yusuke1997/dblp-id-title huggingface dataset:
A methodology for the analysis of differential coexpression across the human lifespan
Quantitative prediction model for affinity of drug-target interactions based on molecular vibrations and overall system of ligand-receptor
Long short-term memory RNN for biomedical named entity recognition
Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm
PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space
Gene finding in metatranscriptomic sequences
Multilayer network alignment based on topological assessment via embeddings
uap: reproducible and robust HTS data analysis
Assigning credit where it is due: an information content score to capture the clinical value of multiplexed assays of variant effect
Improved precision and accuracy for microarrays using updated probe set definitions
Genome-wide detection of short tandem repeat expansions by long-read sequencing
DrImpute: imputing dropout events in single cell RNA sequencing data
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure
Difficulty in inferring microbial community structure based on co-occurrence network approaches
Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction
ProToDeviseR: an automated protein topology scheme generator
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
Analysis of effect of congenic mice on the gene expression under genomic background of BALB/c mice
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions
A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient
AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites
Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification
An automated homology-based approach for identifying transposable elements
A stable gene selection in microarray data analysis
Benchmark study of feature selection strategies for multi-omics data
A hybrid method for the exact planted (l, d) motif finding problem and its parallelization
The evolutionary rate of antibacterial drug targets
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data
OpenMS - An open-source software framework for mass spectrometry
Alignment-free genomic sequence comparison using FCGR and signal processing
DWNN-RLS: regularized least squares method for predicting circRNA-disease associations
Censcyt: censored covariates in differential abundance analysis in cytometry
Stochastic simulations of minimal cells: the Ribocell model
MAESTRO - multi agent stability prediction upon point mutations
Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference
Facilitating functional annotation of chicken microarray data
Chaos game representation for comparison of whole genomes
Multi-TGDR, a multi-class regularization method, identifies the metabolic profiles of hepatocellular carcinoma and cirrhosis infected with hepatitis B or hepatitis C virus
Modeling of cell signaling pathways in macrophages by semantic networks
Multiobjective triclustering of time-series transcriptome data reveals key genes of biological processes
Sample entropy analysis of cervical neoplasia gene-expression signatures
HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data
Do little interactions get lost in dark random forests?
Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data
Annotation depth confounds direct comparison of gene expression across species
Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening
Adaptive gradient scaling: integrating Adam and landscape modification for protein structure prediction
Cascaded classifiers for confidence-based chemical named entity recognition
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach
Dna-storalator: a computational simulator for DNA data storage
Hit integration for identifying optimal spaced seeds
Comparison of sequencing data processing pipelines and application to underrepresented African human populations
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation
m6Acorr: an online tool for the correction and comparison of m 6 A methylation profiles
Reconstructing cancer genomes from paired-end sequencing data
An inferential framework for biological network hypothesis tests
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization
Genome-wide identification and expression analysis of Raffinose synthetase family in cotton
Biomedical semantic text summarizer
Generation of Gene Ontology benchmark datasets with various types of positive signal
Cell4D: a general purpose spatial stochastic simulator for cellular pathways
Paired-end read length lower bounds for genome re-sequencing
CompNet: a GUI based tool for comparison of multiple biological interaction networks
Accurate and highly interpretable prediction of gene expression from histone modifications
ALE: automated label extraction from GEO metadata
TAMEE: data management and analysis for tissue microarrays
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
The effect of rare variants on inflation of the test statistics in case-control analyses
FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families
RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump
Nonlinear preprocessing method for detecting peaks from gas chromatograms
Visual4DTracker: a tool to interact with 3D + t image stacks
BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways
tcR: an R package for T cell receptor repertoire advanced data analysis
Multi-dimensional data integration algorithm based on random walk with restart
The characteristic direction: a geometrical approach to identify differentially expressed genes
Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method
Transformer-based tool recommendation system in Galaxy
An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators
3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data
Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15
On the selection of appropriate distances for gene expression data clustering
Novel deep learning-based solution for identification of prognostic subgroups in liver cancer (Hepatocellular carcinoma)
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Assembling contigs in draft genomes using reversals and block-interchanges
Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison
Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning
LOSTdb: a manually curated multi-omics database for lung cancer research
Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme
PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients
Efficient protein alignment algorithm for protein search
TCC: an R package for comparing tag count data with robust normalization strategies
A parameter-adaptive dynamic programming approach for inferring cophylogenies
Cluster analysis for DNA methylation profiles having a detection threshold
Computational models with thermodynamic and composition features improve siRNA design
DWARF - a data warehouse system for analyzing protein families
A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression
GraphCrunch: A tool for large network analyses
miRAS: a data processing system for miRNA expression profiling study
Combined embedding model for MiRNA-disease association prediction
HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding
WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit
Tandem machine learning for the identification of genes regulated by transcription factors
Predicting MoRFs in protein sequences using HMM profiles
PTMViz: a tool for analyzing and visualizing histone post translational modification data
Transcriptome dynamics-based operon prediction in prokaryotes
MANET: tracing evolution of protein architecture in metabolic networks
Variable selection from a feature representing protein sequences: a case of classification on bacterial type IV secreted effectors
Performance of Web tools for predicting changes in protein stability caused by mutations
IPCO: Inference of Pathways from Co-variance analysis
Prediction of sgRNA on-target activity in bacteria by deep learning
DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma
Accelerating genomic workflows using NVIDIA Parabricks
GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach
An efficient gene selection method for microarray data based on LASSO and BPSO
Physicochemical property space distribution among human metabolites, drugs and toxins
Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions
Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking
GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets
A dynamic Bayesian network approach to protein secondary structure prediction
Validation of a yellow fever vaccine model using data from primary vaccination in children and adults, re-vaccination and dose-response in adults and studies with immunocompromised individuals
Automated methods of predicting the function of biological sequences using GO and BLAST
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides
compomics-utilities: an open-source Java library for computational proteomics
Profiled support vector machines for antisense oligonucleotide efficacy prediction
Analysis of optimal alignments unfolds aligners' bias in existing variant profiles
Phenotyping date palm varieties via leaflet cross-sectional imaging and artificial neural network application
Iterative pruning PCA improves resolution of highly structured populations
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis
Multiscale modeling of mucosal immune responses
SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model
MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model
PESM: predicting the essentiality of miRNAs based on gradient boosting machines and sequences
Steiner tree methods for optimal sub-network identification: an empirical study
IDEA: Interactive Display for Evolutionary Analyses
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces
Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution
ZF-Human Disease Database: A Database for Zebrafish Models of Human Genetic Diseases
PREMIM and EMIM: tools for estimation of maternal, imprinting and interaction effects using multinomial modelling
Screening genome-wide DNA methylation CpG sites via training and testing data utilizing surrogate variables
metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models
Incorporating rich background knowledge for gene named entity classification and recognition
Evaluation of high-throughput functional categorization of human disease genes
Design of a flexible component gathering algorithm for converting cell-based models to graph representations for use in evolutionary search
Frequency distribution of TATA Box and extension sequences on human promoters
Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data
Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts
A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
Multistability in the epithelial-mesenchymal transition network
GTZ: a fast compression and cloud transmission tool optimized for FASTQ files
Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160)
CAREx: context-aware read extension of paired-end sequencing data
DeepASDPred: a CNN-LSTM-based deep learning method for Autism spectrum disorders risk RNA identification
2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments
Improved model quality assessment using ProQ2
Correction to: Multi-template matching: a versatile tool for object-localization in microscopy images
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
How to find simple and accurate rules for viral protease cleavage specificities
A short note on dynamic programming in a band
DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features
Detection of Fused Genes in Eukaryotic Genomes using Gene deFuser: Analysis of the Tetrahymena thermophila genome
Sequence-based information-theoretic features for gene essentiality prediction
HolomiRA: a reproducible pipeline for miRNA binding site prediction in microbial genomes
Automatic generation of gene finders for eukaryotic species
Seahawk: moving beyond HTML in Web-based bioinformatics analysis
BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons
QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Optimized LOWESS normalization parameter selection for DNA microarray data
CellProfiler Analyst: data exploration and analysis software for complex image-based screens
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures
SAGE: String-overlap Assembly of GEnomes
Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis
An analysis of the Sargasso Sea resource and the consequences for database composition
FragViz: visualization of fragmented networks
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life
The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data
The BLUES database: A health disparities registry for pregnant mothers
MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study
External features enriched model for biomedical question answering
GRank: a middleware search engine for ranking genes by relevance to given genes
Predicting protein linkages in bacteria: Which method is best depends on task
cuticleDB: a relational database of Arthropod cuticular proteins
msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation
GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data
A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations
A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions
The Medicago truncatula gene expression atlas web server
Accelerating a cross-correlation score function to search modifications using a single GPU
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
Decoding HMMs using the k best paths: algorithms and applications
An improved procedure for gene selection from microarray experiments using false discovery rate criterion
omicplotR: visualizing omic datasets as compositions
A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model
ArrayQuest: a web resource for the analysis of DNA microarray data
CRF-based models of protein surfaces improve protein-protein interaction site predictions
Generating rate equations for complex enzyme systems by a computer-assisted systematic method
FMLRC: Hybrid long read error correction using an FM-index
ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles
Evaluation of gene expression data generated from expired Affymetrix GeneChip ® microarrays using MAQC reference RNA samples
Circadian signatures in rat liver: from gene expression to pathways
stochprofML: stochastic profiling using maximum likelihood estimation in R
Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers
Predicting transcription factor binding sites using local over-representation and comparative genomics
Ori-Finder: A web-based system for finding oriC s in unannotated bacterial genomes
Boolean implication analysis of single-cell data predicts retinal cell type markers
More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs
HELLO: improved neural network architectures and methodologies for small variant calling
doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows
A modified Stokes-Einstein equation for Aβ aggregation
Explorative search of distributed bio-data to answer complex biomedical questions
Improving Probe Set Selection for Microbial Community Analysis by Leveraging Taxonomic Information of Training Sequences
A comparative review of estimates of the proportion unchanged genes and the false discovery rate
A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles
Comparative evaluation of full-length isoform quantification from RNA-Seq
Effective filtering strategies to improve data quality from population-based whole exome sequencing studies
Emulating complex simulations by machine learning methods
3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions
bioNerDS: exploring bioinformatics' database and software use through literature mining
An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories
Elviz - exploration of metagenome assemblies with an interactive visualization tool
The Korean Bird Information System (KBIS) through open and public participation
Detecting virus-specific effects on post-infection temporal gene expression
Protein remote homology detection based on bidirectional long short-term memory
Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
The Musite open-source framework for phosphorylation-site prediction
Organizing the bacterial annotation space with amino acid sequence embeddings
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches
Global screening of potential Candida albicans biofilm-related transcription factors via network comparison
New time-scale criteria for model simplification of bio-reaction systems
MannDB - A microbial database of automated protein sequence analyses and evidence integration for protein characterization
Adaptable probabilistic mapping of short reads using position specific scoring matrices
Optimizing agent-based transmission models for infectious diseases
A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data
An information-theoretic approach to single cell sequencing analysis
Subcellular location prediction of apoptosis proteins using two novel feature extraction methods based on evolutionary information and LDA
Screening prognostic markers for hepatocellular carcinoma based on pyroptosis-related lncRNA pairs
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
Drug-target interaction prediction based on spatial consistency constraint and graph convolutional autoencoder
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
Comparison of genotype clustering tools with rare variants
JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases
Threshold selection in gene co-expression networks using spectral graph theory techniques
GenESysV: a fast, intuitive and scalable genome exploration open source tool for variants generated from high-throughput sequencing projects
Gene signature-based mapping of immunological systems and diseases
Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture model and statistical model selection
Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites
A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology
Multiconstrained gene clustering based on generalized projections
Species-specific protein sequence and fold optimizations
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
Analysis of sleep traits in knockout mice from the large-scale KOMP2 population using a non-invasive, high-throughput piezoelectric system
Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs
Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies
Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes
CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies
Origins and characterization of variants shared between databases of somatic and germline human mutations
A simple and robust method for connecting small-molecule drugs using gene-expression signatures