yusuke1997/dblp-id-title huggingface dataset:
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
MSDmotif: exploring protein sites and motifs
Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment
Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference
TGF-beta signaling proteins and the Protein Ontology
Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis
Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform
mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences
Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling
Structural characterization of genomes by large scale sequence-structure threading
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction
An integrated approach to the prediction of domain-domain interactions
Correcting nucleotide-specific biases in high-throughput sequencing data
Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment
DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning
Using large-scale perturbations in gene network reconstruction
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases
A classification model for distinguishing copy number variants from cancer-related alterations
Which methods to choose to correct cell types in genome-scale blood-derived DNA methylation data?
Provenance in bioinformatics workflows
Haplo2Ped: a tool using haplotypes as markers for linkage analysis
Correlating gene and protein expression data using Correlated Factor Analysis
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators
Integrative approaches to the prediction of protein functions based on the feature selection
MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling
Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line
An analytic and systematic framework for estimating metabolic flux ratios from 13 C tracer experiments
Asterics: a simple tool for the ExploRation and Integration of omiCS data
Benchmarking the PEPOP methods for mimicking discontinuous epitopes
Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age
Correction: Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network
An experimental study of the intrinsic stability of random forest variable importance measures
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes
CellProfiler 4: improvements in speed, utility and usability
FastProNGS: fast preprocessing of next-generation sequencing reads
Deploying mutation impact text-mining software with the SADI Semantic Web Services framework
Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering
BioPP: a tool for web-publication of biological networks
Linear combination test for gene set analysis of a continuous phenotype
Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches
An assessment on epitope prediction methods for protozoa genomes
SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
TaxMan: a taxonomic database manager
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery
Unsupervised assessment of microarray data quality using a Gaussian mixture model
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
Statistical modelling of CG interdistance across multiple organisms
Protein-protein docking using region-based 3D Zernike descriptors
Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure
Application of amino acid occurrence for discriminating different folding types of globular proteins
SurvivalGWAS_Power: a user friendly tool for power calculations in pharmacogenetic studies with "time to event" outcomes
Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa
Machine learning with naturally labeled data for identifying abbreviation definitions
Piecewise multivariate modelling of sequential metabolic profiling data
A phylogenetic approach for weighting genetic sequences
DeepMF: deciphering the latent patterns in omics profiles with a deep learning method
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
TargetSpy: a supervised machine learning approach for microRNA target prediction
Dynamic simulation of regulatory networks using SQUAD
SNPs3D: Candidate gene and SNP selection for association studies
Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration
Screening drug target combinations in disease-related molecular networks
A graph-based approach for the visualisation and analysis of bacterial pangenomes
Refining intra-protein contact prediction by graph analysis
SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models
Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm
False positive reduction in protein-protein interaction predictions using gene ontology annotations
A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
Automated Terminological and Structural Analysis of Human-Mouse Anatomical Ontology Mappings
Development of large-scale metabolite identification methods for metabolomics
GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms
Assessing statistical significance in causal graphs
Rare variant phasing using paired tumor: normal sequence data
A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction
CNVizard - a lightweight streamlit application for an interactive analysis of copy number variants
Prediction of virus-host protein-protein interactions mediated by short linear motifs
MultiModalGraphics: an R package for graphical integration of multi-omics datasets
Dose-response prediction for in-vitro drug combination datasets: a probabilistic approach
Metabolic pathways variability and sequence/networks comparisons
The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes
Levenshtein error-correcting barcodes for multiplexed DNA sequencing
REW-ISA: unveiling local functional blocks in epi-transcriptome profiling data via an RNA expression-weighted iterative signature algorithm
Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
Predicting substrates of the human breast cancer resistance protein using a support vector machine method
Image-level and group-level models for Drosophila gene expression pattern annotation
RNA motif search with data-driven element ordering
SAPFIR: A webserver for the identification of alternative protein features
Natural Language Processing in aid of FlyBase curators
An effective heuristic for developing hybrid feature selection in high dimensional and low sample size datasets
Shortest triplet clustering: reconstructing large phylogenies using representative sets
A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration
A method for automatically extracting infectious disease-related primers and probes from the literature
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format
MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries
Block network mapping approach to quantitative trait locus analysis
Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity
BioCarian: search engine for exploratory searches in heterogeneous biological databases
A graph-theoretic approach for inparalog detection
Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy
Extension of the Bayesian Alphabet for Genomic Selection
Bacterial network for precise plant stress detection and enhanced crop resilience
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets
The study of muscle remodeling in Drosophila metamorphosis using in vivo microscopy and bioimage informatics
The MULTICOM toolbox for protein structure prediction
Transcriptional programs: Modelling higher order structure in transcriptional control
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments
Online tool for the discrimination of equi-distributions
Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa
Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration
M-pick, a Modularity-based Method for OTU Picking of 16S rRNA Sequences
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
Detection of viral sequence fragments of HIV-1 subfamilies yet unknown
LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model
Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances
Prediction of antibody-antigen interaction based on backbone aware with invariant point attention
Genome-wide DNA polymorphism analyses using VariScan
IRESpy: an XGBoost model for prediction of internal ribosome entry sites
Phylogenetic analysis of Harmonin homology domains
Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes
Computational discovery of direct associations between GO terms and protein domains
Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Temporal dynamics of protein complexes in PPI Networks: a case study using yeast cell cycle dynamics
Genome aliquoting with double cut and join
Detecting gene-gene interactions from GWAS using diffusion kernel principal components
Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers
