yusuke1997/dblp-id-title huggingface dataset:
OmicsARules: a R package for integration of multi-omics datasets via association rules mining
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes
cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets
ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search
Evaluating different methods of microarray data normalization
Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis
Evaluating methods for ranking differentially expressed genes applied to MicroArray Quality Control data
Correction to: Clustering analysis of tumor metabolic networks
Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists
DensityMap: a genome viewer for illustrating the densities of features
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data
TreeRipper web application: towards a fully automated optical tree recognition software
A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition
Mojo hand, a TALEN design tool for genome editing applications
scBubbletree: computational approach for visualization of single cell RNA-seq data
BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips
Spall: accurate and robust unveiling cellular landscapes from spatially resolved transcriptomics data using a decomposition network
Sources of variability and effect of experimental approach on expression profiling data interpretation
OnEX: Exploring changes in life science ontologies
Equivariant score-based generative diffusion framework for 3D molecules
PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data
Cells in Silico - introducing a high-performance framework for large-scale tissue modeling
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data
STON: exploring biological pathways using the SBGN standard and graph databases
Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers
Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness
Measuring similarities between transcription factor binding sites
Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences
A consensus multi-view multi-objective gene selection approach for improved sample classification
Establishing a prognostic model of chromatin modulators and identifying potential drug candidates in renal clear cell patients
Global parameter estimation methods for stochastic biochemical systems
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data
Genome Projector: zoomable genome map with multiple views
Predicting the effect of missense mutations on protein function: analysis with Bayesian networks
Thesaurus-based disambiguation of gene symbols
Biomedical word sense disambiguation with bidirectional long short-term memory and attention-based neural networks
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet
Texture based skin lesion abruptness quantification to detect malignancy
Detecting gene-gene interactions for complex quantitative traits using generalized fuzzy classification
Exploiting sequence labeling framework to extract document-level relations from biomedical texts
Gevab: a prototype genome variation analysis browsing server
A disease-related gene mining method based on weakly supervised learning model
CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions
Evaluation of gene-expression clustering via mutual information distance measure
TranSeqAnnotator: large-scale analysis of transcriptomic data
Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective
Fully moderated t-statistic in linear modeling of mixed effects for differential expression analysis
ElTetrado: a tool for identification and classification of tetrads and quadruplexes
Identification of missing variants by combining multiple analytic pipelines
ideal: an R/Bioconductor package for interactive differential expression analysis
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
Evolutionary conservation of DNA-contact residues in DNA-binding domains
Stepwise iterative maximum likelihood clustering approach
Automatising the analysis of stochastic biochemical time-series
Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling
TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base
RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures
Evaluation of microarray-based DNA methylation measurement using technical replicates: the Atherosclerosis Risk In Communities (ARIC) Study
Probabilistic modeling and machine learning in structural and systems biology
A hierarchical integration deep flexible neural forest framework for cancer subtype classification by integrating multi-omics data
CACSV: a computational web-sever that provides classification for cancer somatic genetic variants from different tissues
Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture
ARTDeco: automatic readthrough transcription detection
Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme
Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals
Automated assessment of biological database assertions using the scientific literature
XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences
Detecting internally symmetric protein structures
Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases
Strobe sequence design for haplotype assembly
SSS-test: a novel test for detecting positive selection on RNA secondary structure
Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis
Gsw-fi: a GLM model incorporating shrinkage and double-weighted strategies for identifying cancer driver genes with functional impact
Exact solving and sensitivity analysis of stochastic continuous time Boolean models
Finding sRNA generative locales from high-throughput sequencing data with NiBLS
Selection of organisms for the co-evolution-based study of protein interactions
Pathological rate matrices: from primates to pathogens
Tracembler - software for in-silico chromosome walking in unassembled genomes
nQuire: a statistical framework for ploidy estimation using next generation sequencing
Optimal Step Length EM Algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping
Correlation test to assess low-level processing of high-density oligonucleotide microarray data
p3d - Python module for structural bioinformatics
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Error statistics of hidden Markov model and hidden Boltzmann model results
Exact biclustering algorithm for the analysis of large gene expression data sets
Negative binomial mixed models for analyzing microbiome count data
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries
QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR
Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data
BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature
BM-BC: a Bayesian method of base calling for Solexa sequence data
BayesFlow: latent modeling of flow cytometry cell populations
Learning genetic epistasis using Bayesian network scoring criteria
LCSkPOA: enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended LCSk++
LASSIE: simulating large-scale models of biochemical systems on GPUs
Semantic role labeling for protein transport predicates
Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages
Automating deployment of several GBrowse instances
llperm: a permutation of regressor residuals test for microbiome data
Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi
Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands
iview: an interactive WebGL visualizer for protein-ligand complex
Reproducibility of mass spectrometry based metabolomics data
Discovering mutated driver genes through a robust and sparse co-regularized matrix factorization framework with prior information from mRNA expression patterns and interaction network
SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome
Conventionally used reference genes are not outstanding for normalization of gene expression in human cancer research
Protein Function Prediction using Text-based Features extracted from the Biomedical Literature: The CAFA Challenge
High-throughput binding affinity calculations at extreme scales
Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters
In silico single strand melting curve: a new approach to identify nucleic acid polymorphisms in Totiviridae
Gene Ontology term overlap as a measure of gene functional similarity
A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: Toward the strict alignment of valid fragments across electrophoretic patterns
HLA-Clus: HLA class I clustering based on 3D structure
Compareads: comparing huge metagenomic experiments
Dynamic incorporation of prior knowledge from multiple domains in biomarker discovery
CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies
Correlating protein function and stability through the analysis of single amino acid substitutions
Recognition of protein/gene names from text using an ensemble of classifiers
Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences
Sketching and sampling approaches for fast and accurate long read classification
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms
Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach
DiscMycoVir: a user-friendly platform for discovering mycoviruses in fungal transcriptomes
A corpus for plant-chemical relationships in the biomedical domain
RESCUE: imputing dropout events in single-cell RNA-sequencing data
DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts
NetMets: software for quantifying and visualizing errors in biological network segmentation
CBMOS: a GPU-enabled Python framework for the numerical study of center-based models
Inferring high-confidence human protein-protein interactions
Analysis of enhanced CT imaging signs and clinicopathological prognostic factors in hepatoid adenocarcinoma of stomach patients with radical surgery: a retrospective study
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number
prot4EST: Translating Expressed Sequence Tags from neglected genomes
hoDCA: higher order direct-coupling analysis
A new set-valued system identification approach to identifying rare genetic variants for ordered categorical phenotype
Resolving the structure of interactomes with hierarchical agglomerative clustering
FERN - a Java framework for stochastic simulation and evaluation of reaction networks
HMM Logos for visualization of protein families
HGDTI: predicting drug-target interaction by using information aggregation based on heterogeneous graph neural network
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology
Fast processing of microscopic images using object-based extended depth of field
Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data
Biologically constrained optimization based cell membrane segmentation in C. elegans embryos
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking
A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
Exploring spatial-frequency-sequential relationships for motor imagery classification with recurrent neural network
TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms
An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome
Model-based cell clustering and population tracking for time-series flow cytometry data
The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results
UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline
FOUNTAIN: A JAVA open-source package to assist large sequencing projects
TOBFAC: the database of tobacco transcription factors
MT-Toolbox: improved amplicon sequencing using molecule tags
A strategy for evaluating pathway analysis methods
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products
Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building
Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study
Fast batch searching for protein homology based on compression and clustering
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics
Structure-based Markov random field model for representing evolutionary constraints on functional sites
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data
A supervised protein complex prediction method with network representation learning and gene ontology knowledge
ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data
Evaluation of a decided sample size in machine learning applications
Differential analysis of biological networks
The admixture maximum likelihood test to test for association between rare variants and disease phenotypes
A comparison of Affymetrix gene expression arrays
UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing
Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53
BASE - 2nd generation software for microarray data management and analysis
Robust double machine learning model with application to omics data
Protopia: a protein-protein interaction tool
Transcription factor site dependencies in human, mouse and rat genomes
PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing
Developing measures for microbial genome assembly quality control
Light-weight reference-based compression of FASTQ data
Thermal face recognition under different conditions
Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis
In silico prediction of potential chemical reactions mediated by human enzymes
Proceedings of the Fourteenth Annual UT- KBRIN Bioinformatics Summit 2015
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
Identifying potential drugs that induce QT prolongation using electronic medical records
Arena3D: visualizing time-driven phenotypic differences in biological systems
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks
Label noise in subtype discrimination of class C G protein-coupled receptors: A systematic approach to the analysis of classification errors
Oral cancer prognosis based on clinicopathologic and genomic markers using a hybrid of feature selection and machine learning methods
MiBiOmics: an interactive web application for multi-omics data exploration and integration
Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?
