Related papers: A new method for identifying vertebrates using onl…
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by progressive cognitive decline and widespread epigenetic dysregulation in the brain. DNA methylation, as a stable yet dynamic epigenetic modification,…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…
Purpose: To use and test a labelling algorithm that operates on two-dimensional (2D) reformations, rather than three-dimensional (3D) data to locate and identify vertebrae. Methods: We improved the Btrfly Net (described by Sekuboyina et al)…
Deep learning (DL) techniques have shown unprecedented success when applied to images, waveforms, and text. Generally, when the sample size ($N$) is much bigger than the number of features ($d$), DL often outperforms other machine learning…
Reliable vertebrae annotations are key to perform analysis of spinal X-ray images. However, obtaining annotation of vertebrae from those images is usually carried out manually due to its complexity (i.e. small structures with varying…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of…
Mitochondrial diseases are currently untreatable due to our limited understanding of their pathology. We study the expression of various mitochondrial proteins in skeletal myofibres (SM) in order to discover processes involved in…
This study analyzes rates and ways of data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on human ancient DNA published between 1988 and 2013. For the most part, data are available in…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
The vertebral levels of the spine provide a useful coordinate system when making measurements of plaque, muscle, fat, and bone mineral density. Correctly classifying vertebral levels with high accuracy is challenging due to the similar…
Several studies suggest strong correlation between different types of cancer and the relative concentration of short circulating RNA sequences (miRNA). Because of short length and low concentration, miRNA detection is not easy. Standard…
Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the…
Understanding how biological communities respond to environmental changes is a key challenge in ecology and ecosystem management. The apparent decline of insect populations necessitates more biomonitoring but the time-consuming sorting and…
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is…
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a biological system is a key element of precision medicine. Indeed it allows to tailor diagnostic, prognostic and treatment choice to individual…
Three-dimensional (3D) ultrasound imaging technique has been applied for scoliosis assessment, but current assessment method only uses coronal projection image and cannot illustrate the 3D deformity and vertebra rotation. The vertebra…