yusuke1997/dblp-id-title huggingface dataset:
Deep learning detection of informative features in tau PET for Alzheimer's disease classification
VEGAWES: variational segmentation on whole exome sequencing for copy number detection
The therapeutic and prognostic role of cuproptosis-related genes in triple negative breast cancer
Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature
Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution
Integrated genomic analysis of biological gene sets with applications in lung cancer prognosis
Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris
A regression system for estimation of errors introduced by confocal imaging into gene expression data in situ
Prediction of essential proteins based on subcellular localization and gene expression correlation
Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data
Imputation reliability on DNA biallelic markers for drug metabolism studies
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data
Ycasd - a tool for capturing and scaling data from graphical representations
L.U.St: a tool for approximated maximum likelihood supertree reconstruction
Structure-based and ligand-based virtual screening of novel methyltransferase inhibitors of the dengue virus
Benchmarking consensus model quality assessment for protein fold recognition
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites
arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays
A quantitative analysis of secondary RNA structure using domination based parameters on trees
Comparison study on statistical features of predicted secondary structures for protein structural class prediction: From content to position
DCJ-RNA - double cut and join for RNA secondary structures
High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs
Biotite: new tools for a versatile Python bioinformatics library
Integrated analysis of gene expression by association rules discovery
Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)
Predictive modeling of gene expression regulation
Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow
A random forest approach to the detection of epistatic interactions in case-control studies
Gene tree correction guided by orthology
Arabidopsis Motif Scanner
MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network
A methodology for exploring biomarker - phenotype associations: application to flow cytometry data and systemic sclerosis clinical manifestations
Detection and reconstruction of tandemly organized de novo copy number variations
SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies
An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data
TagDust2: a generic method to extract reads from sequencing data
GenomeGraphs: integrated genomic data visualization with R
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
Comparative interactions of withanolides and sterols with two members of sterol glycosyltransferases from Withania somnifera
In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function
Using a literature-based NMF model for discovering gene functional relationships
CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments
A data review and re-assessment of ovarian cancer serum proteomic profiling
Biclustering of microarray data with MOSPO based on crowding distance
Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation
BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray data
Predicting protein ligand binding motions with the Conformation Explorer
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics
Identifying pathogenic processes by integrating microarray data with prior knowledge
GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data
Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage
University of Turku in the BioNLP'11 Shared Task
SNPLims: a data management system for genome wide association studies
A kernel-based approach for detecting outliers of high-dimensional biological data
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion
MAPI: towards the integrated exploitation of bioinformatics Web Services
UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
FlowClus: efficiently filtering and denoising pyrosequenced amplicons
Mobilomics in Saccharomyces cerevisiae strains
Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems
Comparison of annotation terms between automated and curated E. coli K12 databases
Ab initio identification of human microRNAs based on structure motifs
ProbFAST: Probabilistic Functional Analysis System Tool
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network
Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
Gene expression profiling of breast cancer survivability by pooled cDNA microarray analysis using logistic regression, artificial neural networks and decision trees
A novel approach to sequence validating protein expression clones with automated decision making
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis
Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping
BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design
Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction
Super-taxon in human microbiome are identified to be associated with colorectal cancer
Deep learning of mutation-gene-drug relations from the literature
Multi-stage gene normalization for full-text articles with context-based species filtering for dynamic dictionary entry selection
An efficient visualization tool for the analysis of protein mutation matrices
A continuous optimization approach for inferring parameters in mathematical models of regulatory networks
Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters
RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data
Gene selection for cancer identification: a decision tree model empowered by particle swarm optimization algorithm
Protein complexes identification based on go attributed network embedding
GECKO: a complete large-scale gene expression analysis platform
Discovery of novel biomarkers and phenotypes by semantic technologies
WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
plethy: management of whole body plethysmography data in R
MARTS-DB: a database of mechanisms and reactions of terpene synthases
FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis
Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli
GPU-based detection of protein cavities using Gaussian surfaces
'PACLIMS': A component LIM system for high-throughput functional genomic analysis
A pairwise residue contact area-based mean force potential for discrimination of native protein structure
FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data
An effective method to resolve ambiguous bisulfite-treated reads
Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis
GeDi: applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes
An effective method for network module extraction from microarray data
An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem
A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
ki67 nuclei detection and ki67-index estimation: a novel automatic approach based on human vision modeling
Global, highly specific and fast filtering of alignment seeds
CompMoby: Comparative MobyDick for detection of cis-regulatory motifs
Unsupervised gene selection using biological knowledge : application in sample clustering
trieFinder: an efficient program for annotating digital gene expression (DGE) tags
Highly improved homopolymer aware nucleotide-protein alignments with 454 data
Predicting protein-ligand binding residues with deep convolutional neural networks
Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers
Gene regulatory network inference based on a nonhomogeneous dynamic Bayesian network model with an improved Markov Monte Carlo sampling
knnAUC: an open-source R package for detecting nonlinear dependence between one continuous variable and one binary variable
PRED-LD: efficient imputation of GWAS summary statistics
RResolver: efficient short-read repeat resolution within ABySS
LDexpress: an online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data
MSCFS: inferring circRNA functional similarity based on multiple data sources
A new pairwise kernel for biological network inference with support vector machines
Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria
Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection
Nonparametric Bayesian clustering to detect bipolar methylated genomic loci
Glycosylator: a Python framework for the rapid modeling of glycans
Universal multilayer network embedding reveals a causal link between GABA neurotransmitter and cancer
Changes in radiomic and radiologic features in meningiomas after radiation therapy
ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization
PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling
A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin loops
Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools
Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability
pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms
Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria
Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
Integrated bioinformatics analysis for conducting a prognostic model and identifying immunotherapeutic targets in gastric cancer
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction
Empirical Bayes analysis of single nucleotide polymorphisms
Significance analysis of microarray transcript levels in time series experiments
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities
ESTIMA, a tool for EST management in a multi-project environment
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration
Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes
DMET-Analyzer: automatic analysis of Affymetrix DMET Data
FindCSV: a long-read based method for detecting complex structural variations
PDZscape: a comprehensive PDZ-protein database
Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions
Computing minimal nutrient sets from metabolic networks via linear constraint solving
The translational network for metabolic disease - from protein interaction to disease co-occurrence
Identifying protein complexes based on an edge weight algorithm and core-attachment structure
A parallel and incremental algorithm for efficient unique signature discovery on DNA databases
Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae
Replicability analysis in genome-wide association studies via Cartesian hidden Markov models
CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope
Prediction of the effects of small molecules on the gut microbiome using machine learning method integrating with optimal molecular features
The effects of normalization on the correlation structure of microarray data
Optimising parallel R correlation matrix calculations on gene expression data using MapReduce
An advanced approach to identify antimicrobial peptides and their function types for penaeus through machine learning strategies
Designing and delivering bioinformatics project-based learning in East Africa
Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants
Microbial identification by mass cataloging
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization
Topological characterization of neuronal arbor morphology via sequence representation: I - motif analysis
SNPlotz: a generic genome plot tool to aid the SNP association studies
Genomic analysis of a rare human tumor
MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
Improved two-stage model averaging for high-dimensional linear regression, with application to Riboflavin data analysis
DynaVenn: web-based computation of the most significant overlap between ordered sets
Triplet supertree heuristics for the tree of life
In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression
Construction of an annotated corpus to support biomedical information extraction
RiboFSM: Frequent subgraph mining for the discovery of RNA structures and interactions
Accelerating the reconstruction of genome-scale metabolic networks
NetiNeti: discovery of scientific names from text using machine learning methods
Calciumnetexplorer: an R package for network analysis of calcium imaging data
Integrating partonomic hierarchies in anatomy ontologies
An approach to large scale identification of non-obvious structural similarities between proteins
PROPER: global protein interaction network alignment through percolation matching
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing
KVFinder: steered identification of protein cavities as a PyMOL plugin
Multicore and GPU algorithms for Nussinov RNA folding
A novel method to assess collagen architecture in skin
Netrank: network-based approach for biomarker discovery
A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images
Batch correction evaluation framework using a-priori gene-gene associations: applied to the GTEx dataset
Toward a more holistic method of genome assembly assessment
ModularBoost: an efficient network inference algorithm based on module decomposition
A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database
Development and validation of a deep learning survival model for cervical adenocarcinoma patients
Joint probabilistic-logical refinement of multiple protein feature predictors
Drug response prediction model using a hierarchical structural component modeling method
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms
Clustering on hierarchical heterogeneous data with prior pairwise relationships
ModuleDigger: an itemset mining framework for the detection of cis -regulatory modules
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure
DescFold: A web server for protein fold recognition
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
Comparison of phylogenetic trees through alignment of embedded evolutionary distances
Testing for treatment effects on gene ontology
Inferring gene regression networks with model trees
Novel deep learning model for more accurate prediction of drug-drug interaction effects
System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution
Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs
CerealsDB 2.0: an integrated resource for plant breeders and scientists
Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms
Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks
Long-distance dependency combined multi-hop graph neural networks for protein-protein interactions prediction
GLUE: a flexible software system for virus sequence data
Simple binary segmentation frameworks for identifying variation in DNA copy number
The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011
Columba: an integrated database of proteins, structures, and annotations
Finding long protein products of alternatively spliced genes
A Population Proportion approach for ranking differentially expressed genes
Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds
Disease candidate gene identification and prioritization using protein interaction networks
Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments
A novel method to identify high order gene-gene interactions in genome-wide association studies: Gene-based MDR
Primary case inference in viral outbreaks through analysis of intra-host variant population
srnaMapper: an optimal mapping tool for sRNA-Seq reads
Erratum to: MetCap: A bioinformatics probe design pipeline for large-scale targeted metagenomics
Biblio-MetReS: A bibliometric network reconstruction application and server
GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs
Allermatch(tm), a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines
Efficient experimental design for uncertainty reduction in gene regulatory networks
Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes
EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance
The MB2 gene family of Plasmodium species has a unique combination of S1 and GTP-binding domains
Considerations when using the significance analysis of microarrays (SAM) algorithm
FFCA: a feasibility-based method for flux coupling analysis of metabolic networks
VIPR: A probabilistic algorithm for analysis of microbial detection microarrays
Fast-Find: A novel computational approach to analyzing combinatorial motifs
Comparative study of unsupervised dimension reduction techniques for the visualization of microarray gene expression data
Cuproptosis-related lncRNA signature for prognostic prediction in patients with acute myeloid leukemia
Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities
Extracting rate changes in transcriptional regulation from MEDLINE abstracts
Identifying tweets of personal health experience through word embedding and LSTM neural network
Scoring functions and enrichment: a case study on Hsp90
A bioinformatics knowledge discovery in text application for grid computing
AEGAN-Pathifier: a data augmentation method to improve cancer classification for imbalanced gene expression data
PRMxAI: protein arginine methylation sites prediction based on amino acid spatial distribution using explainable artificial intelligence
AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis
MRMPro: a web-based tool to improve the speed of manual calibration for multiple reaction monitoring data analysis by mass spectrometry
An effective drug-disease associations prediction model based on graphic representation learning over multi-biomolecular network
Methods for evaluating gene expression from Affymetrix microarray datasets
Dinucleotide controlled null models for comparative RNA gene prediction
Correction: On Bayesian modeling of censored data in JAGS
A targeted solution for estimating the cell-type composition of bulk samples
Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction mention extraction
Gene selection and classification of microarray data using random forest
scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport
Graphle: Interactive exploration of large, dense graphs
EGCPPIS: learning hierarchical equivariant graph representations with contrastive integration for protein-protein interaction site identification
A negative selection heuristic to predict new transcriptional targets
Obnet: Network of semantic associations for obesity
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina
Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases
Removing Noise From Pyrosequenced Amplicons
Analyzing 2D Gel Images using a Two-Component Empirical Bayes Model
Characterisation and correction of signal fluctuations in successive acquisitions of microarray images
DIAMIN: a software library for the distributed analysis of large-scale molecular interaction networks