotations using a compositional approach
HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods
Comut-viz: efficiently creating and browsing comutation plots online
Pattern recognition of topologically associating domains using deep learning
ECMIS: computational approach for the identification of hotspots at protein-protein interfaces
LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches
A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles
REDalign: accurate RNA structural alignment using residual encoder-decoder network
Forecasting the spread of COVID-19 using LSTM network
Shambhala: a platform-agnostic data harmonizer for gene expression data
Indirect association and ranking hypotheses for literature based discovery
An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees
DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing
Impact of RNA structure on the prediction of donor and acceptor splice sites
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
FIGG: Simulating populations of whole genome sequences for heterogeneous data analyses
The UofL Microarray Facility: merger and new location
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics
Exploring supervised and unsupervised methods to detect topics in biomedical text
Utilizing genomic signatures to gain insights into the dynamics of SARS-CoV-2 through Machine and Deep Learning techniques
Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses
GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network
Integrative analysis of gene expression and copy number alterations using canonical correlation analysis
Automated functional classification of experimental and predicted protein structures
ASAView : Database and tool for solvent accessibility representation in proteins
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis
NFPscanner: a webtool for knowledge-based deciphering of biomedical networks
LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting
Identification of gene pairs through penalized regression subject to constraints
Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles
A spatial simulation approach to account for protein structure when identifying non-random somatic mutations
MCCMF: collaborative matrix factorization based on matrix completion for predicting miRNA-disease associations
The distance-profile representation and its application to detection of distantly related protein families
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes
Pathway collages: personalized multi-pathway diagrams
Platform dependence of inference on gene-wise and gene-set involvement in human lung development
Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
Hidden Markov Model Variants and their Application
Cell type discovery and representation in the era of high-content single cell phenotyping
Non-negative matrix factorisation methods for the spectral decomposition of MRS data from human brain tumours
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
Visualization of three-way comparisons of omics data
Predicting effective drug combinations using gradient tree boosting based on features extracted from drug-protein heterogeneous network
Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools
Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics
Discovering collectively informative descriptors from high-throughput experiments
The impact of sample imbalance on identifying differentially expressed genes
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations
Spatio-structural granularity of biological material entities
Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations
Towards Semantic e-Science for Traditional Chinese Medicine
A novel two-way rebalancing strategy for identifying carbonylation sites
TIPred: a novel stacked ensemble approach for the accelerated discovery of tyrosinase inhibitory peptides
Linear MALDI-ToF simultaneous spectrum deconvolution and baseline removal
Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine antibiotic resistance genotypes
Stability and bifurcations in a discrete-time epidemic model with vaccination and vital dynamics
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees
In search of functional association from time-series microarray data based on the change trend and level of gene expression
DCD - a novel plant specific domain in proteins involved in development and programmed cell death
IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data
Sequence-only evolutionary and predicted structural features for the prediction of stability changes in protein mutants
An algebraic language for RNA pseudoknots comparison
On the consistency of orthology relationships
AMYPdb: A database dedicated to amyloid precursor proteins
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules
Optimized permutation testing for information theoretic measures of multi-gene interactions
Attention-based recurrent neural network for influenza epidemic prediction
Prediction and analysis of multiple protein lysine modified sites based on conditional wasserstein generative adversarial networks
MHCSeqNet: a deep neural network model for universal MHC binding prediction
Automated classification of protein subcellular localization in immunohistochemistry images to reveal biomarkers in colon cancer
SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform
GraphOmics: an interactive platform to explore and integrate multi-omics data
Predictive modeling of plant messenger RNA polyadenylation sites
An accurate and interpretable model for siRNA efficacy prediction
Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis
VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams
Gene set bagging for estimating the probability a statistically significant result will replicate
The role of structural parameters in DNA cyclization
UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes
Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA
Optimization algorithms for functional deimmunization of therapeutic proteins
Predicting functionally important SNP classes based on negative selection
A permutable MLP-like architecture for disease prediction from gut metagenomic data
BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes
Large-scale prediction of long disordered regions in proteins using random forests
FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis
A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues
Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures
Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants
Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice
A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes
Protein protein interactions, evolutionary rate, abundance and age
Deep-m5U: a deep learning-based approach for RNA 5-methyluridine modification prediction using optimized feature integration
RNA inverse folding using Monte Carlo tree search
A two-way interface between limited Systems Biology Markup Language and R
A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area
Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks
Reconstruction of ancestral gene orders using intermediate genomes
Automatic identifying and counting blood cells in smear images by using single shot detector and Taguchi method
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation
OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies
A gene based combination test using GWAS summary data
Practicality of identifying mitochondria variants from exome and RNAseq data
A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments
Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis
Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing
Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data
Selected abstracts of "Bioinformatics: from Algorithms to Applications 2020" conference
Missing value imputation in high-dimensional phenomic data: imputable or not, and how?
Semantic web data warehousing for caGrid
Mathematical model of the cell signaling pathway based on the extended Boolean network model with a stochastic process
circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs
nanite: using machine learning to assess the quality of atomic force microscopy-enabled nano-indentation data
A coherent graph-based semantic clustering and summarization approach for biomedical literature and a new summarization evaluation method
Variant detection and the Autism sequencing project
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery
A novel approach to the clustering of microarray data via nonparametric density estimation
Significance analysis of lexical bias in microarray data
NOBLE - Flexible concept recognition for large-scale biomedical natural language processing
Improving the sensitivity of sample clustering by leveraging gene co-expression networks in variable selection
SUPFAM: A database of sequence superfamilies of protein domains
Modeling relaxation experiments with a mechanistic model of gene expression
Multiple non-collinear TF-map alignments of promoter regions
Kerfdr: a semi-parametric kernel-based approach to local false discovery rate estimation
How accurate and statistically robust are catalytic site predictions based on closeness centrality?
ClearFinder: a Python GUI for annotating cells in cleared mouse brain
Emerging strengths in Asia Pacific bioinformatics
BatchPrimer3: A high throughput web application for PCR and sequencing primer design
Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)
Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data
Statistical tools for transgene copy number estimation based on real-time PCR
Motif-guided sparse decomposition of gene expression data for regulatory module identification
Computational identification of ubiquitylation sites from protein sequences
"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis
Detection of suspicious interactions of spiking covariates in methylation data
Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis
metacp: a versatile software package for combining dependent or independent p-values
Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality
MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks
Searching for 3D structural models from a library of biological shapes using a few 2D experimental images
A machine learning-based data mining in medical examination data: a biological features-based biological age prediction model
Real-time data analysis for medical diagnosis using FPGA-accelerated neural networks
The Gaggle: An open-source software system for integrating bioinformatics software and data sources
Bias in error estimation when using cross-validation for model selection
Approximation properties of haplotype tagging
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice
Shortest path counting in probabilistic biological networks
The Proteogenomic Mapping Tool
CoMI: consensus mutual information for tissue-specific gene signatures
Semantic annotation of biological concepts interplaying microbial cellular responses
The value of position-specific scoring matrices for assessment of protein allegenicity
New statistical methods for estimation of recombination fractions in F2 population
Protein complex prediction for large protein protein interaction networks with the Core&Peel method
Game of neutrophils: modeling the balance between apoptosis and necrosis
Natural language processing in text mining for structural modeling of protein complexes
Efficient prediction of human protein-protein interactions at a global scale
The application of compressed sensing on tumor mutation burden calculation from overlapped pooling sequencing data
Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process
An integrated analysis of molecular aberrations in NCI-60 cell lines
CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins
Analysis of breast cancer subtypes by AP-ISA biclustering
A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets
Pegasys: software for executing and integrating analyses of biological sequences
GAM-NGS: genomic assemblies merger for next generation sequencing
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies
Automated recognition and analysis of head thrashes behavior in C. elegans
Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster
TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Composition Profiler: a tool for discovery and visualization of amino acid composition differences
Investigation of dirigent like domains from bacterial genomes
A comparison on effects of normalisations in the detection of differentially expressed genes
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data
Protein domain organisation: adding order
A model of the circadian clock in the cyanobacterium Cyanothece sp. ATCC 51142
CAPL: an efficient association software package using family and case-control data and accounting for population stratification
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
SemaTyP: a knowledge graph based literature mining method for drug discovery
PROMPT: a protein mapping and comparison tool
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug-drug interactions
SFMetrics: an analysis tool for scanning force microscopy images of biomolecules
Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na + symporter family
Structure-sensitive transformer and multi-view graph contrastive learning enhanced prediction of drug-related microbes
Grouping miRNAs of similar functions via weighted information content of gene ontology
SCOWLP classification: Structural comparison and analysis of protein binding regions
Constructing a robust protein-protein interaction network by integrating multiple public databases
A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies
Reordering based integrative expression profiling for microarray classification
TopoICSim: a new semantic similarity measure based on gene ontology
A Java-based tool for the design of classification microarrays
The value of position-specific priors in motif discovery using MEME
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes
HDAPD: a web tool for searching the disease-associated protein structures
ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly
Detecting microsatellites within genomes: significant variation among algorithms
Ribosomal computing: implementation of the computational method
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology
Joint learning sample similarity and correlation representation for cancer survival prediction
Deep user identification model with multiple biometric data
Plaseval: a framework for comparing and evaluating plasmid detection tools
Improved multi-level protein¿protein interaction prediction with semantic-based regularization
Selecting effective siRNA sequences by using radial basis function network and decision tree learning
Fuzzy optimization for identifying antiviral targets for treating SARS-CoV-2 infection in the heart
PathEx: a novel multi factors based datasets selector web tool
Assembly complexity of prokaryotic genomes using short reads
Crystallizing short-read assemblies around seeds
Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays
Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments
An integrative method for scoring candidate genes from association studies: application to warfarin dosing
lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models
Biomedical question answering using semantic relations
TCR-L: an analysis tool for evaluating the association between the T-cell receptor repertoire and clinical phenotypes
Using multi-layer perceptron to identify origins of replication in eukaryotes via informative features
scSemiAE: a deep model with semi-supervised learning for single-cell transcriptomics
DTranNER: biomedical named entity recognition with deep learning-based label-label transition model
HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein
VarDetect: a nucleotide sequence variation exploratory tool
MCM-test: a fuzzy-set-theory-based approach to differential analysis of gene pathways
BioWarehouse: a bioinformatics database warehouse toolkit
Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis
GMASS: a novel measure for genome assembly structural similarity
Bioinformatic identification of novel putative photoreceptor specific cis -elements
Bioinformatics analysis of SARS coronavirus genome polymorphism
Laboratory information management software for engineered mini-protein therapeutic workflow
An integrated ChIP-seq analysis platform with customizable workflows
Metagenomic analysis through the extended Burrows-Wheeler transform
Protein language models can capture protein quaternary state
Marigold: a machine learning-based web app for zebrafish pose tracking
Functional discrimination of membrane proteins using machine learning techniques
Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society