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A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

BackgroundThe growing amount of high dimensional biomolecular data has spawned new statistical and computational models for risk prediction and diseas......

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

Background PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they hav......

A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

BackgroundThe field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial int......

ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

Background: The growing power and ever decreasing cost of RNA sequencing (RNASeq) technologies have resulted in an explosion of RNA-Seq data productio......

Predicting tumour content of liquid biopsies from cell-free DNA

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

BackgroundLiquid biopsy is a minimally-invasive method of sampling bodily fluids, capable of revealing evidence of cancer. The distribution of cell-fr......

lifex-ep: a robust and efficient software for cardiac electrophysiology simulations

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

Background: Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the......

Using transfer learning and dimensionality reduction techniques to improve generalisability of machine-learning predictions of mosquito ages from mid-infrared spectra

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

Background: Old mosquitoes are more likely to transmit malaria than young ones. Therefore, accurate prediction of mosquito population age can drastica......

Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

BackgroundIt remains an important challenge to predict the functional consequences or clinical impacts of genetic variants in human diseases, such as ......

Application of sequence semantic and integrated cellular geography approach to study alternative biogenesis of exonic circular RNA

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

BackgroundConcurrent existence of lncRNA and circular RNA at both nucleus and cytosol within a cell at different proportions is well reported. Previou......

In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both in......

Pan-genome de Bruijn graph using the bidirectional FM-index

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

BackgroundPan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes......

MSLP: mRNA subcellular localization predictor based on machine learning techniques

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

Background: Subcellular localization of messenger RNA (mRNAs) plays a pivotal role in the regulation of gene expression, cell migration as well as in ......

BioLegato: a programmable, object-oriented graphic user interface

期刊: BMC BIOINFORMATICS, 2023; 24 (1)

BackgroundBiologists are faced with an ever-changing array of complex software tools with steep learning curves, often run on High Performance Computi......

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