yusuke1997/dblp-id-title huggingface dataset:
Sparse coding of pathology slides compared to transfer learning with deep neural networks
Identifying candidate genes for variation in sleep-related quantitative traits
A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva
Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem
Genome bioinformatic analysis of nonsynonymous SNPs
STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data
Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles
2D electrophoresis image brightness correction based on gradient interval histogram
ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding
SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis
FCLQC: fast and concurrent lossless quality scores compressor
Decline of protein structure rigidity with interatomic distance
BisoGenet: a new tool for gene network building, visualization and analysis
A functional hierarchical organization of the protein sequence space
StackedEnC-AOP: prediction of antioxidant proteins using transform evolutionary and sequential features based multi-scale vector with stacked ensemble learning
Incorporating representation learning and multihead attention to improve biomedical cross-sentence n-ary relation extraction
PhenoGO: an integrated resource for the multiscale mining of clinical and biological data
Rapid DNA barcoding analysis of large datasets using the composition vector method
Erratum to: How can functional annotations be derived from profiles of phenotypic annotations?
B-LBConA: a medical entity disambiguation model based on Bio-LinkBERT and context-aware mechanism
Evaluation of word embedding models to extract and predict surgical data in breast cancer
A fast and robust hepatocyte quantification algorithm including vein processing
SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
To aggregate or not to aggregate high-dimensional classifiers
moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks
Coconut: covariate-assisted composite null hypothesis testing with applications to replicability analysis of high-throughput experimental data
Gene finding in novel genomes
Functional clustering of yeast proteins from the protein-protein interaction network
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network
Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies
Main findings and advances in bioinformatics and biomedical engineering- IWBBIO 2018
Evaluating the accuracy of protein design using native secondary sub-structures
Ensemble learning for integrative prediction of genetic values with genomic variants
Phylogenetically informed logic relationships improve detection of biological network organization
An SVM-based method for assessment of transcription factor-DNA complex models
An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification
Inferring functional modules of protein families with probabilistic topic models
Optimal clustering with missing values
Illumina error correction near highly repetitive DNA regions improves de novo genome assembly
AnnotateGenomicRegions: a web application
Correction to: cuRnet: an R package for graph traversing on GPU
Estimating copy numbers of alleles from population-scale high-throughput sequencing data
SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis
Integrated structure-based protein interface prediction
reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction
Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions
A linear model for predicting performance of short-read aligners using genome complexity
Model based heritability scores for high-throughput sequencing data
A predictor for predicting Escherichia coli transcriptome and the effects of gene perturbations
FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets
Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression
A comparative evaluation of sequence classification programs
miTAR: a hybrid deep learning-based approach for predicting miRNA targets
A network-based approach for identifying suitable biomarkers for oral immunotherapy of food allergy
In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study
Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana
ODTbrain: a Python library for full-view, dense diffraction tomography
ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery
PepBank - a database of peptides based on sequence text mining and public peptide data sources
AMDORAP: Non-targeted metabolic profiling based on high-resolution LC-MS
BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations
Characterization and sequence prediction of structural variations in α-helix
Knowledge discovery of drug data on the example of adverse reaction prediction
QTL mapping arthritis traits in CXB mice
Erratum to: Predicting the functions of a protein from its ability to associate with other molecules
Features generated for computational splice-site prediction correspond to functional elements
BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology
repDilPCR: a tool for automated analysis of qPCR assays by the dilution-replicate method
A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage
Modeling and mining term association for improving biomedical information retrieval performance
C-Norm: a neural approach to few-shot entity normalization
HISEA: HIerarchical SEed Aligner for PacBio data
Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey
Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems
An ILP solution for the gene duplication problem
Characterization of a Bayesian genetic clustering algorithm based on a Dirichlet process prior and comparison among Bayesian clustering methods
Protein disorder prediction by condensed PSSM considering propensity for order or disorder
Automated smoother for the numerical decoupling of dynamics models
MTG-Link: leveraging barcode information from linked-reads to assemble specific loci
A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
GLOSSI: a method to assess the association of genetic loci-sets with complex diseases
TooT-T: discrimination of transport proteins from non-transport proteins
BioMoby extensions to the Taverna workflow management and enactment software
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Quality control, analysis and secure sharing of Luminex(R) immunoassay data using the open source LabKey Server platform
SeqClone: sequential Monte Carlo based inference of tumor subclones
TreeQNet: a webserver for Treatment evaluation with Quantified Network
SuiteMSA: Visual Tools for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation
Noncoding RNA gene detection using comparative sequence analysis
BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion
Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum
Bayesian graphical models for computational network biology
Neuroimaging feature extraction using a neural network classifier for imaging genetics
Empirical methods for the validation of time-to-event mathematical models taking into account uncertainty and variability: application to EGFR + lung adenocarcinoma
Colony size measurement of the yeast gene deletion strains for functional genomics
A machine learning approach for predicting methionine oxidation sites
Using tree diversity to compare phylogenetic heuristics
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
Towards integrative gene functional similarity measurement
Estimates of introgression as a function of pairwise distances
Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction
Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses
Using machine learning to determine the correlation between physiological and environmental parameters and the induction of acute mountain sickness
iDMET: network-based approach for integrating differential analysis of cancer metabolomics
ProteoModlR for functional proteomic analysis
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
Clinical Bioinformatics: challenges and opportunities
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants
ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies
Clustering exact matches of pairwise sequence alignments by weighted linear regression
MPprimer: a program for reliable multiplex PCR primer design
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Determining anion-quadrupole interactions among protein, DNA, and ligand molecules
The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation
A high-throughput pipeline for the design of real-time PCR signatures
DeepSort: deep convolutional networks for sorting haploid maize seeds
Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions
clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape
Performance of epistasis detection methods in semi-simulated GWAS
False discovery rate estimation using candidate peptides for each spectrum
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
Fully automated pipeline for detection of sex linked genes using RNA-Seq data
A quality metric for homology modeling: the H-factor
Network-enabled gene expression analysis
A base composition analysis of natural patterns for the preprocessing of metagenome sequences
Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks
A novel computational strategy for DNA methylation imputation using mixture regression model (MRM)
Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach
Introducing difference recurrence relations for faster semi-global alignment of long sequences
A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics
Integer programming for selecting set of informative markers in paternity inference
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
Representative transcript sets for evaluating a translational initiation sites predictor
Discrete wavelet transform de-noising in eukaryotic gene splicing
Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks
Prediction of novel miRNAs and associated target genes in Glycine max
Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
Automated identification of copepods using digital image processing and artificial neural network
Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella
Profile analysis and prediction of tissue-specific CpG island methylation classes
Methylmap: visualization of modified nucleotides for large cohort sizes
Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
On validation and invalidation of biological models
Transcriptional regulation at a glance
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies
Analysis of AML genes in dysregulated molecular networks
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization
Identifying microRNA targets in different gene regions
Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains
Lists2Networks: Integrated analysis of gene/protein lists
Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'
Predicting enhancers with deep convolutional neural networks
Conserved residue clusters at protein-protein interfaces and their use in binding site identification
Testing for mean and correlation changes in microarray experiments: an application for pathway analysis
A multitask bi-directional RNN model for named entity recognition on Chinese electronic medical records
S-conLSH: alignment-free gapped mapping of noisy long reads
G-InforBIO: integrated system for microbial genomics
GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM
Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data
VANet: a medical image fusion model based on attention mechanism to assist disease diagnosis
Effective selection of informative SNPs and classification on the HapMap genotype data
CRISP: correlation-refined image segmentation process
Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses
Predicting tumour content of liquid biopsies from cell-free DNA
Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins
Automatic symptom name normalization in clinical records of traditional Chinese medicine
SVhet: towards accurate detection of germline heterozygous deletions using short reads
Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods
Analyzing miRNA co-expression networks to explore TF-miRNA regulation
AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids
GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases
Improvement of alignment accuracy utilizing sequentially conserved motifs
Improving model construction of profile HMMs for remote homology detection through structural alignment
TrypanoCyc - a metabolic pathway database for Trypanosoma brucei
Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework
Erratum to: Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations
Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing
A fuzzy method for RNA-Seq differential expression analysis in presence of multireads
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation
A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities
Alternative empirical Bayes models for adjusting for batch effects in genomic studies
A robust data scaling algorithm to improve classification accuracies in biomedical data
A directed weighted network-based method for drug combinations identification using drug-target and inter-target regulation
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins
Biological relevance of CNV calling methods using familial relatedness including monozygotic twins
Evaluation of top-down mass spectral identification with homologous protein sequences
NGS-Logistics: data infrastructure for efficient analysis of NGS sequence variants across multiple centers
QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis
In-silico design of an immunoinformatics based multi-epitope vaccine against Leishmania donovani
RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins
Hsp90/Cdc37 Chaperone/co-chaperone complex, a novel junction anticancer target elucidated by the mode of action of herbal drug Withaferin A
Topic modeling for cluster analysis of large biological and medical datasets
Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos
A hybrid deep learning framework for bacterial named entity recognition with domain features
A new and updated resource for codon usage tables
Modeling methylation dynamics with simultaneous changes in CpG islands
COMBImage2: a parallel computational framework for higher-order drug combination analysis that includes automated plate design, matched filter based object counting and temporal data mining
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings
Significance evaluation in factor graphs
Significance testing in ridge regression for genetic data
Rigorous assessment and integration of the sequence and structure based features to predict hot spots
Discovering functional interaction patterns in protein-protein interaction networks
Quality assessment of peptide tandem mass spectra
The Otto Warburg International Summer School and Workshop on Networks and Regulation
Comprehensive host-pathogen protein-protein interaction network analysis
Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen
PILER-CR: Fast and accurate identification of CRISPR repeats
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
An automated protocol for modelling peptide substrates to proteases
A novel method for gathering and prioritizing disease candidate genes based on construction of a set of disease-related MeSH(R) terms
Identifying disease associations via genome-wide association studies
CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays
Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities
EvoRSR: an integrated system for exploring evolution of RNA structural robustness
Properties and identification of antibiotic drug targets
A structural SVM approach for reference parsing
Evolutionary algorithms for the selection of single nucleotide polymorphisms
On optimal comparability editing with applications to molecular diagnostics
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction
Optimum contribution selection for animal breeding and conservation: the R package optiSel
Supervised Regularized Canonical Correlation Analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery
Using transfer learning and dimensionality reduction techniques to improve generalisability of machine-learning predictions of mosquito ages from mid-infrared spectra
A two-stage approach for improved prediction of residue contact maps
Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence
In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function
A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
Large-scale labeling and assessment of sex bias in publicly available expression data
A-Prot: protein structure modeling using MSA transformer
Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors
DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors
BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly
Comparison of computational methods for identifying translation initiation sites in EST data
Computational modelling of chromosomally clustering protein domains in bacteria
SNPInterForest: A new method for detecting epistatic interactions
VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers
Random KNN feature selection - a fast and stable alternative to Random Forests
Systematic classification of non-coding RNAs by epigenomic similarity
Spectral consensus strategy for accurate reconstruction of large biological networks
Improved accuracy assessment for 3D genome reconstructions
T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System
FUNYBASE: a FUNgal phYlogenomic dataBASE
Identification of discriminative characteristics for clusters from biologic data with InforBIO software
A genetic algorithm-based boolean delay model of intracellular signal transduction in inflammation
DNI-MDCAP: improvement of causal MiRNA-disease association prediction based on deep network imputation
Appearance frequency modulated gene set enrichment testing
A Method of Gene Expression Data Partitioning for the Construction of Context-Sensitive PBNs
A virus-target host proteins recognition method based on integrated complexes data and seed extension