yusuke1997/dblp-id-title huggingface dataset:
Improved packing of protein side chains with parallel ant colonies
A mixed-effects stochastic model reveals clonal dominance in gene therapy safety studies
Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome
Algebraic Dynamic Programming over general data structures
DFLAT: functional annotation for human development
PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing
Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species
Statistical analysis of microarray gene expression data from a mouse model of toxoplasmosis
SDM-assist software to design site-directed mutagenesis primers introducing "silent" restriction sites
Integrating biological data - the Distributed Annotation System
Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human
DSD - An integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities
Reuse of structural domain-domain interactions in protein networks
Simultant: simultaneous curve fitting of functions and differential equations using analytical gradient calculations
Signaling pathways have an inherent need for noise to acquire information
Bayesian probabilistic network modeling from multiple independent replicates
Deep learning approach for cancer subtype classification using high-dimensional gene expression data
Core and periphery structures in protein interaction networks
A quantization method based on threshold optimization for microarray short time series
Extracting drug-drug interactions from biomedical texts
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
VarBin, a novel method for classifying true and false positive variants in NGS data
Tabular deep learning: a comparative study applied to multi-task genome-wide prediction
Integrated network reconstruction, visualization and analysis using YANAsquare
Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association
Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data
MiPepid: MicroPeptide identification tool using machine learning
A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers
Shape-IT: new rapid and accurate algorithm for haplotype inference
NmSEER V2.0: a prediction tool for 2′-O-methylation sites based on random forest and multi-encoding combination
SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data
A unified STR profiling system across multiple species with whole genome sequencing data
Model averaging strategies for structure learning in Bayesian networks with limited data
CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
Evolutionary sequence analysis of complete eukaryote genomes
FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments
An interactive tool for visualization of relationships between gene expression profiles
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
Genotyping and inflated type I error rate in genome-wide association case/control studies
Publisher Correction to: TrancriptomeReconstructoR: data‑driven annotation of complex transcriptomes
GRAPHIE: graph based histology image explorer
Preface to the BMC-CIBB 2015-16 special issue
Fast motif recognition via application of statistical thresholds
Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation
Open-Target Sparse Sensing of Biological Agents using DNA Microarray
Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers
The parameter sensitivity of random forests
USMPep: universal sequence models for major histocompatibility complex binding affinity prediction
Automated selection of homologs to track the evolutionary history of proteins
Using natural language processing and machine learning to identify breast cancer local recurrence
Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models
Classification of protein-protein association rates based on biophysical informatics
flowDiv: a new pipeline for analyzing flow cytometric diversity
BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology
Discovering semantic features in the literature: a foundation for building functional associations
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data
Predicting stage-specific cancer related genes and their dynamic modules by integrating multiple datasets
Integrated entropy-based approach for analyzing exons and introns in DNA sequences
Exploratory analysis of genomic segmentations with Segtools
A weighted string kernel for protein fold recognition
Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data
SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
MiRTif: a support vector machine-based microRNA target interaction filter
Variable selection for binary classification using error rate p -values applied to metabolomics data
GeneXplorer: an interactive web application for microarray data visualization and analysis
Generalized gene co-expression analysis via subspace clustering using low-rank representation
A novel candidate disease gene prioritization method using deep graph convolutional networks and semi-supervised learning
On the computational modeling of the innate immune system
Unexpected observations after mapping LongSAGE tags to the human genome
IView: introgression library visualization and query tool
DePolymerase Predictor (DePP): a machine learning tool for the targeted identification of phage depolymerases
How large B-factors can be in protein crystal structures
Fregene: Simulation of realistic sequence-level data in populations and ascertained samples
The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure
Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data
NEDD: a network embedding based method for predicting drug-disease associations
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique
Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion
Automatic classification of protein structures using low-dimensional structure space mappings
Biclustering of gene expression data by non-smooth non-negative matrix factorization
In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches
SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes
An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in Acute Myeloid Leukemia
Prediction of antigenic epitopes on protein surfaces by consensus scoring
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito
Survival models with preclustered gene groups as covariates
Modelling study of dimerization in mammalian defensins
Scellpam: an R package/C++ library to perform parallel partitioning around medoids on scRNAseq data sets
EDGE 3 : A web-based solution for management and analysis of Agilent two color microarray experiments
RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression
A tool for analyzing and visualizing ribo-seq data at the isoform level
MELTING, a flexible platform to predict the melting temperatures of nucleic acids
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis
Evaluation of gene importance in microarray data based upon probability of selection
Potent bace-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies
Measures of co-expression for improved function prediction of long non-coding RNAs
EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib
WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations
Novel image markers for non-small cell lung cancer classification and survival prediction
Data hosting infrastructure for primary biodiversity data
Masakari: visualization supported statistical analysis of genome segmentations
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments
kruX: matrix-based non-parametric eQTL discovery
AVID: An integrative framework for discovering functional relationships among proteins
Disease ontologies for knowledge graphs
Rare copy number variant analysis in case-control studies using snp array data: a scalable and automated data analysis pipeline
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data
DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference
Multiple-platform data integration method with application to combined analysis of microarray and proteomic data
Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis
De novo inference of stratification and local admixture in sequencing studies
Multi-objective data enhancement for deep learning-based ultrasound analysis
A database and API for variation, dense genotyping and resequencing data
MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline
estimateR: an R package to estimate and monitor the effective reproductive number
Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database
In silico design of targeted SRM-based experiments
TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins
LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs
A Bayesian method for comparing and combining binary classifiers in the absence of a gold standard
Generalized probabilistic canonical correlation analysis for multi-modal data integration with full or partial observations
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment
Enhancing the prediction of protein pairings between interacting families using orthology information
Integrating mean and variance heterogeneities to identify differentially expressed genes
Finite mixture clustering of human tissues with different levels of IGF-1 splice variants mRNA transcripts
GO-Diff: Mining functional differentiation between EST-based transcriptomes
MARS: Microarray analysis, retrieval, and storage system
Simple integrative preprocessing preserves what is shared in data sources
Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems
Taxanorm: a novel taxa-specific normalization approach for microbiome data
Pollux: platform independent error correction of single and mixed genomes
Drug response prediction using graph representation learning and Laplacian feature selection
Using local gene expression similarities to discover regulatory binding site modules
Speeding Disease Gene Discovery with SUSPECTS
Evaluation of classification in single cell atac-seq data with machine learning methods
Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing
PaSS: a sequencing simulator for PacBio sequencing
Temporal classification of short time series data
EVEREST: automatic identification and classification of protein domains in all protein sequences
Learning biological network using mutual information and conditional independence
SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions
SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets
Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data
A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors
Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation
Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma
Haplotype-based autoencoders can reduce the dataset dimension and estimate haplotype block effects in different crop species
Additive risk survival model with microarray data
Predicting chemosensitivity using drug perturbed gene dynamics
Evaluating genome architecture of a complex region via generalized bipartite matching
Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
lifex-ep: a robust and efficient software for cardiac electrophysiology simulations
GONOME: measuring correlations between GO terms and genomic positions
DGDTA: dynamic graph attention network for predicting drug-target binding affinity
Global multiple protein-protein interaction network alignment by combining pairwise network alignments
Prediction of epigenetically regulated genes in breast cancer cell lines
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes
Modeling gene regulatory network motifs using statecharts
MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction
dRiskKB: a large-scale disease-disease risk relationship knowledge base constructed from biomedical text
Automatically extracting functionally equivalent proteins from SwissProt
Correction to: IonCRAM: a reference-based compression tool for ion torrent sequence files
Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs
Automatic detection of diffusion modes within biological membranes using back-propagation neural network
