yusuke1997/dblp-id-title huggingface dataset:
Comparison, alignment, and synchronization of cell line information between CLO and EFO
CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies
CorDiffViz: an R package for visualizing multi-omics differential correlation networks
Oculus: faster sequence alignment by streaming read compression
A statistical framework for integrating two microarray data sets in differential expression analysis
Construction of an RNA modification-related gene predictive model associated with prognosis and immunity in gastric cancer
CODA (CrossOver Distribution Analyzer): quantitative characterization of crossover position patterns along chromosomes
Assessing and selecting gene expression signals based upon the quality of the measured dynamics
BioSet2Vec: extraction of k-mer dictionaries from multiple sets of biological sequences via big data technologies
Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches
PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases
Using indirect protein interactions for the prediction of Gene Ontology functions
Living longer by dieting: analysis of transcriptional response after caloric restriction
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations
Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination
PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data
Identifying GPCR-drug interaction based on wordbook learning from sequences
GO for gene documents
Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts
Theoretical characterisation of strand cross-correlation in ChIP-seq
How to make the most of NE dictionaries in statistical NER
NCMHap: a novel method for haplotype reconstruction based on Neutrosophic c-means clustering
Correction: Fitting Gaussian mixture models on incomplete data
Acute stress reduces population-level metabolic and proteomic variation
Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing
Supervised promoter recognition: a benchmark framework
Prediction of protein binding sites in protein structures using hidden Markov support vector machine
RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
The BioCyc Metabolic Network Explorer
Lag penalized weighted correlation for time series clustering
Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks
Gene network inference using continuous time Bayesian networks: a comparative study and application to Th17 cell differentiation
How can functional annotations be derived from profiles of phenotypic annotations?
Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data
Applying unmixing to gene expression data for tumor phylogeny inference
COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator
Exploring community structure in biological networks with random graphs
RNA-binding residues prediction using structural features
Molecular analysis of Trypanosoma cruzi isolates obtained from raccoons in Warren and Barren counties of Kentucky
DUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples
Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective
Identifying hypermethylated CpG islands using a quantile regression model
An improved alignment-free model for dna sequence similarity metric
Fine-tuning structural RNA alignments in the twilight zone
A resource-saving collective approach to biomedical semantic role labeling
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)
Knowledge Discovery and interactive Data Mining in Bioinformatics - State-of-the-Art, future challenges and research directions
Epidemic prediction of dengue fever based on vector compartment model and Markov chain Monte Carlo method
An adaptive method for cDNA microarray normalization
Wound area measurement with 3D transformation and smartphone images
Novel m7G-related lncRNA signature for predicting overall survival in patients with gastric cancer
Extended Newick: it is time for a standard representation of phylogenetic networks
Unsupervised outlier detection applied to SARS-CoV-2 nucleotide sequences can identify sequences of common variants and other variants of interest
Spectral classification of short numerical exon and intron sequences
Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments
An integrated system for genetic analysis
Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings
Analysis of mass spectrometry data using sub-spectra
Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines
A novel procedure on next generation sequencing data analysis using text mining algorithm
Estimating true evolutionary distances under rearrangements, duplications, and losses
Stratification bias in low signal microarray studies
The meaning of alignment: lessons from structural diversity
Bioclipse 2: A scriptable integration platform for the life sciences
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
PDA-PRGCN: identification of Piwi-interacting RNA-disease associations through subgraph projection and residual scaling-based feature augmentation
Gene set enrichment analysis for multiple continuous phenotypes
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases
An Entropy-based gene selection method for cancer classification using microarray data
Clone temporal centrality measures for incomplete sequences of graph snapshots
PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants
Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data
First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA
The 3of5 web application for complex and comprehensive pattern matching in protein sequences
RNA-clique: a method for computing genetic distances from RNA-seq data
Estimate haplotype frequencies in pedigrees
