yusuke1997/dblp-id-title huggingface dataset:
Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy
UrQt: an efficient software for the Unsupervised Quality trimming of NGS data
METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
Improving pan-genome annotation using whole genome multiple alignment
Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy
sciReptor: analysis of single-cell level immunoglobulin repertoires
Comparing sequences without using alignments: application to HIV/SIV subtyping
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks
-In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1
Computational modeling of phagocyte transmigration for foreign body responses to subcutaneous biomaterial implants in mice
ANAT 2.0: reconstructing functional protein subnetworks
Are scale-free networks robust to measurement errors?
Integrative relational Machine-Learning Approach for Understanding Drug Side-Effect Profiles
Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms
Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure
Generalized box-plot for root growth ensembles
Similarities and differences between variants called with human reference genome HG19 or HG38
Scientific workflow optimization for improved peptide and protein identification
ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies
Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes
Exact score distribution computation for ontological similarity searches
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning
Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens
MTar: a computational microRNA target prediction architecture for human transcriptome
Optimized ancestral state reconstruction using Sankoff parsimony
Visual cavity analysis in molecular simulations
Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study
Identification of long non-coding transcripts with feature selection: a comparative study
A voting-based machine learning approach for classifying biological and clinical datasets
Systematic analysis identifies XRCC4 as a potential immunological and prognostic biomarker associated with pan-cancer
A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution
CPMI: comprehensive neighborhood-based perturbed mutual information for identifying critical states of complex biological processes
SAveRUNNER: an R-based tool for drug repurposing
LSI based framework to predict gene regulatory information
deltaXpress (ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data
Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB)
An equivalence approach to the integrative analysis of feature lists
SeqHound: biological sequence and structure database as a platform for bioinformatics research
Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry
Identifying network biomarkers of cancer by sample-specific differential network
Performance of a genetic algorithm for mass spectrometry proteomics
Efficient and low-complexity variable-to-variable length coding for DNA storage
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks
CLAG: an unsupervised non hierarchical clustering algorithm handling biological data
Gram-positive and gram-negative subcellular localization using rotation forest and physicochemical-based features
Meta-analysis of gene expression changes in response to radiation exposure
Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information
Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
IMOS: improved Meta-aligner and Minimap2 On Spark
The BioAssay network and its implications to future therapeutic discovery
Computational method using heterogeneous graph convolutional network model combined with reinforcement layer for MiRNA-disease association prediction
PRCFX-DT: a new graph-based approach for feature selection and classification of genomic sequences
Extensive parent-of-origin genetic effects on fetal growth
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data
Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations
Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics
Estimating statistical significance of local protein profile-profile alignments
DNA-based watermarks using the DNA-Crypt algorithm
xCAPT5: protein-protein interaction prediction using deep and wide multi-kernel pooling convolutional neural networks with protein language model
ccImpute: an accurate and scalable consensus clustering based algorithm to impute dropout events in the single-cell RNA-seq data
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
A classification model for lncRNA and mRNA based on k-mers and a convolutional neural network
Discovery of moiety preference by Shapley value in protein kinase family using random forest models
CLOVE: classification of genomic fusions into structural variation events
GRLGRN: graph representation-based learning to infer gene regulatory networks from single-cell RNA-seq data
Overview of BioCreAtIvE: critical assessment of information extraction for biology
Use of normalization methods for analysis of microarrays containing a high degree of gene effects
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments
Protein annotation as term categorization in the gene ontology using word proximity networks
DAE-CFR: detecting microRNA-disease associations using deep autoencoder and combined feature representation
AtlasGrabber: a software facilitating the high throughput analysis of the human protein atlas online database
Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map
A novel Mixture Model Method for identification of differentially expressed genes from DNA microarray data
Growing functional modules from a seed protein via integration of protein interaction and gene expression data
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it
On the PATHGROUPS approach to rapid small phylogeny
Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology
Real-time audio and visual display of the Coronavirus genome
Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types
Accuracy of structure-based sequence alignment of automatic methods
A cis-regulatory logic simulator
cosinoRmixedeffects: an R package for mixed-effects cosinor models
MetaBar - a tool for consistent contextual data acquisition and standards compliant submission
Isoform specific gene expression analysis of KRAS in the prognosis of lung adenocarcinoma patients
RDb2C2: an improved method to identify the residue-residue pairing in β strands
AGeNNT: annotation of enzyme families by means of refined neighborhood networks
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients
MiRNATIP: a SOM-based miRNA-target interactions predictor
Network-based analysis of transcriptional profiles from chemical perturbations experiments
Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations
Haplotype-based quantitative trait mapping using a clustering algorithm
Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data
Processing methods for differential analysis of LC/MS profile data
Is automatic detection of hidden knowledge an anomaly?