Selected proceedings of the 2009 Summit on Translational Bioinformatics
GenClust: A genetic algorithm for clustering gene expression data
flowEMMi: an automated model-based clustering tool for microbial cytometric data
Single sample scoring of molecular phenotypes
Prediction of drug-disease associations based on ensemble meta paths and singular value decomposition
ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data
MathDAMP: a package for differential analysis of metabolite profiles
Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors : An In-silico Study
Multistable switches and their role in cellular differentiation networks
Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data
Mabs, a suite of tools for gene-informed genome assembly
Completing a genomic characterisation of microscopic tumour samples with copy number
Multi-class boosting for the analysis of multiple incomplete views on microbiome data
An integrated pharmacokinetics ontology and corpus for text mining
SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics
Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease
TMFUF: a triple matrix factorization-based unified framework for predicting comprehensive drug-drug interactions of new drugs
PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data
Improved machine learning method for analysis of gas phase chemistry of peptides
M 3 G: Maximum Margin Microarray Gridding
Simplifying gene trees for easier comprehension
Multi-scaled self-attention for drug-target interaction prediction based on multi-granularity representation
Germline contamination and leakage in whole genome somatic single nucleotide variant detection
Investigating selection on viruses: a statistical alignment approach
Analyses of domains and domain fusions in human proto-oncogenes
Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer
Exploration of biological network centralities with CentiBiN
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves
A comparison study on feature selection of DNA structural properties for promoter prediction
A meta-learning approach for B-cell conformational epitope prediction
Combining active learning and semi-supervised learning techniques to extract protein interaction sentences
Genomic and immunogenomic analysis of three prognostic signature genes in LUAD
Text Detective: a rule-based system for gene annotation in biomedical texts
CNN-Siam: multimodal siamese CNN-based deep learning approach for drug‒drug interaction prediction
Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms
Prediction of protein-binding areas by small-world residue networks and application to docking
Identifying and mitigating batch effects in whole genome sequencing data
An EM algorithm to improve the estimation of the probability of clonal relatedness of pairs of tumors in cancer patients
A linear memory algorithm for Baum-Welch training
Detecting differentially expressed genes for syndromes by considering change in mean and dispersion simultaneously
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach
Assistant diagnosis with Chinese electronic medical records based on CNN and BiLSTM with phrase-level and word-level attentions
Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations
SEQSIM: A novel bioinformatics tool for comparisons of promoter regions - a case study of calcium binding protein spermatid associated 1 (CABS1)
BarWare: efficient software tools for barcoded single-cell genomics
Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays
Performance of random forest when SNPs are in linkage disequilibrium
LocateP: Genome-scale subcellular-location predictor for bacterial proteins
Predicting breast cancer using an expression values weighted clinical classifier
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'
SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction
Efficient implied alignment
GPU-accelerated iterative reconstruction for limited-data tomography in CBCT systems
A machine learning model for classifying G-protein-coupled receptors as agonists or antagonists
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans
CNV-TV: A robust method to discover copy number variation from short sequencing reads
Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data
Identification of indels in next-generation sequencing data
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature
The partitioned LASSO-patternsearch algorithm with application to gene expression data
A knowledge discovery object model API for Java
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art
TABASCO: A single molecule, base-pair resolved gene expression simulator
PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction
Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization
PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios
SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution
Small protein complex prediction algorithm based on protein-protein interaction network segmentation
Deep learning for cancer type classification and driver gene identification
Comparison of codon usage in mycobacteriophages with and without tRNAs in their genomes
TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
Spatial registration of neuron morphologies based on maximization of volume overlap
Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles
Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies
Structure and function predictions of the Msa protein in Staphylococcus aureus
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry
A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time
Pan-cancer analysis of SYNGR2 with a focus on clinical implications and immune landscape in liver hepatocellular carcinoma
Keras R-CNN: library for cell detection in biological images using deep neural networks
Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data
Machine learning and statistics shape a novel path in archaeal promoter annotation
Factors affecting the accuracy of a class prediction model in gene expression data