[HTML][HTML] Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

J Lloyd-Price, C Arze, AN Ananthakrishnan… - Nature, 2019 - nature.com
Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect
several million individuals worldwide. Crohn's disease and ulcerative colitis are complex …

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

BF Tan, C Ng, JP Nshimyimana, LL Loh… - Frontiers in …, 2015 - frontiersin.org
Water quality is an emergent property of a complex system comprised of interacting
microbial populations and introduced microbial and chemical contaminants. Studies …

Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability

A Uzonyi, D Dierks, R Nir, OS Kwon, U Toth, I Barbosa… - Molecular cell, 2023 - cell.com
Summary N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-
uniformly distributed across the transcriptome, yet the basis for its selective deposition is …

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

P Ma, HM Amemiya, LL He, SJ Gandhi, R Nicol… - Cell, 2023 - cell.com
We introduce BacDrop, a highly scalable technology for bacterial single-cell RNA
sequencing that has overcome many challenges hindering the development of scRNA-seq …

[HTML][HTML] A deep learning approach to antibiotic discovery

JM Stokes, K Yang, K Swanson, W Jin, A Cubillos-Ruiz… - Cell, 2020 - cell.com
Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to
discover new antibiotics. To address this challenge, we trained a deep neural network …

[HTML][HTML] RNA promotes the formation of spatial compartments in the nucleus

SA Quinodoz, JW Jachowicz, P Bhat, N Ollikainen… - Cell, 2021 - cell.com
RNA, DNA, and protein molecules are highly organized within three-dimensional (3D)
structures in the nucleus. Although RNA has been proposed to play a role in nuclear …

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

V Maini Rekdal, EN Bess, JE Bisanz, PJ Turnbaugh… - Science, 2019 - science.org
INTRODUCTION Parkinson's disease is a debilitating neurological condition affecting more
than 1% of the global population aged 60 and above. The primary medication used to treat …

Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine

DF Rojas-Tapias, EM Brown, ER Temple… - Nature …, 2022 - nature.com
Colonization of the intestine by oral microbes has been linked to multiple diseases such as
inflammatory bowel disease and colon cancer, yet mechanisms allowing expansion in this …

[HTML][HTML] Second-strand synthesis-based massively parallel scRNA-seq reveals cellular states and molecular features of human inflammatory skin pathologies

TK Hughes, MH Wadsworth, TM Gierahn, T Do… - Immunity, 2020 - cell.com
High-throughput single-cell RNA-sequencing (scRNA-seq) methodologies enable
characterization of complex biological samples by increasing the number of cells that can be …

Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus

SA Quinodoz, N Ollikainen, B Tabak, A Palla… - Cell, 2018 - cell.com
Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current
methods for studying genome-wide structure are based on proximity ligation. However, this …