Analyzing high-dimensional cytometry data using FlowSOM

K Quintelier, A Couckuyt, A Emmaneel, J Aerts… - Nature protocols, 2021 - nature.com
The dimensionality of cytometry data has strongly increased in the last decade, and in many
situations the traditional manual downstream analysis becomes insufficient. The field is …

HIV–host cell interactions

SK Masenga, BC Mweene, E Luwaya, L Muchaili… - Cells, 2023 - mdpi.com
The development of antiretroviral drugs (ARVs) was a great milestone in the management of
HIV infection. ARVs suppress viral activity in the host cell, thus minimizing injury to the cells …

Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination

RK Suryawanshi, IP Chen, T Ma, AM Syed, N Brazer… - Nature, 2022 - nature.com
Abstract SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although
individuals infected with Delta are at risk of developing severe lung disease, infection with …

SARS-CoV-2-specific T cells exhibit phenotypic features of helper function, lack of terminal differentiation, and high proliferation potential

J Neidleman, X Luo, J Frouard, G Xie, G Gill… - Cell Reports …, 2020 - cell.com
Summary Convalescing coronavirus disease 2019 (COVID-19) patients mount robust T cell
responses against SARS-CoV-2, suggesting an important role of T cells in viral clearance …

[HTML][HTML] Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19

J Neidleman, X Luo, AF George, M McGregor, J Yang… - Cell Reports, 2021 - cell.com
Although T cells are likely players in severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) immunity, little is known about the phenotypic features of SARS-CoV-2 …

mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status

J Neidleman, X Luo, M McGregor, G Xie, V Murray… - Elife, 2021 - elifesciences.org
While mRNA vaccines are proving highly efficacious against SARS-CoV-2, it is important to
determine how booster doses and prior infection influence the immune defense they elicit …

Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

J Neidleman, X Luo, J Frouard, G Xie, F Hsiao, T Ma… - Elife, 2020 - elifesciences.org
The latent reservoir is a major barrier to HIV cure. As latently infected cells cannot be
phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we …

Single-cell glycomics analysis by CyTOF-Lec reveals glycan features defining cells differentially susceptible to HIV

T Ma, M McGregor, L Giron, G Xie, AF George… - Elife, 2022 - elifesciences.org
High-parameter single-cell phenotyping has enabled in-depth classification and
interrogation of immune cells, but to date has not allowed for glycan characterization. Here …

Endometrial responses to bacterial and viral infection: a scoping review

CV Lindsay, JA Potter, AA Grimshaw… - Human …, 2023 - academic.oup.com
BACKGROUND The endometrium is a highly dynamic tissue that undergoes dramatic
proliferation and differentiation monthly in order to prepare the uterus for implantation and …

Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood

J Vallvé-Juanico, AF George, S Sen, R Thomas… - BMC medicine, 2022 - Springer
Background Endometriosis is a chronic, estrogen-dependent disorder where inflammation
contributes to disease-associated symptoms of pelvic pain and infertility. Immune …