yusuke1997/dblp-id-title huggingface dataset:
A statistical approach to identify, monitor, and manage incomplete curated data sets
Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons
GIW and InCoB are advancing bioinformatics in the Asia-Pacific
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
Mining differential top-k co-expression patterns from time course comparative gene expression datasets
A novel R-package graphic user interface for the analysis of metabonomic profiles
Validation and functional annotation of expression-based clusters based on gene ontology
Harshlight: a "corrective make-up" program for microarray chips
Natural computation meta-heuristics for the in silico optimization of microbial strains
Differential analysis of combinatorial protein complexes with CompleXChange
Simulating the decentralized processes of the human immune system in a virtual anatomy model
GASP: Gapped Ancestral Sequence Prediction for proteins
Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome
A sensitive short read homology search tool for paired-end read sequencing data
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment
CoCoNUT: an efficient system for the comparison and analysis of genomes
Cancer module genes ranking using kernelized score functions
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information
A highly efficient multi-core algorithm for clustering extremely large datasets
Seqcrawler: biological data indexing and browsing platform
Latent network-based representations for large-scale gene expression data analysis
Frnakenstein: multiple target inverse RNA folding
An analysis of allele sharing in a region of linkage with bipolar affective disorder
SyntTax: a web server linking synteny to prokaryotic taxonomy
pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods
Zipper plot: visualizing transcriptional activity of genomic regions
General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms
In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus
A flexible ancestral genome reconstruction method based on gapped adjacencies
ARPIR: automatic RNA-Seq pipelines with interactive report
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes
NIFTI: An evolutionary approach for finding number of clusters in microarray data
EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection
Correction: Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data
Correction: On triangle inequalities of correlation-based distances for gene expression profiles
Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms
MDAT- Aligning multiple domain arrangements
GeneViTo: Visualizing gene-product functional and structural features in genomic datasets
EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation
ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense
CRA toolbox: software package for conditional robustness analysis of cancer systems biology models in MATLAB
Estimating heterogeneous treatment effect by balancing heterogeneity and fitness
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest
Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering
Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data
Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements
Fast NJ-like algorithms to deal with incomplete distance matrices
Efficiently Gap-Filling Reaction Networks
SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data
CirGO: an alternative circular way of visualising gene ontology terms
Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design
Protein structure search and local structure characterization
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets
Proposal of supervised data analysis strategy of plasma miRNAs from hybridisation array data with an application to assess hemolysis-related deregulation
PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords
Hybrid approaches for the detection of networks of critical residues involved in functional motions in protein families
Centroid based clustering of high throughput sequencing reads based on n-mer counts
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
A comprehensive comparison of comparative RNA structure prediction approaches
RCPred: RNA complex prediction as a constrained maximum weight clique problem
Integrative investigation of metabolic and transcriptomic data
ncDLRES: a novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet
Consensus clustering applied to multi-omics disease subtyping
Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel
Gene expression prediction using low-rank matrix completion
A domain-based approach to predict protein-protein interactions
A robustness metric for biological data clustering algorithms
Leveraging graph topology and semantic context for pharmacovigilance through twitter-streams
Computed tomography angiography-based analysis of high-risk intracerebral haemorrhage patients by employing a mathematical model
Solving the molecular distance geometry problem with inaccurate distance data
Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction
Modelling the correlation between the activities of adjacent genes in drosophila
scDIOR: single cell RNA-seq data IO software
N-terminal sequence-based prediction of subcellular location
ProGenExpress: Visualization of quantitative data on prokaryotic genomes
2dSpAn-Auto: an automated tool for analysis of two-dimensional dendritic spine images
Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists
Virtual reality assisted microscopy data visualization and colocalization analysis
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data
Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential
Applications of machine learning for simulations of red blood cells in microfluidic devices
NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data
GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data
Comparative evaluation of gene-set analysis methods
Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments
Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression
Event extraction on PubMed scale
Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data
The road not taken: retreat and diverge in local search for simplified protein structure prediction
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph
Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts
Computing paths and cycles in biological interaction graphs
Stepwise kinetic equilibrium models of quantitative polymerase chain reaction
Fast and robust multiple sequence alignment with phylogeny-aware gap placement
A novel phenotype imputation method with copula model
iGPSe: A visual analytic system for integrative genomic based cancer patient stratification
High dimensional model representation of log-likelihood ratio: binary classification with expression data
Exploring the membrane potential of a simple dual membrane system by using a constant electric field
HDBStat!: A platform-independent software suite for statistical analysis of high dimensional biology data
Beyond rotamers: a generative, probabilistic model of side chains in proteins
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools
Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing
Selecting informative subsets of sparse supermatrices increases the chance to find correct trees
Evaluation and integration of existing methods for computational prediction of allergens
Erratum to: BayesFlow: latent modeling of flow cytometry cell populations
How to balance the bioinformatics data: pseudo-negative sampling
SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images
ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes
Logical modelling and analysis of the budding yeast cell cycle
Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer
Fast computation of distance estimators
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila
A stochastic context free grammar based framework for analysis of protein sequences
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome
Integration of multi-omics data for prediction of phenotypic traits using random forest
iSeqQC: a tool for expression-based quality control in RNA sequencing
A CoD-based stationary control policy for intervening in large gene regulatory networks
Regression based predictor for p53 transactivation
A methodology for detecting the orthology signal in a PPI network at a functional complex level
Evaluation of normalization methods for microarray data
RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
Cluster correlation based method for lncRNA-disease association prediction
SingleScan: a comprehensive resource for single-cell sequencing data processing and mining
