Related papers: The Phylogenetic LASSO and the Microbiome
The advances of next-generation sequencing technology have accelerated study of the microbiome and stimulated the high throughput profiling of metagenomes. The large volume of sequenced data has encouraged the rise of various studies for…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
Next-generation sequencing technologies have enhanced the scope of Internet-of-Things (IoT) to include genomics for personalized medicine through the increased availability of an abundance of genome data collected from heterogeneous sources…
There is a growing awareness of the important roles that microbial communities play in complex biological processes. Modern investigation of these often uses next generation sequencing of metagenomic samples to determine community…
The widespread collection of data from mobile and wearable devices has created unprecedented opportunities to study human behavior in fine temporal resolution. One common structure for such data is categorical sequences: ordered,…
Background: Understanding the relationship between the Omics and the phenotype is a central problem in precision medicine. The high dimensionality of metabolomics data challenges learning algorithms in terms of scalability and…
The Lasso has become a benchmark data analysis procedure, and numerous variants have been proposed in the literature. Although the Lasso formulations are stated so that overall prediction error is optimized, no full control over the…
Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
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 last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
Access to individual-level health data is essential for gaining new insights and advancing science. In particular, modern methods based on artificial intelligence rely on the availability of and access to large datasets. In the health…
Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global alignment algorithms…
Recent advances in high-throughput sequencing technologies have enabled the extraction of multiple features that depict patient samples at diverse and complementary molecular levels. The generation of such data has led to new challenges in…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
High-throughput microarray and sequencing technology have been used to identify disease subtypes that could not be observed otherwise by using clinical variables alone. The classical unsupervised clustering strategy concerns primarily the…
The intricate relationship between genetic variation and human diseases has been a focal point of medical research, evidenced by the identification of risk genes regarding specific diseases. The advent of advanced genome sequencing…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
This paper studies high-dimensional regression models with lasso when data is sampled under multi-way clustering. First, we establish convergence rates for the lasso and post-lasso estimators. Second, we propose a novel inference method…