yusuke1997/dblp-id-title huggingface dataset:
Semi-supervised adaptive-height snipping of the hierarchical clustering tree
DEEPSEN: a convolutional neural network based method for super-enhancer prediction
Detecting differential expression in microarray data: comparison of optimal procedures
Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
Identification of differentially expressed genes by means of outlier detection
Evaluation of the effectiveness of simple nuclei-segmentation methods on Caenorhabditis elegans embryogenesis images
Predicting protein function via downward random walks on a gene ontology
Constructing a database for the relations between CNV and human genetic diseases via systematic text mining
Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems
A robust approach to optimizing multi-source information for enhancing genomics retrieval performance
Finding gene regulatory network candidates using the gene expression knowledge base
GObar: A Gene Ontology based analysis and visualization tool for gene sets
Quantitative inference of dynamic regulatory pathways via microarray data
BSMAP: whole genome bisulfite sequence MAPping program
Network based transcription factor analysis of regenerating axolotl limbs
Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS
Detecting false positive sequence homology: a machine learning approach
A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network
Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis
Assessment of disease named entity recognition on a corpus of annotated sentences
TAMA: improved metagenomic sequence classification through meta-analysis
ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions
Current approaches to gene regulatory network modelling
Multi-view feature representation and fusion for drug-drug interactions prediction
FM-test: a fuzzy-set-theory-based approach to differential gene expression data analysis
CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins
pSuc-EDBAM: Predicting lysine succinylation sites in proteins based on ensemble dense blocks and an attention module
Statistical issues in the analysis of Illumina data
Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data
A novel collaborative filtering model for LncRNA-disease association prediction based on the Naïve Bayesian classifier
BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity
Extending pathways and processes using molecular interaction networks to analyse cancer genome data
Machine learning techniques in disease forecasting: a case study on rice blast prediction
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
Processing genome scale tabular data with wormtable
Introducing the f 0 % method: a reliable and accurate approach for qPCR analysis
Computer-assisted evaluation of small airway disease in CT scans of Iran-Iraq war victims of chemical warfare by a locally developed software: comparison between different quantitative methods
Using least median of squares for structural superposition of flexible proteins
Word sense disambiguation for event trigger word detection in biomedicine
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment
Quasi-linear score for capturing heterogeneous structure in biomarkers
Analysis of circular genome rearrangement by fusions, fissions and block-interchanges
Solu: a cloud platform for real-time genomic pathogen surveillance
Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets
TAP score: torsion angle propensity normalization applied to local protein structure evaluation
Fast and SNP-aware short read alignment with SALT
Tracing retinal vessel trees by transductive inference
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
Analysis of lifestyle and metabolic predictors of visceral obesity with Bayesian Networks
Improving prediction of burial state of residues by exploiting correlation among residues
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
Prediction of lung cancer using gene expression and deep learning with KL divergence gene selection
Mining on Alzheimer's diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing
SPARQL Assist language-neutral query composer
Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver
Score regularization for peptide identification
Zim4rv: an R package to modeling zero-inflated count phenotype on regional-based rare variants
CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements
A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study
A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes
BayesPeak: Bayesian analysis of ChIP-seq data
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
BIPAD: A web server for modeling bipartite sequence elements
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes
Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction
Redefining the high variable genes by optimized LOESS regression with positive ratio
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach
Mapping eQTL by leveraging multiple tissues and DNA methylation
Latent class distributional regression for the estimation of non-linear reference limits from contaminated data sources
A bioengineering approach for rational vaccine design towards the Ebola Virus
MethPed: an R package for the identification of pediatric brain tumor subtypes
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
A Bayesian approach to determine the composition of heterogeneous cancer tissue
Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy
Development of quantitative and continuous measure for severity degree of Alzheimer's disease evaluated from MRI images of 761 human brains
A multivariate approach to the integration of multi-omics datasets
Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model
GenMAPP 2: new features and resources for pathway analysis
Finding genomic ontology terms in text using evidence content
CLASS: constrained transcript assembly of RNA-seq reads
HOME: a histogram based machine learning approach for effective identification of differentially methylated regions
SCOPIT: sample size calculations for single-cell sequencing experiments
Segmentum: a tool for copy number analysis of cancer genomes
miRTissue ce : extending miRTissue web service with the analysis of ceRNA-ceRNA interactions
A foundation for reference models for drug combinations with an application to Loewe's reference model
Integrative disease classification based on cross-platform microarray data
Identification of common coexpression modules based on quantitative network comparison
Comprehensive characterization of an individual's LINE-1 insertion profile using next generation sequencing data
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions
Genomes as geography: using GIS technology to build interactive genome feature maps
Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs
Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway
Revealing hidden information in osteoblast's mechanotransduction through analysis of time patterns of critical events
Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm
Statistical methodology for the analysis of dye-switch microarray experiments
Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?