A quantitative genetic and epigenetic model of complex traits
CNV Radar: an improved method for somatic copy number alteration characterization in oncology
minet : A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information
Cell_motility: a cross-platform, open source application for the study of cell motion paths
DISMISS: detection of stranded methylation in MeDIP-Seq data
Identifying essential proteins from protein-protein interaction networks based on influence maximization
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures
An effective correlation-based data modeling framework for automatic diabetes prediction using machine and deep learning techniques
The genomic features that affect the lengths of 5' untranslated regions in multicellular eukaryotes
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores
Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method
bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
Genotype determination for polymorphisms in linkage disequilibrium
Mild cognitive impairment understanding: an empirical study by data-driven approach
Predicting biological pathways of chemical compounds with a profile-inspired approach
Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel
An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks
DBMLoc: a Database of proteins with multiple subcellular localizations
An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma
Assessing local structural perturbations in proteins
Modeling the interactions of Alzheimer-related genes from the whole brain microarray data and diffusion tensor images of human brain
Statistical methods and resources for biomarker discovery using metabolomics
Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions
A shortcut for multiple testing on the directed acyclic graph of gene ontology
LTRharvest , an efficient and flexible software for de novo detection of LTR retrotransposons
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
Network-based prediction of polygenic disease genes involved in cell motility
An efficient genome-wide association test for multivariate phenotypes based on the Fisher combination function
DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD
Mechanism-aware imputation: a two-step approach in handling missing values in metabolomics
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive"
3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison
Breast cancer prediction using genome wide single nucleotide polymorphism data
Selection of optimal quantile protein biomarkers based on cell-level immunohistochemistry data
Density-based parallel skin lesion border detection with webCL
Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology
FogBank: a single cell segmentation across multiple cell lines and image modalities
Clustering metagenomic sequences with interpolated Markov models
CONFOLD2: improved contact-driven ab initio protein structure modeling
ProLego: tool for extracting and visualizing topological modules in protein structures
nPoRe: n-polymer realigner for improved pileup-based variant calling
Galba: genome annotation with miniprot and AUGUSTUS
Highlights from the 5 th International Society for Computational Biology Student Council Symposium at the 17 th Annual International Conference on Intelligent Systems for Molecular Biology and the 8 th European Conference on Computational Biology
Biotite: a unifying open source computational biology framework in Python
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
Prioritization of gene regulatory interactions from large-scale modules in yeast
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics
iRefIndex: A consolidated protein interaction database with provenance
A Two-Step Hierarchical Hypothesis Set Testing Framework, with Applications to Gene Expression Data on Ordered Categories
ConEVA: a toolbox for comprehensive assessment of protein contacts
The MG-RAST API explorer: an on-ramp for RESTful query composition
MultiSeq: unifying sequence and structure data for evolutionary analysis
abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis
SamPler - a novel method for selecting parameters for gene functional annotation routines
SNPeBoT: a tool for predicting transcription factor allele specific binding
baredSC: Bayesian approach to retrieve expression distribution of single-cell data
Comparison of PGH 2 binding site in prostaglandin synthases
Fast detection of de novo copy number variants from SNP arrays for case-parent trios
A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment
A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model
FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries
An integrated network visualization framework towards metabolic engineering applications
Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information
Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine
Prediction of protein-protein interactions between viruses and human by an SVM model
Gene functional similarity search tool (GFSST)
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Enhanced JBrowse plugins for epigenomics data visualization
HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example
Open Biomedical Ontology-based Medline exploration
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface
Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory
Application of transfer learning for cancer drug sensitivity prediction
Evaluating the accuracy of a functional SNP annotation system
A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates
mmquant: how to count multi-mapping reads?
