yusuke1997/dblp-id-title huggingface dataset:
Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data
Predicting co-complexed protein pairs using genomic and proteomic data integration
Linguistic feature analysis for protein interaction extraction
GenHap: a novel computational method based on genetic algorithms for haplotype assembly
Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data
Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan
A cross-validation scheme for machine learning algorithms in shotgun proteomics
NetSeekR: a network analysis pipeline for RNA-Seq time series data
Genes with human-specific features are primarily involved with brain, immune and metabolic evolution
GMFilter and SXTestPlate: software tools for improving the SNPlex TM genotyping system
BorreliaBase: a phylogeny-centered browser of Borrelia genomes
A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction
Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database
Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information
MKDESIGNER and TASEQ: a set of tools for plant genotyping by targeted amplicon sequencing
The Protein-DNA Interface database
Predicting phenotypic traits of prokaryotes from protein domain frequencies
ISVASE: identification of sequence variant associated with splicing event using RNA-seq data
Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets
Statistical shape analysis of tap roots: a methodological case study on laser scanned sugar beets
Predicting the functions of a protein from its ability to associate with other molecules
Conversion from electrocardiosignals to equivalent electrical sources on heart surface
Predicting drug characteristics using biomedical text embedding
Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model
R.ROSETTA: an interpretable machine learning framework
ORENZA: a web resource for studying ORphan ENZyme activities
Reverse active learning based atrous DenseNet for pathological image classification
Fractal-based analysis of optical coherence tomography data to quantify retinal tissue damage
Volumetric macromolecule identification in cryo-electron tomograms using capsule networks
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages
Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions
StrAuto: automation and parallelization of STRUCTURE analysis
Comparative study on gene set and pathway topology-based enrichment methods
Prediction of RNA-binding amino acids from protein and RNA sequences
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism
Analysis of cancer metabolism with high-throughput technologies
Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction
flowClust: a Bioconductor package for automated gating of flow cytometry data
Text-mining, milk proteins and nutraceutical potential - the MilkER project
Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)
Relating gene expression data on two-component systems to functional annotations in Escherichia coli
Bidirectional long short-term memory with CRF for detecting biomedical event trigger in FastText semantic space
Statistical analysis of a Bayesian classifier based on the expression of miRNAs
A tensor-based bi-random walks model for protein function prediction
Selecting normalization genes for small diagnostic microarrays
SNVstory: inferring genetic ancestry from genome sequencing data
A fragment based method for modeling of protein segments into cryo-EM density maps
The identification of informative genes from multiple datasets with increasing complexity
Prediction of amyloid fibril-forming segments based on a support vector machine
Mild cognitive impairment prediction based on multi-stream convolutional neural networks
MIA: Mutual Information Analyzer, a graphic user interface program that calculates entropy, vertical and horizontal mutual information of molecular sequence sets
PAGE: Parametric Analysis of Gene Set Enrichment
Clinlabomics: leveraging clinical laboratory data by data mining strategies
Extracting the abstraction pyramid from complex networks
rCUR: an R package for CUR matrix decomposition
A correlated motif approach for finding short linear motifs from protein interaction networks
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information
The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion
A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model
ResBoost: characterizing and predicting catalytic residues in enzymes
Genotyping common and rare variation using overlapping pool sequencing
A survey of protein interaction data and multigenic inherited disorders
VASCo: computation and visualization of annotated protein surface contacts
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction
A random forest based computational model for predicting novel lncRNA-disease associations
CARMA: A platform for analyzing microarray datasets that incorporate replicate measures
A statistical normalization method and differential expression analysis for RNA-seq data between different species
Integrating diverse biological and computational sources for reliable protein-protein interactions
A new method for identifying bivariate differential expression in high dimensional microarray data using quadratic discriminant analysis
Ranking genomic features using an information-theoretic measure of epigenetic discordance
classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes
Prediction of twin-arginine signal peptides
An evaluation of statistical methods for DNA methylation microarray data analysis
Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB
SwarmTCR: a computational approach to predict the specificity of T cell receptors
iGenSig-Rx: an integral genomic signature based white-box tool for modeling cancer therapeutic responses using multi-omics data
MBAT: A scalable informatics system for unifying digital atlasing workflows
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding
ncDENSE: a novel computational method based on a deep learning framework for non-coding RNAs family prediction
MultiSETTER: web server for multiple RNA structure comparison
Characterization of pathogenic germline mutations in human Protein Kinases
Concept annotation in the CRAFT corpus
Reference-free deconvolution of DNA methylation data and mediation by cell composition effects
Identifying metabolic enzymes with multiple types of association evidence