Correction to: An introduction to new robust linear and monotonic correlation coefficients
Correction to: NoRCE: non‑coding RNA sets cis enrichment tool
ADAGE signature analysis: differential expression analysis with data-defined gene sets
Data mining tools for Salmonella characterization: application to gel-based fingerprinting analysis
Unexpected variations in translation initiation machinery
PTPD: predicting therapeutic peptides by deep learning and word2vec
Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci
The NTD Nanoscope: potential applications and implementations
Effects of error-correction of heterozygous next-generation sequencing data
Learning biophysically-motivated parameters for alpha helix prediction
An application of kernel methods to variety identification based on SSR markers genetic fingerprinting
Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants
Neuron anatomy structure reconstruction based on a sliding filter
SBMLmod: a Python-based web application and web service for efficient data integration and model simulation
Improved residue contact prediction using support vector machines and a large feature set
Incorporating Ab Initio energy into threading approaches for protein structure prediction
GTB - an online genome tolerance browser
Frequent occurrence of recognition Site-like sequences in the restriction endonucleases
Sarcopenia negatively affects hip structure analysis variables in a group of Lebanese postmenopausal women
Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment
SPIDR: small-molecule peptide-influenced drug repurposing
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
On reliable discovery of molecular signatures
htSNPer1.0: software for haplotype block partition and htSNPs selection
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database
Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions
Closha: bioinformatics workflow system for the analysis of massive sequencing data
Sifter-T: A scalable framework for phylogenomic probabilistic protein domain functional annotation
Determination of strongly overlapping signaling activity from microarray data
ERD: a fast and reliable tool for RNA design including constraints
ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data
Prediction of protein-protein interaction types using association rule based classification
Multiple phenotype association tests based on sliced inverse regression
Dynamical modeling of uncertain interaction-based genomic networks
CellTrackVis: interactive browser-based visualization for analyzing cell trajectories and lineages
ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble
Equivalent input produces different output in the UniFrac significance test
PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks
Widespread evidence of viral miRNAs targeting host pathways
Accounting for uncertainty when assessing association between copy number and disease: a latent class model
Multi-scale Gaussian representation and outline-learning based cell image segmentation
Automated cell segmentation in FIJI® using the DRAQ5 nuclear dye
Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm
A unified computational model for revealing and predicting subtle subtypes of cancers
ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis
Multi-dimensional discovery of biomarker and phenotype complexes
Dissecting complex transcriptional responses using pathway-level scores based on prior information
CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data
Development of an automatic Classification Scheme for Disease-related Enzyme Information
Classification epitopes in groups based on their protein family
RF_Purify: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression
Gene function classification using Bayesian models with hierarchy-based priors
Using neural networks to support high-quality evidence mapping
Optimal experiment selection for parameter estimation in biological differential equation models
Variation in structural location and amino acid conservation of functional sites in protein domain families
A fast parallel algorithm for finding the longest common sequence of multiple biosequences
Iterative rank-order normalization of gene expression microarray data
More powerful significant testing for time course gene expression data using functional principal component analysis approaches
Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes
Detecting sequence dependent transcriptional pauses from RNA and protein number time series
uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts
Parallel multi-swarm cooperative particle swarm optimization for protein-ligand docking and virtual screening
MATLIGN: a motif clustering, comparison and matching tool
Extension of the COG and arCOG databases by amino acid and nucleotide sequences
Short paired-end reads trump long single-end reads for expression analysis
A new algorithm to train hidden Markov models for biological sequences with partial labels
Analysis of superfamily specific profile-profile recognition accuracy
Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis
Inference of regulatory networks with a convergence improved MCMC sampler
D-Light on promoters: A client-server system for the analysis and visualization of cis-regulatory elements
Accelerated maximum likelihood parameter estimation for stochastic biochemical systems
Variation of geometrical and physicochemical properties in protein binding pockets and their ligands
Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data
Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype
Dynamic variable selection in SNP genotype autocalling from APEX microarray data
VKCDB: Voltage-gated potassium channel database
