yusuke1997/dblp-id-title huggingface dataset:
Instance-based error correction for short reads of disease-associated genes
Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device
PreDisorder: ab initio sequence-based prediction of protein disordered regions
ASH structure alignment package: Sensitivity and selectivity in domain classification
DeBasher: a flow-based programming bash extension for the implementation of complex and interactive workflows with stateful processes
Clustering the annotation space of proteins
DryMass: handling and analyzing quantitative phase microscopy images of spherical, cell-sized objects
The structural and content aspects of abstracts versus bodies of full text journal articles are different
Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures
An interaction-motif-based scoring function for protein-ligand docking
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs
Statistical representation models for mutation information within genomic data
SIGMA 2 : A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes
Correlation between structure and temperature in prokaryotic metabolic networks
Protein localization prediction using random walks on graphs
Developing the novel bioinformatics algorithms to systematically investigate the connections among survival time, key genes and proteins for Glioblastoma multiforme
LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference
Cauchy hyper-graph Laplacian nonnegative matrix factorization for single-cell RNA-sequencing data analysis
Integrating protein localization with automated signaling pathway reconstruction
Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes
Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum
Integrated multi-level quality control for proteomic profiling studies using mass spectrometry
linkedISA: semantic representation of ISA-Tab experimental metadata
Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses
Penalized partial least squares for pleiotropy
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts
Analysis of amplicon-based NGS data from neurological disease gene panels: a new method for allele drop-out management
A method for rapid similarity analysis of RNA secondary structures
BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi
Utilizing heart rate variability to predict ICU patient outcome in traumatic brain injury
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
Clover: a clustering-oriented de novo assembler for Illumina sequences
Merging microarray data from separate breast cancer studies provides a robust prognostic test
FDC-SP as a diagnostic and prognostic biomarker and modulates immune infiltrates in renal cell carcinoma
PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship
From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways
Exploring attractor bifurcations in Boolean networks
smsMap: mapping single molecule sequencing reads by locating the alignment starting positions
Hybrid clustering for microarray image analysis combining intensity and shape features
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence
Predicting the pathogenicity of bacterial genomes using widely spread protein families
Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species
Protein-DNA docking with a coarse-grained force field
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data
CRANet: a comprehensive residual attention network for intracranial aneurysm image classification
Wavelet-based identification of DNA focal genomic aberrations from single nucleotide polymorphism arrays
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations
The impact of quantitative optimization of hybridization conditions on gene expression analysis
Resolving repeat families with long reads
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes
Exploration of multivariate analysis in microbial coding sequence modeling
From raw data to data-analysis for magnetic resonance spectroscopy - the missing link: jMRUI2XML
Efficient use of unlabeled data for protein sequence classification: a comparative study
Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis
Integrative analysis of time course metabolic data and biomarker discovery
Estimating the annotation error rate of curated GO database sequence annotations
CoNVEX: copy number variation estimation in exome sequencing data using HMM
The Genopolis Microarray Database
ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures
Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus
SEEG assistant: a 3DSlicer extension to support epilepsy surgery
Toponomics method for the automated quantification of membrane protein translocation
Kalign - an accurate and fast multiple sequence alignment algorithm
IRIS: a method for reverse engineering of regulatory relations in gene networks
Integrating phenotype and gene expression data for predicting gene function
Enhancing the accuracy of knowledge discovery: a supervised learning method
VSGdb: a database for trypanosome variant surface glycoproteins, a large and diverse family of coiled coil proteins
DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis
A Bayesian approach for inducing sparsity in generalized linear models with multi-category response
MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction
Correction: Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly
Local cell metrics: a novel method for analysis of cell-cell interactions
Automated identification of Monogeneans using digital image processing and K-nearest neighbour approaches
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions
The use of novel selectivity metrics in kinase research
Using context to improve protein domain identification
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Protein subcellular localization prediction based on compartment-specific features and structure conservation
CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis
Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations
Modeling genomic data with type attributes, balancing stability and maintainability
The G protein-coupled receptors in the pufferfish Takifugu rubripes
Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks
CNNH_PSS: protein 8-class secondary structure prediction by convolutional neural network with highway
Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization
Numerical integration methods and layout improvements in the context of dynamic RNA visualization
Spectral phenotyping of embryonic development reveals integrative thermodynamic responses
DTreePred: an online viewer based on machine learning for pathogenicity prediction of genomic variants
A joint use of pooling and imputation for genotyping SNPs
Correction to: Mining a stroke knowledge graph from literature
AfterQC: automatic filtering, trimming, error removing and quality control for fastq data
A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes
CASTELO: clustered atom subtypes aided lead optimization - a combined machine learning and molecular modeling method
pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing
XRate: a fast prototyping, training and annotation tool for phylo-grammars
Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data
The Secrets of a Functional Synapse - From a Computational and Experimental Viewpoint
VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces
Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
A comprehensive database for integrated analysis of omics data in autoimmune diseases
Extracting a biologically latent space of lung cancer epigenetics with variational autoencoders
Selection of optimal reference genes for normalization in quantitative RT-PCR
Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data
Rigorous optimisation of multilinear discriminant analysis with Tucker and PARAFAC structures
Predicting gene function using hierarchical multi-label decision tree ensembles
Accurate prediction of protein enzymatic class by N-to-1 Neural Networks
Meta-analysis of gene expression microarrays with missing replicates
Application of the geographic population structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas
BioNLP Shared Task - The Bacteria Track
The behaviour of random forest permutation-based variable importance measures under predictor correlation
PathFinder: mining signal transduction pathway segments from protein-protein interaction networks
Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB
A benchmark for statistical microarray data analysis that preserves actual biological and technical variance
Investigating mathematical models of immuno-interactions with early-stage cancer under an agent-based modelling perspective
Measuring rank robustness in scored protein interaction networks
Identification and characterization of conserved lncRNAs in human and rat brain
A flexible statistical model for alignment of label-free proteomics data - incorporating ion mobility and product ion information
Scalable transcriptomics analysis with Dask: applications in data science and machine learning
Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment
Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data
MI-GWAS: a SAS platform for the analysis of inherited and maternal genetic effects in genome-wide association studies using log-linear models
An Iterative Approach of Protein Function Prediction
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions
The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words
DeepACLSTM: deep asymmetric convolutional long short-term memory neural models for protein secondary structure prediction
VIGLA-M: visual gene expression data analytics
Understanding molecular recognition and epitope prediction from Information Theoretic approach
NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data
Normalization of ChIP-seq data with control
Comparative network stratification analysis for identifying functional interpretable network biomarkers
A temporal precedence based clustering method for gene expression microarray data
Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression
A two-phase procedure for non-normal quantitative trait genetic association study
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications
PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome
HCS-Neurons: identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening
Codon pair bias in prokaryotic and eukaryotic genomes
pHisPred: a tool for the identification of histidine phosphorylation sites by integrating amino acid patterns and properties
A hybrid Stacking-SMOTE model for optimizing the prediction of autistic genes
Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach
Analysis of oligonucleotide array experiments with repeated measures using mixed models
Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
Graph algorithms for machine learning: a case-control study based on prostate cancer populations and high throughput transcriptomic data
A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences
Single-cell classification using graph convolutional networks
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing
MHSNMF: multi-view hessian regularization based symmetric nonnegative matrix factorization for microbiome data analysis
Predicting potential adverse events using safety data from marketed drugs
A genetic algorithm-Bayesian network approach for the analysis of metabolomics and spectroscopic data: application to the rapid detection of Bacillus spores and identification of Bacillus species
RAE1 is a prognostic biomarker and is correlated with clinicopathological characteristics of patients with hepatocellular carcinoma
Valection: design optimization for validation and verification studies
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins
Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
New concepts for building vocabulary for cell image ontologies
Model order selection for bio-molecular data clustering
IGDD: a database of intronless genes in dicots
VaMiAnalyzer: an open source, Python-based application for analysis of 3D in vitro vasculogenic mimicry assays
LabKey Server: An open source platform for scientific data integration, analysis and collaboration
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies
GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor
Spectral gene set enrichment (SGSE)
nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets
TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use
GEMINI: a computationally-efficient search engine for large gene expression datasets
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
Training text chunkers on a silver standard corpus: can silver replace gold?
GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences
IPO: a tool for automated optimization of XCMS parameters
DAS Writeback: A Collaborative Annotation System
Efficient alignment of RNA secondary structures using sparse dynamic programming
Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding
Meta-Analysis Based on Weighted Ordered P-values for Genomic Data with Heterogeneity
MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Ca only models, Alternative alignments, and Non-sequential alignments
Inferring time-dependent population growth rates in cell cultures undergoing adaptation
VisualRepbase: an interface for the study of occurrences of transposable element families
Non-linear mapping for exploratory data analysis in functional genomics
A novel scan statistics approach for clustering identification and comparison in binary genomic data
Comparative studies of high-throughput biological graphs
Trimming of mammalian transcriptional networks using network component analysis
Detection of recurrent rearrangement breakpoints from copy number data
FastqPuri: high-performance preprocessing of RNA-seq data
Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files
Boosting accuracy of automated classification of fluorescence microscope images for location proteomics
Identifying interactions in the time and frequency domains in local and global networks - A Granger Causality Approach
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
A model-based approach to selection of tag SNPs
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements
Linking microarray reporters with protein functions
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource
The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets
Machine learning predicts nucleosome binding modes of transcription factors
Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays
Local conservation scores without a priori assumptions on neutral substitution rates
tarSVM: Improving the accuracy of variant calls derived from microfluidic PCR-based targeted next generation sequencing using a support vector machine
Brain antibody sequence evaluation (BASE): an easy-to-use software for complete data analysis in single cell immunoglobulin cloning
Integrating GPCR-specific information with full text articles
ICGRM: integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset
Studying the functional conservation of cis-regulatory modules and their transcriptional output
Mutagenesis Objective Search and Selection Tool (MOSST): an algorithm to predict structure-function related mutations in proteins
Genotyping microsatellites in next-generation sequencing data
Identifying pleiotropic genes in genome-wide association studies from related subjects using the linear mixed model and Fisher combination function
Flanking signal and mature peptide residues influence signal peptide cleavage
refMLST: reference-based multilocus sequence typing enables universal bacterial typing
PyConvU-Net: a lightweight and multiscale network for biomedical image segmentation
TSSAR: TSS annotation regime for dRNA-seq data
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes
TCP: a tool for designing chimera proteins based on the tertiary structure information
An efficient and extensible approach for compressing phylogenetic trees
Evaluating imputation methods for single-cell RNA-seq data
LSTrAP: efficiently combining RNA sequencing data into co-expression networks
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition
Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework
A scalable machine-learning approach to recognize chemical names within large text databases
Light-RCV: a lightweight read coverage viewer for next generation sequencing data
JCoDA: a tool for detecting evolutionary selection
zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm
Community-driven computational biology with Debian Linux
Evaluation of a large-scale biomedical data annotation initiative
Alternative splicing and protein function
Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
Mining protein networks for synthetic genetic interactions
Exploiting protein flexibility to predict the location of allosteric sites
Discovering local patterns of co - evolution: computational aspects and biological examples
Extract antibody and antigen names from biomedical literature
CellECT: cell evolution capturing tool
From sequence to enzyme mechanism using multi-label machine learning
Predicting overlapping protein complexes based on core-attachment and a local modularity structure
BESST - Efficient scaffolding of large fragmented assemblies
Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
MPD: multiplex primer design for next-generation targeted sequencing
MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin
SigUNet: signal peptide recognition based on semantic segmentation
Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Stability of the core domain of p53: insights from computer simulations
Unifying generative and discriminative learning principles
SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data
FPGA-based accelerator for adaptive banded event alignment in nanopore sequencing data analysis
Statistical extraction of Drosophila cis -regulatory modules using exhaustive assessment of local word frequency
Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis
Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
Comparison of small n statistical tests of differential expression applied to microarrays
Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms
Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
Novel definition files for human GeneChips based on GeneAnnot
Discovering relationships among dispersed repeats using spatial association rule mining
Robust gene selection methods using weighting schemes for microarray data analysis