yusuke1997/dblp-id-title huggingface dataset:
Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets
Visualization methods for differential expression analysis
Two new ArrayTrack libraries for personalized biomedical research
Measuring similarity between gene interaction profiles
Local protein structure prediction using discriminative models
Establishment and validation of a predictive model of preeclampsia based on transcriptional signatures of 43 genes in decidua basalis and peripheral blood
Novel computational analysis of protein binding microarray data identifies direct targets of Nkx2.2 in the pancreas
VIRI: a visualization tool for tree reconciliations
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages
A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph
expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer
Identifying hypothetical genetic influences on complex disease phenotypes
Statistical methods for quantitative mass spectrometry proteomic experiments with labeling
Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis
Single sample pathway analysis in metabolomics: performance evaluation and application
Drug activity prediction using multiple-instance learning via joint instance and feature selection
Identification and correction of systematic error in high-throughput sequence data
The Drosophila Gene Expression Tool (DGET) for expression analyses
Normalization of oligonucleotide arrays based on the least-variant set of genes
A systematic comparison of the MetaCyc and KEGG pathway databases
Application of Petri net based analysis techniques to signal transduction pathways
phyloMDA: an R package for phylogeny-aware microbiome data analysis
BASE: a web service for providing compound-protein binding affinity prediction datasets with reduced similarity bias
Validating module network learning algorithms using simulated data
Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction
A systematic evaluation of nucleotide properties for CRISPR sgRNA design
Fine-tuning anti-tumor immunotherapies via stochastic simulations
Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction
A scalable, knowledge-based analysis framework for genetic association studies
A general modular framework for gene set enrichment analysis
A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns
Optimizing spatio-temporal correlation structures for modeling food security in Africa: a simulation-based investigation
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management
Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function
A-MADMAN: Annotation-based microarray data meta-analysis tool
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23
Coverage statistics for sequence census methods
Multiplatform biomarker identification using a data-driven approach enables single-sample classification
A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network
Highlights from the 5th Symposium on Biological Data Visualization: Part 1
A comprehensive assessment of N-terminal signal peptides prediction methods
A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data
LncRNA HOTAIR-mediated Wnt/β-catenin network modeling to predict and validate therapeutic targets for cartilage damage
Expression profiling of human renal carcinomas with functional taxonomic analysis
Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life
A Computational model for compressed sensing RNAi cellular screening
Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer
Methodology for biomarker discovery with reproducibility in microbiome data using machine learning
XHM: A system for detection of potential cross hybridizations in DNA microarrays
A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants
Analysis of the role of retrotransposition in gene evolution in vertebrates
Systematic assignment of thermodynamic constraints in metabolic network models
Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences
Full cyclic coordinate descent: solving the protein loop closure problem in C alpha space
Efficient digest of high-throughput sequencing data in a reproducible report
cgMSI: pathogen detection within species from nanopore metagenomic sequencing data
Accurate genome relative abundance estimation for closely related species in a metagenomic sample
WEBnm@: a web application for normal mode analyses of proteins
BirdsEyeView (BEV): graphical overviews of experimental data
PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly
PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability
Identification of gene expression patterns using planned linear contrasts
MAVEN: Motion Analysis and Visualization of Elastic Networks and Structural Ensembles
Ensemble classifier based on context specific miRNA regulation modules: a new method for cancer outcome prediction
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
QTREDS: a Ruby on Rails-based platform for omics laboratories
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data
Robust subspace structure discovery for cell type identification in scRNA-seq data
Functional and genetic analysis of the colon cancer network
PseUI: Pseudouridine sites identification based on RNA sequence information
GenomeViz: visualizing microbial genomes
Meta-analysis of breast cancer microarray studies in conjunction with conserved cis -elements suggest patterns for coordinate regulation
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia
Bioinformatics research at BGRS-2018
MPAgenomics: an R package for multi-patient analysis of genomic markers
PathwayBooster: a tool to support the curation of metabolic pathways
Fractal feature selection model for enhancing high-dimensional biological problems
Cancer immune control dynamics: a clinical data driven model of systemic immunity in patients with metastatic melanoma
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout
SurvivalGWAS_SV: software for the analysis of genome-wide association studies of imputed genotypes with "time-to-event" outcomes
The evolutionary origin of protein complexes
WinHAP2: an extremely fast haplotype phasing program for long genotype sequences
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach
Asc-Seurat: analytical single-cell Seurat-based web application