An optimized algorithm for detecting and annotating regional differential methylation
GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees
Prediction of microbial phenotypes based on comparative genomics
Exploring the transcription factor activity in high-throughput gene expression data using RLQ analysis
Bioinformatics research in the Asia Pacific: a 2007 update
Learning a confidence score and the latent space of a new supervised autoencoder for diagnosis and prognosis in clinical metabolomic studies
In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines: evidence of a possible putative protective effect
Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments
Sorting out inherent features of head-to-head gene pairs by evolutionary conservation
MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
Classifying breast cancer subtypes on multi-omics data via sparse canonical correlation analysis and deep learning
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor
Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning
Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders
COMBImage: a modular parallel processing framework for pairwise drug combination analysis that quantifies temporal changes in label-free video microscopy movies
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning
Towards precise classification of cancers based on robust gene functional expression profiles
Ranking near-native candidate protein structures via random forest classification
DTI-MHAPR: optimized drug-target interaction prediction via PCA-enhanced features and heterogeneous graph attention networks
Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines
Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research
Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection
Quantitative sequence-function relationships in proteins based on gene ontology
Correction to: binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions
BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing
Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing
Time-series alignment by non-negative multiple generalized canonical correlation analysis
Using expression arrays for copy number detection: an example from E. coli
In silico vaccine design and epitope mapping of New Delhi metallo-beta-lactamase (NDM): an immunoinformatics approach
A comparative study of topology-based pathway enrichment analysis methods
PB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site
Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells
Tigmint: correcting assembly errors using linked reads from large molecules
Analysis of multiple phenotypes in genome-wide genetic mapping studies
EnsInfer: a simple ensemble approach to network inference outperforms any single method
PyBDA: a command line tool for automated analysis of big biological data sets
Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)
Set-theory based benchmarking of three different variant callers for targeted sequencing
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature
A deep learning approach to bilingual lexicon induction in the biomedical domain
SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses
PADB : Published Association Database
Mining multi-item drug adverse effect associations in spontaneous reporting systems
OMeta: an ontology-based, data-driven metadata tracking system
Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization
Prediction of 8-state protein secondary structures by a novel deep learning architecture
CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments
Identifying set-wise differential co-expression in gene expression microarray data
solveME: fast and reliable solution of nonlinear ME models
Community-driven development for computational biology at Sprints, Hackathons and Codefests
Riboswitch Detection Using Profile Hidden Markov Models
Insights into mammalian transcription control by systematic analysis of ChIP sequencing data
GeneBins: a database for classifying gene expression data, with application to plant genome arrays
From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration
An application of machine learning with feature selection to improve diagnosis and classification of neurodegenerative disorders
Considerations in the identification of functional RNA structural elements in genomic alignments
Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences
Modelling cell type-specific lncRNA regulatory network in autism with Cycle
CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes
In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)
iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding
NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences
A methodology for global validation of microarray experiments
Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes
Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks
LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics
An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions
MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes
Web-Based Metabolic Network Visualization with a Zooming User Interface
Fractionation statistics
Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)
Resolving deconvolution ambiguity in gene alternative splicing
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
CP-CHARM: segmentation-free image classification made accessible
FASIMU: flexible software for flux-balance computation series in large metabolic networks
Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery
Identifying protein complexes directly from high-throughput TAP data with Markov random fields
Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization