yusuke1997/dblp-id-title huggingface dataset:
A truncated nuclear norm and graph-Laplacian regularized low-rank representation method for tumor clustering and gene selection
Filtering high-throughput protein-protein interaction data using a combination of genomic features
GeneRIF indexing: sentence selection based on machine learning
MR-KPA: medication recommendation by combining knowledge-enhanced pre-training with a deep adversarial network
CausNet: generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints
Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge
Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Mapping side chain interactions at protein helix termini
variancePartition: interpreting drivers of variation in complex gene expression studies
Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection
Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection
TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data
CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network
Dual channel rank-based intensity weighting for quantitative co-localization of microscopy images
CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies
Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures
Selection of antisense oligonucleotides based on multiple predicted target mRNA structures
Anatomy of enzyme channels
Effect of stochasticity on coinfection dynamics of respiratory viruses
InteroPORC: an automated tool to predict highly conserved protein interaction networks
PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms
aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data
WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration
A lightweight hierarchical convolution network for brain tumor segmentation
Inferring activity changes of transcription factors by binding association with sorted expression profiles
Multiple graph regularized protein domain ranking
Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery
DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder
Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases
Bioimage classification with subcategory discriminant transform of high dimensional visual descriptors
Hydrophobic pulses predict transmembrane helix irregularities and channel transmembrane units
Empirical Bayesian models for analysing molecular serotyping microarrays
Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data
IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics
The strength of co-authorship in gene name disambiguation
An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology
A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants
An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction
SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis
Searching for transcription factor binding sites in vector spaces
Nonparametric methods for the analysis of single-color pathogen microarrays
wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool
A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models
New Bandwidth Selection Criterion for Kernel PCA: Approach to Dimensionality Reduction and Classification Problems
Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100
Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data
dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond
SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures
Prediction of the burial status of transmembrane residues of helical membrane proteins
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads
Impact of data resolution on three-dimensional structure inference methods
Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses
Distance-based functional criticality in the human brain: intelligence and emotional intelligence
Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies
Predicting active enhancers with DNA methylation and histone modification
Reduction of supervision for biomedical knowledge discovery
Chromosomal clustering of a human transcriptome reveals regulatory background
pblat: a multithread blat algorithm speeding up aligning sequences to genomes
FragGeneScanRs: faster gene prediction for short reads
Transfer learning for accelerated failure time model with microarray data
Identification of pathogen genomic variants through an integrated pipeline
Bioinformatics analysis of immune response to group A streptococcal sepsis integrating quantitative trait loci mapping with genome-wide expression studies
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets
Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes
Reproducibility of gene expression across generations of Affymetrix microarrays
Detection of biological switches using the method of Gröebner bases
Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data
barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection
A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells
NIPS workshop on New Problems and Methods in Computational Biology
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
ChIPbinner: an R package for analyzing broad histone marks binned in uniform windows from ChIP-Seq or CUT&RUN/TAG data
ComiRNet: a web-based system for the analysis of miRNA-gene regulatory networks
Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene
Global haplotype partitioning for maximal associated SNP pairs
Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
The sensitivity and significance analysis of parameters in the model of pH regulation on lactic acid production by Lactobacillus bulgaricus
miRA: adaptable novel miRNA identification in plants using small RNA sequencing data
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping
In Silico Evaluation of Predicted Regulatory Interactions in Arabidopsis thaliana
Phase analysis of circadian-related genes in two tissues
Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
Exploiting sparseness in de novo genome assembly
A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes
Oligomeric protein structure networks: insights into protein-protein interactions
Taxonomy-aware feature engineering for microbiome classification
Strategies for analyzing highly enriched IP-chip datasets
PSMIX: an R package for population structure inference via maximum likelihood method
Optimal alpha reduces error rates in gene expression studies: a meta-analysis approach
SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes
In-silico prediction of disorder content using hybrid sequence representation
Data-driven encoding for quantitative genetic trait prediction
Improving protein fold recognition using the amalgamation of evolutionary-based and structural based information
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses
Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets
CONAN: copy number variation analysis software for genome-wide association studies
Orthogonal projections to latent structures as a strategy for microarray data normalization
Amino acid function and docking site prediction through combining disease variants, structure alignments, sequence alignments, and molecular dynamics: a study of the HMG domain
Modeling expression quantitative trait loci in data combining ethnic populations
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics
A knowledge-based decision support system in bioinformatics: an application to protein complex extraction
Structuring and extracting knowledge for the support of hypothesis generation in molecular biology
Estimation of sequencing error rates in short reads
TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas
Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps
Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data
Bacillus anthracis genome organization in light of whole transcriptome sequencing
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation
Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality
Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR
ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently
phyloXML: XML for evolutionary biology and comparative genomics
WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis
A sui generis QA approach using RoBERTa for adverse drug event identification
Prediction of protein structural class with Rough Sets
Recruitment of rare 3 -grams at functional sites: Is this a mechanism for increasing enzyme specificity?
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories
Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis
A Formal MIM Specification and Tools for the Common Exchange of MIM Diagrams: an XML-Based Format, an API, and a Validation Method
BBCAnalyzer: a visual approach to facilitate variant calling
PCA-based population structure inference with generic clustering algorithms
solGS: a web-based tool for genomic selection
Improved prediction of gene expression through integrating cell signalling models with machine learning
Semi-automatic conversion of BioProp semantic annotation to PASBio annotation
ZDOG: zooming in on dominating genes with mutations in cancer pathways
Expression cartography of human tissues using self organizing maps
Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes
Translation regulation by RNA stem-loops can reduce gene expression noise
Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications
GeNESiS: gene network evolution simulation software
SPdb - a signal peptide database
High-resolution genetic mapping with pooled sequencing
A theoretical entropy score as a single value to express inhibitor selectivity
A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality
CoSMoS: Conserved Sequence Motif Search in the proteome
An integrated approach to understand apicomplexan metabolism from their genomes
NGS data vectorization, clustering, and finding key codons in SARS-CoV-2 variations
Digital sorting of complex tissues for cell type-specific gene expression profiles
clonevdjseq: A workflow and bioinformatics management system for sequencing, archiving, and analysis of VDJ sequences from clonal libraries
Weakly supervised learning of biomedical information extraction from curated data
A supervised learning method for classifying methylation disorders
Random generalized linear model: a highly accurate and interpretable ensemble predictor
A covert authentication and security solution for GMOs
uPEPperoni: An online tool for upstream open reading frame location and analysis of transcript conservation
MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets
Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines
General deep learning model for detecting diabetic retinopathy
Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Weakly supervised video-based cardiac detection for hypertensive cardiomyopathy
SynBioTools: a one-stop facility for searching and selecting synthetic biology tools
Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data
hsegHMM: hidden Markov model-based allele-specific copy number alteration analysis accounting for hypersegmentation
Microarray scanner calibration curves: characteristics and implications
SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis
RDFScape: Semantic Web meets Systems Biology
A quantitatively-modeled homozygosity mapping algorithm, qHomozygosityMapping, utilizing whole genome single nucleotide polymorphism genotyping data
Predicting nucleosome positioning using a duration Hidden Markov Model
Sequence Analysis In Promoter Regions
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes
EzMAP: Easy Microbiome Analysis Platform
FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
Menoci: lightweight extensible web portal enhancing data management for biomedical research projects
Convergent evolution in structural elements of proteins investigated using cross profile analysis
Correction: Maptcha: an efficient parallel workflow for hybrid genome scaffolding
FluConvert and IniFlu: a suite of integrated software to identify novel signatures of emerging influenza viruses with increasing risk
tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data
Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line
Automated ensemble assembly and validation of microbial genomes
AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
A novel approach to the analysis of Overall Survival (OS) as response with Progression-Free Interval (PFI) as condition based on the RNA-seq expression data in The Cancer Genome Atlas (TCGA)
Shape based kinetic outlier detection in real-time PCR
Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways
A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification
Epi-GTBN: an approach of epistasis mining based on genetic Tabu algorithm and Bayesian network
Spectral estimation in unevenly sampled space of periodically expressed microarray time series data
Data capture in bioinformatics: requirements and experiences with Pedro
ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites
Enhanced protein domain discovery using taxonomy
BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation
A systematic comparison of genome-scale clustering algorithms
BioWMS: a web-based Workflow Management System for bioinformatics
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies
Efficient algorithms for biological stems search
Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
Integrating the interactome and the transcriptome of Drosophila
Modeling gene expression measurement error: a quasi-likelihood approach
Estimation of the methylation pattern distribution from deep sequencing data
A fast read alignment method based on seed-and-vote for next generation sequencing
Human gene expression sensitivity according to large scale meta-analysis
Inferring microRNA and transcription factor regulatory networks in heterogeneous data
InCoB2010 - 9 th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010
Correction: Improving somatic exome sequencing performance by biological replicates
In silico analysis of a family of extracellular polysaccharide deacetylases involved in virulence of pathogenic gram-positive cocci
Shared probe design and existing microarray reanalysis using PICKY
On the potential of models for location and scale for genome-wide DNA methylation data
Measuring similarities between gene expression profiles through new data transformations
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
Stochastic sequence-level model of coupled transcription and translation in prokaryotes
In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase
Metabolic disassembler for understanding and predicting the biosynthetic units of natural products
An extensible six-step methodology to automatically generate fuzzy DSSs for diagnostic applications
SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost
Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling
Bipartite graph-based collaborative matrix factorization method for predicting miRNA-disease associations
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier
AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip (r) platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples
A gene profiling deconvolution approach to estimating immune cell composition from complex tissues
Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach
The relationship between protein sequences and their gene ontology functions
SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database
PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization
ProteinNet: a standardized data set for machine learning of protein structure
Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces
PoSE: visualization of patterns of sequence evolution using PAML and MATLAB
A Bayesian model for gene family evolution
Multi-omic analysis of signalling factors in inflammatory comorbidities
EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction
A lightweight classification of adaptor proteins using transformer networks
Cellstitch: 3D cellular anisotropic image segmentation via optimal transport
Optimised amino acid specific weighting factors for unbound protein docking
Integrating gene set analysis and nonlinear predictive modeling of disease phenotypes using a Bayesian multitask formulation
On the expansion of "dangerous" gene families in vertebrates
RNA secondary structure prediction with convolutional neural networks
Precise detection of rearrangement breakpoints in mammalian chromosomes
Ensemble outlier detection and gene selection in triple-negative breast cancer data
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation
Correction to: The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure
Multiple virtual screening approaches for finding new Hepatitis c virus RNA-dependent RNA polymerase inhibitors: Structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors
Top Scoring Pairs for Feature Selection in Machine Learning and Applications to Cancer Outcome Prediction
Modular composition predicts kinase/substrate interactions
New directions in biomedical text annotation: definitions, guidelines and corpus construction
Probabilistic modeling methods for cell-free DNA methylation based cancer classification
Analysis of nanopore detector measurements using Machine-Learning methods, with application to single-molecule kinetic analysis
Deep-ProBind: binding protein prediction with transformer-based deep learning model
maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
FUSE: a profit maximization approach for functional summarization of biological networks
Robust probabilistic superposition and comparison of protein structures
Exploring the boundaries: gene and protein identification in biomedical text
The effects of multiple features of alternatively spliced exons on the K A /K S ratio test
Corpus annotation for mining biomedical events from literature
Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets
Epiviz: a view inside the design of an integrated visual analysis software for genomics
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
In the light of deep coalescence: revisiting trees within networks