HoxPred: automated classification of Hox proteins using combinations of generalised profiles
Integrating text mining into high-throughput assay analysis
GARS: Genetic Algorithm for the identification of a Robust Subset of features in high-dimensional datasets
Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search
Robust test method for time-course microarray experiments
PseudoGeneQuest - Service for identification of different pseudogene types in the human genome
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study
Isabl Platform, a digital biobank for processing multimodal patient data
Estimation of data-specific constitutive exons with RNA-Seq data
Predicting disease genes based on multi-head attention fusion
SparkBLAST: scalable BLAST processing using in-memory operations
Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task
cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes
Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis
MI-MAAP: marker informativeness for multi-ancestry admixed populations
Profiling alternatively spliced mRNA isoforms for prostate cancer classification
Erratum to: An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome
Prediction of MHC class I binding peptides, using SVMHC
MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications
FlexOracle: predicting flexible hinges by identification of stable domains
Roast: a tool for reference-free optimization of supertranscriptome assemblies
Inferring biological networks with output kernel trees
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning
Alignment and clustering of phylogenetic markers - implications for microbial diversity studies
DNACLUST: accurate and efficient clustering of phylogenetic marker genes
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature
Heterogeneous computing for epidemiological model fitting and simulation
PhyloScape: interactive and scalable visualization platform for phylogenetic trees
Vindel: a simple pipeline for checking indel redundancy
Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective
Near-membrane ensemble elongation in the proline-rich LRP6 intracellular domain may explain the mysterious initiation of the Wnt signaling pathway
Identification of miRNA biomarkers for breast cancer by combining ensemble regularized multinomial logistic regression and Cox regression
OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs
Improved variance estimation of classification performance via reduction of bias caused by small sample size
Integrating data and knowledge to identify functional modules of genes: a multilayer approach
A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems
Visualization methods for statistical analysis of microarray clusters
Statistical analysis of multiple significance test methods for differential proteomics
Unsupervised image segmentation for microarray spots with irregular contours and inner holes
A composite genome approach to identify phylogenetically informative data from next-generation sequencing
Detection of divergent genes in microbial aCGH experiments
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis
The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes
Exploration of m 6 A methylation regulators as epigenetic targets for immunotherapy in advanced sepsis
MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification
Abstraction-based segmental simulation of reaction networks using adaptive memoization
BreakNet: detecting deletions using long reads and a deep learning approach
Computational evaluation of TIS annotation for prokaryotic genomes
Selecting control genes for RT-QPCR using public microarray data
CollaboNet: collaboration of deep neural networks for biomedical named entity recognition
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
Estimation of tumor heterogeneity using CGH array data
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations
DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection
Reconstructing the modular recombination history of Staphylococcus aureus phages
Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins
Algorithm of OMA for large-scale orthology inference
Probabilistic retrieval and visualization of biologically relevant microarray experiments
SDAR: a practical tool for graphical analysis of two-dimensional data
DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data
Predicting rifampicin resistance mutations in bacterial RNA polymerase subunit beta based on majority consensus
Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources
Better quality score compression through sequence-based quality smoothing
Construction of dynamic probabilistic protein interaction networks for protein complex identification
Freeprotmap: waiting-free prediction method for protein distance map
ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples
Survey statistics of automated segmentations applied to optical imaging of mammalian cells
Towards an automatic classification of protein structural domains based on structural similarity
Protein complex detection in PPI networks based on data integration and supervised learning method
Sequence-based prediction of protein protein interaction using a deep-learning algorithm