Tetranucleotide usage in mycobacteriophage genomes: alignment-free methods to cluster phage and infer evolutionary relationships
Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression
GENPPI: standalone software for creating protein interaction networks from genomes
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010
Microarray-based gene set analysis: a comparison of current methods
Correction to: HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment
Wildfire: distributed, Grid-enabled workflow construction and execution
Trimming of sequence reads alters RNA-Seq gene expression estimates
Scoring docking conformations using predicted protein interfaces
CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints
Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles
Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach
Proteome scanning to predict PDZ domain interactions using support vector machines
FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking
Combining heterogeneous data sources for accurate functional annotation of proteins
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization
Integrating neighbor clustering, coexpression clustering and subsystems analysis to define dynamic changes in regulatory networks associated with group A streptococcal sociomicrobiology and niche adaptation
Formatt: Correcting Protein Multiple Structural Alignments by Incorporating Sequence Alignment
Identification of functionally related genes using data mining and data integration: a breast cancer case study
Target-small decoy search strategy for false discovery rate estimation
Ontology based molecular signatures for immune cell types via gene expression analysis
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models
MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data
Statistical power of phylo-HMM for evolutionarily conserved element detection
Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
The rainfall plot: its motivation, characteristics and pitfalls
Simple regression models as a threshold for selecting AFLP loci with reduced error rates
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models
HLAscan: genotyping of the HLA region using next-generation sequencing data
Classifying early and late mild cognitive impairment stages of Alzheimer's disease by fusing default mode networks extracted with multiple seeds
BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics
Skittle: A 2-Dimensional Genome Visualization Tool
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model
Advances and challenges in Bioinformatics and Biomedical Engineering: IWBBIO 2020
EnzML: multi-label prediction of enzyme classes using InterPro signatures
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
Subgroup and outlier detection analysis
Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect
SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures
Ambivalent covariance models
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation
scSemiAAE: a semi-supervised clustering model for single-cell RNA-seq data
A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data
GeneTools - application for functional annotation and statistical hypothesis testing
Joint analysis of scATAC-seq datasets using epiConv
PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity
BHCox: Bayesian heredity-constrained Cox proportional hazards models for detecting gene-environment interactions
m6A-TCPred: a web server to predict tissue-conserved human m 6 A sites using machine learning approach
PuTmiR: A database for extracting neighboring transcription factors of human microRNAs
NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm
Tractable RNA-ligand interaction kinetics
Learning to rank-based gene summary extraction
Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors
Predicting protein-protein interactions via multivariate mutual information of protein sequences
Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs
RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory
GCAC: galaxy workflow system for predictive model building for virtual screening
Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry
Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding
Cancer bioinformatics: A new approach to systems clinical medicine
Clustering of protein domains for functional and evolutionary studies
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors
EasyKASP: a simple and fast tool for KASP primer design
BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems
GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA
Deep learning models for bacteria taxonomic classification of metagenomic data
System level visualization of eQTLs and pQTLs
OVAS: an open-source variant analysis suite with inheritance modelling
Dual graph convolutional neural network for predicting chemical networks
Integration of open source software tools for the in silico design of metabolic pathways using flux balance analysis - an application to the production of recombinant human proteins
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
A mixture of feature experts approach for protein-protein interaction prediction
TopHat-Recondition: a post-processor for TopHat unmapped reads
Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data
Clustering evolving proteins into homologous families
IRProfiler - a software toolbox for high throughput immune receptor profiling
VariVis: a visualisation toolkit for variation databases
Ranked retrieval of segmented nuclei for objective assessment of cancer gene repositioning
Accelerated probabilistic inference of RNA structure evolution
Towards accurate modeling of noncovalent interactions for protein rigidity analysis
Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm
KnotAli: informed energy minimization through the use of evolutionary information
Predicting MiRNA-disease associations by multiple meta-paths fusion graph embedding model
The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data
Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification
Bayesian clustering and feature selection for cancer tissue samples
On the dynamical aspects of local translation at the activated synapse
Multilocus association mapping using generalized ridge logistic regression
Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
Structure-Revealing Data Fusion
LeARN: a platform for detecting, clustering and annotating non-coding RNAs
repo: an R package for data-centered management of bioinformatic pipelines
Internet-based profiler system as integrative framework to support translational research
Research on drug-drug interaction prediction using capsule neural network based on self-attention mechanism
Novel knowledge-based mean force potential at the profile level
Genome wide identification of regulatory motifs in Bacillus subtilis
Discovery of error-tolerant biclusters from noisy gene expression data
Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads
Hybrid MM/SVM structural sensors for stochastic sequential data
GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization
SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem
Moment based gene set tests
Fast and accurate microRNA search using CNN
A distance based multisample test for high-dimensional compositional data with applications to the human microbiome
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining
Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
Brick plots: an intuitive platform for visualizing multiparametric immunophenotyped cell clusters
GeVaDSs - decision support system for novel Genetic Vaccine development process
Canary: an atomic pipeline for clinical amplicon assays
Attention mechanism enhanced LSTM with residual architecture and its application for protein-protein interaction residue pairs prediction
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145
Next generation models for storage and representation of microbial biological annotation
BicPAMS: software for biological data analysis with pattern-based biclustering
PCirc: random forest-based plant circRNA identification software
Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
WISH-R- a fast and efficient tool for construction of epistatic networks for complex traits and diseases
Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data
HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research
Peptide binding predictions for HLA DR, DP and DQ molecules
A core-attachment based method to detect protein complexes in PPI networks
Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool
Gamevar.f90: a software package for calculating individual gametic diversity
Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks