Leveraging human microbiomes for disease prediction and treatment

HA Tegegne, TC Savidge - Trends in Pharmacological Sciences, 2024 - cell.com
The human microbiome consists of diverse microorganisms that inhabit various body sites.
As these microbes are increasingly recognized as key determinants of health, there is …

Graph-based self-supervised learning for repeat detection in metagenomic assembly

A Azizpour, A Balaji, TJ Treangen, S Segarra - Genome research, 2024 - genome.cshlp.org
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome
assembly and sequence alignment. This is particularly true for metagenomic data, in which …

[HTML][HTML] Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses

G Banerjee, SR Papri, P Banerjee - STAR protocols, 2024 - Elsevier
Constructing metagenome-assembled genomes (MAGs) from complex metagenomic
samples involves a series of bioinformatics operations, each requiring deep bioinformatics …

Capturing variation in metagenomic assembly graphs with MetaCortex

S Martin, M Ayling, L Patrono, M Caccamo… - …, 2023 - academic.oup.com
Motivation The assembly of contiguous sequence from metagenomic samples presents a
particular challenge, due to the presence of multiple species, often closely related, at varying …

KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome

N Sapoval, M Tanevski… - Pacific Symposium on …, 2024 - pmc.ncbi.nlm.nih.gov
The microbes present in the human gastrointestinal tract are regularly linked to human
health and disease outcomes. Thanks to technological and methodological advances in …

SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens

A Balaji, Y Liu, MG Nute, B Hu, A D. Kappell… - Proceedings of the 14th …, 2023 - dl.acm.org
The COVID-19 pandemic forever underscored the need for bio-surveillance platforms
capable of rapidly detecting emerging pathogens. Oxford Nanopore Technology (ONT) …

Scalable Implicit Graphon Learning

A Azizpour, N Zilberstein, S Segarra - arxiv preprint arxiv:2410.17464, 2024 - arxiv.org
Graphons are continuous models that represent the structure of graphs and allow the
generation of graphs of varying sizes. We propose Scalable Implicit Graphon Learning …

[HTML][HTML] Substitution of Soybean Meal with Azolla pinnata Meal Improves Gut Histomorphology and Growth Performance in Commercial Broilers

FU Khan, R Ullah, L Kinkpe, SU Hassan… - Brazilian Journal of …, 2024 - SciELO Brasil
The rising cost and environmental impact of conventional protein sources in poultry feed
necessitate exploration of sustainable alternatives. Azolla pinnata (AP), a nutrient-rich …

GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly

A Azizpour, A Balaji, TJ Treangen… - … Conference on Research …, 2024 - Springer
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome
assembly and sequence alignment. This is particularly true for metagenomic data, where …

SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens

A Balaji, Y Liu, MG Nute, B Hu, A Kappell… - bioRxiv, 2023 - biorxiv.org
The COVID-19 pandemic forever underscored the need for biosurveillance platforms
capable of rapid detection of previously unseen pathogens. Oxford Nanopore Technology …