Properties of Metabolic Graphs: Biological Organization or Representation Artifacts?
Efficient Bayesian approach for multilocus association mapping including gene-gene interactions
Keanu: a novel visualization tool to explore biodiversity in metagenomes
A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps
Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function
A standardized approach for exact CT-based three-dimensional position analysis in the distal tibiofibular joint
Joint haplotype assembly and genotype calling via sequential Monte Carlo algorithm
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources
An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds
Probabilistic drug connectivity mapping
REMAS: a new regression model to identify alternative splicing events from exon array data
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction
SwitchFinder - a novel method and query facility for discovering dynamic gene expression patterns
Incorporating functional inter-relationships into protein function prediction algorithms
A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies
Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold
Barcode identification for single cell genomics
Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design
In silico docking of urokinase plasminogen activator and integrins
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
Inferring cellular networks - a review
renz: An R package for the analysis of enzyme kinetic data
histoneHMM: Differential analysis of histone modifications with broad genomic footprints
LimiTT: link miRNAs to targets
PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms
Normalization and experimental design for ChIP-chip data
Semantic interoperability: ontological unpacking of a viral conceptual model
Pan-genome de Bruijn graph using the bidirectional FM-index
Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes
Nested Stochastic Block Models applied to the analysis of single cell data
Estimation of the number of extreme pathways for metabolic networks
Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks
Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss
Predicting zinc binding at the proteome level
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes
A multitask transfer learning framework for the prediction of virus-human protein-protein interactions
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
Linked open data-based framework for automatic biomedical ontology generation
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens
Locating tandem repeats in weighted sequences in proteins
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets
Artificial neural network approach for selection of susceptible single nucleotide polymorphisms and construction of prediction model on childhood allergic asthma
OREMPdb: a semantic dictionary of computational pathway models
GPRED-GC: a Gene PREDiction model accounting for 5 ′ - 3 ′ GC gradient
Extracting Genetic Pathways From Text and Grounding at the Spatio-Temporal Level
Discovering motifs that induce sequencing errors
Issues in learning an ontology from text
Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples
Prediction of cis / trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function
A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins
SuperMimic - Fitting peptide mimetics into protein structures
RAG: RNA-As-Graphs web resource
Identification of large disjoint motifs in biological networks
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence
Genome plasticity and systems evolution in Streptomyces
A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator
YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast
Inferring slowly-changing dynamic gene-regulatory networks
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Read mapping on de Bruijn graphs
A comparative study of survival models for breast cancer prognostication revisited: the benefits of multi-gene models
Granger causality vs. dynamic Bayesian network inference: a comparative study
mrSNP: Software to detect SNP effects on microRNA binding
In silico investigation into dendritic cell regulation of CD8Treg mediated killing of Th1 cells in murine experimental autoimmune encephalomyelitis
Ovarian cancer classification based on dimensionality reduction for SELDI-TOF data
Promoter prediction in E. coli based on SIDD profiles and Artificial Neural Networks
Sensitivity of CNN image analysis to multifaceted measurements of neurite growth
MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data
SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations
A maximum likelihood framework for protein design
Goldsurfer2 (Gs2): A comprehensive tool for the analysis and visualization of genome wide association studies
Interpretive time-frequency analysis of genomic sequences
Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV
A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates
Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical application to genomic and metagenomic projects
A whitening approach to probabilistic canonical correlation analysis for omics data integration
Protein structure based prediction of catalytic residues
ClassifieR 2.0: expanding interactive gene expression-based stratification to prostate and high-grade serous ovarian cancer
Integration of scRNA-seq data by disentangled representation learning with condition domain adaptation
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations
A probabilistic approach for pediatric epilepsy diagnosis using brain functional connectivity networks
BRANEnet: embedding multilayer networks for omics data integration
Analysing RNA-kinetics based on folding space abstraction
Parametric bootstrapping for biological sequence motifs
GOFFA: Gene Ontology For Functional Analysis - A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data
Advancing translational research with the Semantic Web
Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks
petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker's yeast
Consensus properties for the deep coalescence problem and their application for scalable tree search
A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database
Highlighting computations in bioscience and bioinformatics: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB07)
Aryana-bs: context-aware alignment of bisulfite-sequencing reads
CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization
Potential based, spatial simulation of dynamically nested particles
Bayesian coestimation of phylogeny and sequence alignment
Efficient identification of mutations that potentially confer treatment resistance through computational derivation
Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics
pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
Identification of markers associated with global changes in DNA methylation regulation in cancers
Functional module detection by functional flow pattern mining in protein interaction networks
Simultaneous phylogeny reconstruction and multiple sequence alignment
Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions
The C 1 C 2 : A framework for simultaneous model selection and assessment
Robust joint analysis allowing for model uncertainty in two-stage genetic association studies
Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life
Parameter estimations of sigmoidal models of cancer
A novel miRNA-based classification model of risks and stages for clear cell renal cell carcinoma patients
CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes
SIMAT: GC-SIM-MS data analysis tool
Scuba: scalable kernel-based gene prioritization
GraphDNA: a Java program for graphical display of DNA composition analyses
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads
Automatic detection of false annotations via binary property clustering
StaRTrEK: in silico estimation of RNA half-lives from genome-wide time-course experiments without transcriptional inhibition
miTarget: microRNA target gene prediction using a support vector machine
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis
Choosing the best heuristic for seeded alignment of DNA sequences
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data
Dinosolve: a protein disulfide bonding prediction server using context-based features to enhance prediction accuracy
MetaLook: a 3D visualisation software for marine ecological genomics
ImaGene: a convolutional neural network to quantify natural selection from genomic data
Cluster stability scores for microarray data in cancer studies
Sequence motif finder using memetic algorithm
ImageJ2: ImageJ for the next generation of scientific image data
Extraction of phylogenetic network modules from the metabolic network
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses
An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS
The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy
"TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis
GenGraph: a python module for the simple generation and manipulation of genome graphs
NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks
A compartmentalized approach to the assembly of physical maps
Heuristic algorithms for feature selection under Bayesian models with block-diagonal covariance structure
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments
Random forest methodology for model-based recursive partitioning: the mobForest package for R
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments
A novel modality contribution confidence-enhanced multimodal deep learning framework for multiomics data
Adapting machine-learning algorithms to design gene circuits
Computational identification of biologically functional non-hairpin GC-helices in human Argonaute mRNA
Application of an efficient Bayesian discretization method to biomedical data
Gene expression based prototype for automatic tumor prediction
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
Stochastic epigenetic outliers can define field defects in cancer
PCP-GC-LM: single-sequence-based protein contact prediction using dual graph convolutional neural network and convolutional neural network
Identification of expression patterns in the progression of disease stages by integration of transcriptomic data
Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix
Human limits in machine learning: prediction of potato yield and disease using soil microbiome data
Genome-wide prediction, display and refinement of binding sites with information theory-based models
HMM-ModE - Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences
OscoNet: inferring oscillatory gene networks
Enhancing navigation in biomedical databases by community voting and database-driven text classification