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat
Logarithmic gap costs decrease alignment accuracy
MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria
Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks
Effects of sample size on robustness and prediction accuracy of a prognostic gene signature
Software tool for 3D extraction of germinal centers
WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding
Robust structure measures of metabolic networks that predict prokaryotic optimal growth temperature
Convert your favorite protein modeling program into a mutation predictor: "MODICT"
DiffCoRank: a comprehensive framework for discovering hub genes and differential gene co-expression in brain implant-associated tissue responses
Transfer posterior error probability estimation for peptide identification
A novel procedure for statistical inference and verification of gene regulatory subnetwork
VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing
Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs
Predicting subcellular location of protein with evolution information and sequence-based deep learning
Conformal novelty detection for multiple metabolic networks
Prediction of drug's anatomical therapeutic chemical (ATC) code by constructing biological profiles of ATC codes
Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments
Transcriptional profiling of CD4 T-lymphocytes reveals abnormal gene expression in young prediabetic NOD mice
Query3d: a new method for high-throughput analysis of functional residues in protein structures
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods
Quantification of the variation in percentage identity for protein sequence alignments
Clinical Synopsis Search in OMIM
SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions
Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment
An improved filtering algorithm for big read datasets and its application to single-cell assembly
An edit script for taxonomic classifications
Pripper: prediction of caspase cleavage sites from whole proteomes
Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data
FAAST: Flow-space Assisted Alignment Search Tool
IAOseq: inferring abundance of overlapping genes using RNA-seq data
Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology
Integrated analysis identifies oxidative stress-related lncRNAs associated with progression and prognosis in colorectal cancer
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks
Fold change rank ordering statistics: a new method for detecting differentially expressed genes
FUNC: a package for detecting significant associations between gene sets and ontological annotations
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring
HotSwap for bioinformatics: A STRAP tutorial
Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis
Automatic workflow for the classification of local DNA conformations
StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase
Solving the master equation for Indels
Non-small-cell lung cancer classification via RNA-Seq and histology imaging probability fusion
MetaMine - A tool to detect and analyse gene patterns in their environmental context
An analysis of simple computational strategies to facilitate the design of functional molecular information processors
MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data
On the distribution of cycles and paths in multichromosomal breakpoint graphs and the expected value of rearrangement distance
Aristotle: stratified causal discovery for omics data
Detection of transposable elements by their compositional bias
Structured learning for spatial information extraction from biomedical text: bacteria biotopes
A domain-centric solution to functional genomics via dcGO Predictor
SCFIA: A Statistical Corresponding Feature Identification Algorithm for LC/MS
On finding minimal absent words
Processing SPARQL queries with regular expressions in RDF databases
Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions
Robust MS quantification method for phospho-peptides using 18 O/ 16 O labeling
Toward computational modelling on immune system function
Feature selection environment for genomic applications
GIBA: a clustering tool for detecting protein complexes
COSNet i : ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model
Isomorphism and similarity for 2-generation pedigrees
MicroRNA dysregulational synergistic network: discovering microRNA dysregulatory modules across subtypes in non-small cell lung cancers
Prediction of antimicrobial peptides toxicity based on their physico-chemical properties using machine learning techniques
A semi-parametric statistical model for integrating gene expression profiles across different platforms
Seq-ing improved gene expression estimates from microarrays using machine learning
A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards
NanoSNP: A computational platform for high throughput Quantum Dot encoded microsphere SNP genotyping
Rearrangement analysis of multiple bacterial genomes
ACO: lossless quality score compression based on adaptive coding order
Convergent algorithms for protein structural alignment
Utilization of two sample t -test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies
Global inference of disease-causing single nucleotide variants from exome sequencing data
Fast and efficient short read mapping based on a succinct hash index
A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study
Detection of protein catalytic residues at high precision using local network properties
A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance
Fast genomic prediction of breeding values using parallel Markov chain Monte Carlo with convergence diagnosis
Maximum expected accuracy structural neighbors of an RNA secondary structure
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps
DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data
The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
htsint: a Python library for sequencing pipelines that combines data through gene set generation
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature
Prediction of hot spots in protein-DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting
On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types
Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)
JNets: Exploring networks by integrating annotation
A consensus-based ensemble approach to improve transcriptome assembly
Mapping small molecule binding data to structural domains
An integrated network of microRNA and gene expression in ovarian cancer
Metacells untangle large and complex single-cell transcriptome networks
Fast splice site detection using information content and feature reduction
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes
2D-EM clustering approach for high-dimensional data through folding feature vectors
Protein structure prediction based on particle swarm optimization and tabu search strategy
Feature selection algorithm based on dual correlation filters for cancer-associated somatic variants
Normal uniform mixture differential gene expression detection for cDNA microarrays
Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family
A hybrid approach to protein folding problem integrating constraint programming with local search
Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks
Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
New tools to analyze overlapping coding regions
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities
Scanner calibration revisited
AutoFACT: An Auto matic F unctional A nnotation and C lassification T ool
Repeat-aware modeling and correction of short read errors
Deep learning-based metabolomics data study of prostate cancer
PatternLab for proteomics: a tool for differential shotgun proteomics
JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
Multiple roles of apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) in human tumors: a pan-cancer analysis
ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites
Large-scale mining disease comorbidity relationships from post-market drug adverse events surveillance data
Using the longest significance run to estimate region-specific p-values in genetic association mapping studies
Uncovering extensive post-translation regulation during human cell cycle progression by integrative multi-'omics analysis
Structural Measures for Network Biology Using QuACN
Preliminary nanopore cheminformatics analysis of aptamer-target binding strength
SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation
A Three Stage Integrative Pathway Search ( TIPS (c) ) framework to identify toxicity relevant genes and pathways
Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging
Improving variant calling by incorporating known genetic variants into read alignment
Predicting cancer involvement of genes from heterogeneous data
Phylogeny based discovery of regulatory elements
Longitudinal linear combination test for gene set analysis
Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs
Reproducible Clusters from Microarray Research: Whither?
BITS 2015: the annual meeting of the Italian Society of Bioinformatics
Hierarchical Naive Bayes for genetic association studies
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development
GenomicLayers: sequence-based simulation of epi-genomes
Benchmarking tools for the alignment of functional noncoding DNA
Estimating parameters for generalized mass action models with connectivity information
BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
PileLine: a toolbox to handle genome position information in next-generation sequencing studies
Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach
LinkedImm: a linked data graph database for integrating immunological data
Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments
Microarray results: how accurate are they?
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems
Novel deep learning-based transcriptome data analysis for drug-drug interaction prediction with an application in diabetes
Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data
MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes
Evaluation of genomic island predictors using a comparative genomics approach
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens
Separating common from distinctive variation
A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression
flowCore: a Bioconductor package for high throughput flow cytometry
De Bruijn Superwalk with Multiplicities Problem is NP-hard
Transfer learning for genotype-phenotype prediction using deep learning models
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model
A mixture model approach to sample size estimation in two-sample comparative microarray experiments
GESPA: classifying nsSNPs to predict disease association
Gene regulatory networks modelling using a dynamic evolutionary hybrid
Answering open questions in biology using spatial genomics and structured methods
Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes
Multimodal hybrid convolutional neural network based brain tumor grade classification
An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays
Ontology-based, Tissue MicroArray oriented, image centered tissue bank
Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiaebased on codon composition
A novel approach for haplotype-based association analysis using family data
PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel
Evolutionary relationships between heme-binding ferredoxin α + β barrels
Fast computation of the eigensystem of genomic similarity matrices
Genomic data sampling and its effect on classification performance assessment
GENETAG: a tagged corpus for gene/protein named entity recognition
A multi-stage weakly supervised design for spheroid segmentation to explore mesenchymal stem cell differentiation dynamics
PubMatrix: a tool for multiplex literature mining
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach
Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes
Prediction of protein-protein binding site by using core interface residue and support vector machine
Struct2Graph: a graph attention network for structure based predictions of protein-protein interactions
Recursive model for dose-time responses in pharmacological studies
MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism
SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks
Automatic segmentation of large-scale CT image datasets for detailed body composition analysis
Searching for protein variants with desired properties using deep generative models
Parallel short sequence assembly of transcriptomes