Breast cancer prediction with transcriptome profiling using feature selection and machine learning methods
OMetaNet: an efficient hybrid deep learning model based on multimodal data fusion and contrastive learning for predicting 2'-O-methylation sites in human RNA
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences
Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis
Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction
CastNet: a systems-level sequence evolution simulator
Grouping of genomic markers in populations with family structure
Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature
H3AGWAS: a portable workflow for genome wide association studies
A New Method for Modeling Coalescent Processes with Recombination
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins
Noise-injected neural networks show promise for use on small-sample expression data
Inferring homologous protein-protein interactions through pair position specific scoring matrix
Building gene expression profile classifiers with a simple and efficient rejection option in R
CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes
CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis
The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases
Enriching for Correct Prediction of Biological Processes Using a Combination of Diverse Classifiers
SFESA: a web server for pairwise alignment refinement by secondary structure shifts
Databases of homologous gene families for comparative genomics
Reconstructing phylogeny from metabolic substrate-product relationships
HiCdat: a fast and easy-to-use Hi-C data analysis tool
A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior
Risk prediction for dermatomyositis-associated hepatocellular carcinoma
ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval
A statistical approach to selecting and confirming validation targets in -omics experiments
Merged consensus clustering to assess and improve class discovery with microarray data
Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants
Locational distribution of gene functional classes in Arabidopsis thaliana
Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking
NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis
HIV drug resistance prediction with weighted categorical kernel functions
gcaPDA: a haplotype-resolved diploid assembler
Evaluation of BioCreAtIvE assessment of task 2
A novel evolutionary model for constructing gene coexpression networks with comprehensive features
Automatic detection of anchor points for multiple sequence alignment
Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project
Publisher Correction to: Three-dimensional tumor growth in time-varying chemical fields: a modeling framework and theoretical study
OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data
Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes
Reviewer acknowledgement 2013
Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia
Data handling strategies for high throughput pyrosequencers
Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data
SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'
Prediction of neddylation sites from protein sequences and sequence-derived properties
Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature
HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics
Graphical models for inferring single molecule dynamics
Structural features based genome-wide characterization and prediction of nucleosome organization
Gel2DE - A software tool for correlation analysis of 2D gel electrophoresis data
A novel multiple kernel fuzzy topic modeling technique for biomedical data
Model-based clustering with certainty estimation: implication for clade assignment of influenza viruses
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Automated generation of heuristics for biological sequence comparison
Colocalization by cross-correlation, a new method of colocalization suited for super-resolution microscopy
Critical assessment of on-premise approaches to scalable genome analysis
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data
Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties
Achieving large and distant ancestral genome inference by using an improved discrete quantum-behaved particle swarm optimization algorithm
Experimenting with database segmentation size vs time performance for mpiBLAST on an IBM HS21 blade cluster
Normalized N50 assembly metric using gap-restricted co-linear chaining
Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells
Reconstructing a SuperGeneTree minimizing reconciliation
DconnLoop: a deep learning model for predicting chromatin loops based on multi-source data integration
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases
Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach
AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
Toward a standard formal semantic representation of the model card report
Detecting PCOS susceptibility loci from genome-wide association studies via iterative trend correlation based feature screening
Discriminative topological features reveal biological network mechanisms
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases
Accelerating the annotation of sparse named entities by dynamic sentence selection
Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila
SVM clustering
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
Predicting DNA binding protein-drug interactions based on network similarity
XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data
Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies
Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms
Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress
Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods
QuickPed: an online tool for drawing pedigrees and analysing relatedness
A unified framework for estimating parameters of kinetic biological models
BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics
Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks
An Integrative Approach to Ortholog Prediction for Disease-Focused and Other Functional Studies
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
Automated FingerPrint Background removal: FPB
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences
Detailed protein sequence alignment based on Spectral Similarity Score (SSS)
Protein complexes detection based on node local properties and gene expression in PPI weighted networks
Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology
Shared data science infrastructure for genomics data
KF-NIPT: K-mer and fetal fraction-based estimation of chromosomal anomaly from NIPT data
Outer membrane proteins can be simply identified using secondary structure element alignment
PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli
In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance
Annotation and query of tissue microarray data using the NCI Thesaurus
BioInfer: a corpus for information extraction in the biomedical domain
The functional importance of disease-associated mutation
Probabilistic quotient's work and pharmacokinetics' contribution: countering size effect in metabolic time series measurements
BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features
Network inference with ensembles of bi-clustering trees
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb
An efficient algorithm to perform multiple testing in epistasis screening
Large-scale multiple testing in genome-wide association studies via region-specific hidden Markov models
Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations
ClineHelpR: an R package for genomic cline outlier detection and visualization
VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals
SPECTRA: a tool for enhanced brain wave signal recognition
microTaboo: a general and practical solution to the k-disjoint problem
A permutation-based multiple testing method for time-course microarray experiments
Minimalist ensemble algorithms for genome-wide protein localization prediction
VADR: validation and annotation of virus sequence submissions to GenBank
Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses
Arabidopsis gene co-expression network and its functional modules
A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs
Gene regulatory network modeling via global optimization of high-order dynamic Bayesian network
Identifying host-specific amino acid signatures for influenza A viruses using an adjusted entropy measure
SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes
GenAp: a distributed SQL interface for genomic data
A (fire)cloud-based DNA methylation data preprocessing and quality control platform
circGPA: circRNA functional annotation based on probability-generating functions