MACSIMS : multiple alignment of complete sequences information management system
Semantic integration to identify overlapping functional modules in protein interaction networks
Phage spanins: diversity, topological dynamics and gene convergence
CFMDS: CUDA-based fast multidimensional scaling for genome-scale data
Unintended consequences of existential quantifications in biomedical ontologies
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data
MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane
An integrative variant analysis suite for whole exome next-generation sequencing data
Grading amino acid properties increased accuracies of single point mutation on protein stability prediction
CytoConverter: a web-based tool to convert karyotypes to genomic coordinates
Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources
The BeeBiome data portal provides easy access to bee microbiome information
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest
MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues
Learning an enriched representation from unlabeled data for protein-protein interaction extraction
SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data
The Second International Symposium on Languages in Biology and Medicine (LBM) 2007
Identification of gene expression profiles associated with prognostic groups of patients with Merkel cell carcinoma
Family reunion via error correction: an efficient analysis of duplex sequencing data
A likelihood ratio test for changes in homeolog expression bias
On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation
Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling
A Fourier Transformation based Method to Mine Peptide Space for Antimicrobial Activity
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
Modeling the covariates effects on the hazard function by piecewise exponential artificial neural networks: an application to a controlled clinical trial on renal carcinoma
The maximum clique enumeration problem: algorithms, applications, and implementations
An unbiased kinship estimation method for genetic data analysis
Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts
Constraint Logic Programming approach to protein structure prediction
pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files
A multiobjective approach to the genetic code adaptability problem
An improved approach to infer protein-protein interaction based on a hierarchical vector space model
CLUSS: Clustering of protein sequences based on a new similarity measure
Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor
Prognostic risk assessment model and drug sensitivity analysis of colon adenocarcinoma (COAD) based on immune-related lncRNA pairs
RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics
MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI
"GenotypeColour TM " : colour visualisation of SNPs and CNVs
Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression
Network analysis of human protein location
Evaluation of two-step iterative resampling procedure for internal validation of genome-wide association studies
Efficient design of meganucleases using a machine learning approach
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases
Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation
DM-MOGA: a multi-objective optimization genetic algorithm for identifying disease modules of non-small cell lung cancer
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes
p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data
Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
FANTOM: Functional and taxonomic analysis of metagenomes
Measure transcript integrity using RNA-seq data
A statistical method to identify recombination in bacterial genomes based on SNP incompatibility
Boolean factor graph model for biological systems: the yeast cell-cycle network
Polygenic risk prediction based on singular value decomposition with applications to alcohol use disorder
QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure
Boosting the discriminatory power of sparse survival models via optimization of the concordance index and stability selection
pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties
MSpectraAI: a powerful platform for deciphering proteome profiling of multi-tumor mass spectrometry data by using deep neural networks
Genome comparison using Gene Ontology (GO) with statistical testing
h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
Erratum to: 'NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology'
YSMR: a video tracking and analysis program for bacterial motility
SEGT-GO: a graph transformer method based on PPI serialization and explanatory artificial intelligence for protein function prediction
Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes
Comparative analysis of similarity measurements in miRNAs with applications to miRNA-disease association predictions
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case
Bayesian Semiparametric Regression Models to Characterize Molecular Evolution
Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data
Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO
ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures
A novel meta-analysis based on data augmentation and elastic data shared lasso regularization for gene expression
Multi-task genomic prediction using gated residual variable selection neural networks
Testing gene set enrichment for subset of genes: Sub-GSE
Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization
Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking
Large-scale localization of touching somas from 3D images using density-peak clustering
Structuring an event ontology for disease outbreak detection
Context-dependent transcriptional regulations between signal transduction pathways
Ideal adaptive control in biological systems: an analysis of $\mathbb {P}$-invariance and dynamical compensation properties
Bioclipse: an open source workbench for chemo- and bioinformatics
PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets
Population substructure in Cache County, Utah: the Cache County study
Can large language models understand molecules?
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data
State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?
SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis
Twadn: an efficient alignment algorithm based on time warping for pairwise dynamic networks
svist4get: a simple visualization tool for genomic tracks from sequencing experiments
PTIGS-IdIt, a system for species identification by DNA sequences of the psbA-trnH intergenic spacer region
GWAMA: software for genome-wide association meta-analysis
QPath: a method for querying pathways in a protein-protein interaction network
Predicting conserved protein motifs with Sub-HMMs
Ultra-fast sequence clustering from similarity networks with SiLiX
Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span
Exploiting expression patterns across multiple tissues to map expression quantitative trait loci
Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies
Deblender: a semi-/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data
Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population
Domain-based small molecule binding site annotation
A novel approach to detect hot-spots in large-scale multivariate data
Spotting effect in microarray experiments
Sealer: a scalable gap-closing application for finishing draft genomes
Metadata mapping and reuse in caBIG TM
A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
Exploiting large-scale drug-protein interaction information for computational drug repurposing
Genome rearrangements with duplications
Prediction of scaffold proteins based on protein interaction and domain architectures
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features
Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information
Selection of entropy-measure parameters for knowledge discovery in heart rate variability data
Functionally informative tag SNP selection using a pareto-optimal approach: playing the game of life
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery
Handling missing rows in multi-omics data integration: multiple imputation in multiple factor analysis framework
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data
Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum
Markov chain Monte Carlo for active module identification problem
'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences
SPINGO: a rapid species-classifier for microbial amplicon sequences
GraphFind: enhancing graph searching by low support data mining techniques
TRAMbio: a flexible python package for graph rigidity analysis of macromolecules
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
Discriminative structural approaches for enzyme active-site prediction
CLoDSA: a tool for augmentation in classification, localization, detection, semantic segmentation and instance segmentation tasks
Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data
Topological structure analysis of chromatin interaction networks
Evaluation of potential role of vitamin C in differential skeletal development between female and male mice using a mouse model
Bivariate segmentation of SNP-array data for allele-specific copy number analysis in tumour samples
A new protein linear motif benchmark for multiple sequence alignment software
TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
A principal components method constrained by elementary flux modes: analysis of flux data sets
Dual-channel heterogeneous feature fusion neural network for the prediction of post-transcriptional gene expression in Escherichia coli
Investigation of CRS-associated cytokines in CAR-T therapy with meta-GNN and pathway crosstalk
Evolving stochastic context-free grammars for RNA secondary structure prediction
A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism
Phamerator: a bioinformatic tool for comparative bacteriophage genomics
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens
Function approximation approach to the inference of reduced NGnet models of genetic networks
Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data
Extraction of semantic biomedical relations from text using conditional random fields
Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses
Identifying representative drug resistant mutants of HIV
GOParGenPy: a high throughput method to generate Gene Ontology data matrices
Computational approaches to protein inference in shotgun proteomics
Finding local communities in protein networks
PFASUM: a substitution matrix from Pfam structural alignments
The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
Concentration optimization of combinatorial drugs using Markov chain-based models
Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control
A Bayesian network approach to feature selection in mass spectrometry data
Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA
PaperBot: open-source web-based search and metadata organization of scientific literature
Efficient algorithms for reconstructing gene content by co-evolution
A novel approach for biomarker selection and theintegration of repeated measures experiments from two assays
PIVOT: platform for interactive analysis and visualization of transcriptomics data
FIND: A new software tool and development platform for enhanced multicolor flow analysis
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification
Examination of hydrogen cross-feeders using a colonic microbiota model
Analysis on multi-domain cooperation for predicting protein-protein interactions
An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads
Using quality scores and longer reads improves accuracy of Solexa read mapping
ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces
A big data approach to metagenomics for all-food-sequencing
Identifying stress responsive genes using overlapping communities in co-expression networks