Comparative analysis of commonly used bioinformatics software based on omics

M Xu, C Xu, M Chen, Z Xiao, Y Wang, Y Xu, D Xu - Gene Reports, 2023 - Elsevier
As a widely used technology at the intersection of multiple disciplines in the field of natural
sciences, bioinformatics has received much attention from scholars for its development and …

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data

C Guccione, L Patel, Y Tomofuji, D McDonald… - Nature …, 2025 - nature.com
As next-generation sequencing technologies produce deeper genome coverages at lower
costs, there is a critical need for reliable computational host DNA removal in metagenomic …

Transforming Big Data into AI‐ready data for nutrition and obesity research

DM Thomas, R Knight, JA Gilbert, MC Cornelis… - …, 2024 - Wiley Online Library
Abstract Objective Big Data are increasingly used in obesity and nutrition research to gain
new insights and derive personalized guidance; however, this data in raw form are often not …

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing

NM Ghiasi, M Sadrosadati, H Mustafa… - 2024 ACM/IEEE 51st …, 2024 - ieeexplore.ieee.org
Metagenomics, the study of the genome sequences of diverse organisms in a common
environment, has led to significant advances in many fields. Since the species present in a …

A simple solid media assay for detection of synergy between bacteriophages and antibiotics

E Khong, JJ Oh, JM Jimenez, R Liu… - Microbiology …, 2024 - Am Soc Microbiol
The emergence of antibiotic-resistant bacteria (ARB) has necessitated the development of
alternative therapies to deal with this global threat. Bacteriophages (viruses that target …

Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus)

C Tang-Wing, I Mohanty, MK Bryant, K Makowski… - Msystems, 2024 - journals.asm.org
Gastrointestinal diseases are the most frequently reported clinical problems in captive
common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal …

MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing

NM Ghiasi, M Sadrosadati, H Mustafa… - arXiv preprint arXiv …, 2023 - arxiv.org
Metagenomics has led to significant advancements in many fields. Metagenomic analysis
commonly involves the key tasks of determining the species present in a sample and their …

Salient: Ultra-fast fpga-based short read alignment

B Khaleghi, T Zhang, C Martino… - … Conference on Field …, 2022 - ieeexplore.ieee.org
State-of-the-art high-throughput DNA sequencers output terabytes of short reads that
typically need to be aligned to a reference genome in order to perform downstream …

A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain

L Khatib, SJ Song, AH Dilmore, JG Sanders… - bioRxiv, 2024 - biorxiv.org
Emerging research suggests that diet plays a vital role in shaping the composition and
function of the gut microbiota. While significant efforts have been made to identify general …