BAMSE: Bayesian model selection for tumor phylogeny inference among multiple samples
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease
Identification of native protein structures captured by principal interactions
Subfamily specific conservation profiles for proteins based on n-gram patterns
An innovative approach for testing bioinformatics programs using metamorphic testing
rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci
R/BHC: fast Bayesian hierarchical clustering for microarray data
Extraction of Genetic Networks (GN) Using Static Bayesian Belief Networks From Genome-Wide Temporal Microarray Data
Efficient analysis of large datasets and sex bias with ADMIXTURE
Investigating the effect of paralogs on microarray gene-set analysis
Statistical significance of cis-regulatory modules
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs
Correction: Splice site identification using probabilistic parameters and SVM classification
Theoretical and quantitative aspects of iron acquisition by a bovine isolate of Pasteurella multocida A: 3
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs
Multiclass discovery in array data
Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control
Markov Chain Ontology Analysis (MCOA)
OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons
The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature
Multiview clustering of multi-omics data integration by using a penalty model
Enabling network inference methods to handle missing data and outliers
Genome wide analysis of sex difference in gene expression profiles of bone formations
StructRNAfinder: an automated pipeline and web server for RNA families prediction
Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised
SeqAnt: A web service to rapidly identify and annotate DNA sequence variations
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
A pan-cancer analysis of collagen VI family on prognosis, tumor microenvironment, and its potential therapeutic effect
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides
rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses
The road to linking genomics and proteomics of pathogenic bacteria: from binary protein complexes to interaction pathways
SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment
Bio-semantic relation extraction with attention-based external knowledge reinforcement
Development of a literature informed Bayesian machine learning method for feature extraction and classification
BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes
ChemiRs: a web application for microRNAs and chemicals
Improving interoperability between microbial information and sequence databases
Hierarchical clustering of maximum parsimony reconciliations
Error-correcting properties of the SOLiD Exact Call Chemistry
Adaptive loss-guided multi-stage residual ASPP for lesion segmentation and disease detection in cucumber under complex backgrounds
Combining calls from multiple somatic mutation-callers
Signal extraction from movies of honeybee brain activity: the ImageBee plugin for KNIME
PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data
Differential meta-analysis of RNA-seq data from multiple studies
Knowledge-guided convolutional networks for chemical-disease relation extraction
An SVM-based system for predicting protein subnuclear localizations
A hidden Markov model for detecting multi-gene chromatin domains
Automatically annotating documents with normalized gene lists
Correction: Disease candidate gene identification and prioritization using protein interaction networks
Obtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples
Optical map guided genome assembly
Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes
Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
SAUTE: sequence assembly using target enrichment
On the detection of functionally coherent groups of protein domains with an extension to protein annotation
A short tutorial in analyzing NGS data of cancer genomes for somatic mutation calling
deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes
Predicting essential proteins based on subcellular localization, orthology and PPI networks
Clustering ionic flow blockade toggles with a Mixture of HMMs
Cgaln: fast and space-efficient whole-genome alignment
Finding regulatory elements and regulatory motifs: a general probabilistic framework
Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)
3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics
Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes
AdmixSim 2: a forward-time simulator for modeling complex population admixture
Stereochemical errors and their implications to molecular dynamics simulations
SMOTE for high-dimensional class-imbalanced data
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction
Improved computations for relationship inference using low-coverage sequencing data
Assignment of structural domains in proteins using diffusion kernels on graphs
G+C content dominates intrinsic nucleosome occupancy
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks
Effects of filtering by Present call on analysis of microarray experiments
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
A controlled comparison of thickness, volume and surface areas from multiple cortical parcellation packages
MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species
Stepwise classification of cancer samples using clinical and molecular Data
Identification of sequence motifs significantly associated with antisense activity
Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers
Comparative studies of differential gene calling using RNA-Seq data
Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study
PeakRanger: A cloud-enabled peak caller for ChIP-seq data
A novel approach toward optimal workflow selection for DNA methylation biomarker discovery
Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research for pathway discovery
Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society
Medians seek the corners, and other conjectures
MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data
Delayed impact: ISI's citation tracking choices are keeping scientists in the dark
Estimating colocalization probability from limited summary statistics
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle
Prediction of disease-related miRNAs by voting with multiple classifiers
TMM@: a web application for the analysis of transmembrane helix mobility
Pan-Tetris: an interactive visualisation for Pan-genomes
A comprehensive system for evaluation of remote sequence similarity detection
Comparative analysis of non-classically secreted proteins in Botrytis cinerea and symbiotic fungus Laccaria bicolor
HPD: an online integrated human pathway database enabling systems biology studies
Predicting anticancer synergistic drug combinations based on multi-task learning
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks
A novel representation of RNA secondary structure based on element-contact graphs
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
PChopper: High Throughput Peptide Prediction For MRM/SRM Transition Design
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision