Innate Mucosal Sensing & Shaping of the Human Microbiome

A cloaked human stem-cell-derived neural graft capable of functional integration and immune evasion in rodent models

C Pavan, KC Davidson, N Payne, S Frausin, CPJ Hunt, N Moriarty, M Berrocal Rubio, Z Elahi, AT Quattrocchi, KD Abu-Bonsrah, L Wang, W Clow, H Yang, M Pellegrini, CA Wells, LH Thompson, A Nagy, CL Parish

2025-05-01

Human pluripotent stem cell (hPSC)-derived therapies are a realistic possibility for numerous disorders, including Parkinson's dis..

Efficient generation of human dendritic cells from induced pluripotent stem cell by introducing a feeder-free expansion step for hematopoietic progenitors

Z Elahi, V Jameson, M Sakkas, SK Butcher, JD Mintern, KJ Radford, CA Wells

2025-05-01

Dendritic cells (DCs) are rare innate immune cells that are essential regulators of antitumor, antiviral, and vaccine responses by..

Discovery of NRG1-VII: the myeloid-derived class of NRG1

MA Berrocal-Rubio, YDJ Pawer, M Dinevska, R De Paoli-Iseppi, SS Widodo, J Gleeson, N Rajab, W De Nardo, J Hallab, A Li, T Mantamadiotis, MB Clark, CA Wells

2024-08-29

The growth factor Neuregulin-1 (NRG1) has pleiotropic roles in proliferation and differentiation of the stem cell niche in differe..

Stemformatics data portal enables transcriptional benchmarking of lab-derived myeloid cells

J Choi, SK Butcher, PW Angel, J Bransfield, J Barry, N Faux, B Shaban, P Pillai, A Michalewicz, CA Wells

2024-06-11

Stemformatics.org has been serving the stem cell research community for over a decade, by making it easy for users to find and vie..

IsoVis - a webserver for visualization and annotation of alternative RNA isoforms

Ching Yin Wan, Jack Davis, Manveer Chauhan, Josie Gleeson, Yair DJ Prawer, Ricardo De Paoli-Iseppi, Christine A Wells, Jarny Choi, Michael B Clark

2024-01-01

Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Maki..

Disease-specific loss of microbial cross-feeding interactions in the human gut

VR Marcelino, C Welsh, C Diener, EL Gulliver, EL Rutten, RB Young, EM Giles, SM Gibbons, C Greening, SC Forster

2023-12-01

Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feedi..

The status of the human gene catalogue.

Paulo Amaral, Silvia Carbonell-Sala, Francisco M De La Vega, Tiago Faial, Adam Frankish, Thomas Gingeras, Roderic Guigo, Jennifer L Harrow, Artemis G Hatzigeorgiou, Rory Johnson, Terence D Murphy, Mihaela Pertea, Kim D Pruitt, Shashikant Pujar, Hazuki Takahashi, Igor Ulitsky, Ales Varabyou, Christine A Wells, Mark Yandell, Piero Carninci

2023-10-01

Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years..

Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease

GL D'Adamo, M Chonwerawong, LJ Gearing, VR Marcelino, JA Gould, EL Rutten, SM Solari, PWR Khoo, TJ Wilson, T Thomason, EL Gulliver, PJ Hertzog, EM Giles, SC Forster

2023-07-18

Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolut..

Extensive genome analysis identifies novel plasmid families in Clostridium perfringens

EL Gulliver, V Adams, VR Marcelino, J Gould, EL Rutten, DR Powell, RB Young, GL D’adamo, J Hemphill, SM Solari, SA Revitt-Mills, S Munn, T Jirapanjawat, C Greening, JC Boer, KL Flanagan, M Kaldhusdal, M Plebanski, KB Gibney, RJ Moore

2023-04-01

Globally, the anaerobic bacterium Clostridium perfringens causes severe disease in a wide array of hosts; however, C. perfrin-gens..

The Human Dendritic Cell Atlas: An Integrated Transcriptional Tool to Study Human Dendritic Cell Biology

Z Elahi, PW Angel, SK Butcher, N Rajab, J Choi, Y Deng, JD Mintern, K Radford, CA Wells

2022-12-15

Dendritic cells (DCs) are functionally diverse and are present in most adult tissues, but deep understanding of human DC biology i..

Manipulation of epithelial cell architecture by the bacterial pathogens Listeria and Shigella

EL Hartland, D Ghosal, C Giogha

2022-12-01

Subversion of the host cell cytoskeleton is a virulence attribute common to many bacterial pathogens. On mucosal surfaces, bacteri..

expam - high-resolution analysis of metagenomes using distance trees

SM Solari, RB Young, VR Marcelino, SC Forster

2022-10-15

Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented res..

Access and Visualise High Quality Gene Expression Data with Stemformatics

J Choi, CA Wells

2022-01-01

Stemformatics is an established online gene expression data portal containing hundreds of carefully curated and annotated datasets..

The microbiome and host mucosal interactions in urinary tract diseases

B Jones-Freeman, M Chonwerawong, VR Marcelino, AV Deshpande, SC Forster, MR Starkey

2021-07-01

The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of ..

Key Technologies for Progressing Discovery of Microbiome-Based Medicines

RB Young, VR Marcelino, M Chonwerawong, EL Gulliver, SC Forster

2021-06-22

A growing number of experimental and computational approaches are illuminating the “microbial dark matter” and uncovering the inte..

An integrated analysis of human myeloid cells identifies gaps in in vitro models of in vivo biology

N Rajab, PW Angel, Y Deng, J Gu, V Jameson, M Kurowska-Stolarska, S Milling, CM Pacheco, M Rutar, AL Laslett, KA Lê Cao, J Choi, CA Wells

2021-06-08

The Stemformatics myeloid atlas is an integrated transcriptome atlas of human macrophages and dendritic cells that systematically ..

A simple, scalable approach to building a cross-platform transcriptome atlas

PW Angel, N Rajab, Y Deng, CM Pacheco, T Chen, KA Lê Cao, J Choi, CA Wells

2020-09-01

Gene expression atlases have transformed our understanding of the development, composition and function of human tissues. New tech..