Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Applications of single-cell RNA sequencing in drug discovery and development

B Van de Sande, JS Lee, E Mutasa-Gottgens… - Nature Reviews Drug …, 2023 - nature.com
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods,
together with associated computational tools and the growing availability of public data …

Single-cell spatial landscapes of the lung tumour immune microenvironment

M Sorin, M Rezanejad, E Karimi, B Fiset, L Desharnais… - Nature, 2023 - nature.com
Single-cell technologies have revealed the complexity of the tumour immune
microenvironment with unparalleled resolution,,,,,,,–. Most clinical strategies rely on …

T cell responses to SARS-CoV-2

A Sette, J Sidney, S Crotty - Annual review of immunology, 2023 - annualreviews.org
A large body of evidence generated in the last two and a half years addresses the roles of T
cells in SARS-CoV-2 infection and following vaccination. Infection or vaccination induces …

Viral persistence, reactivation, and mechanisms of long COVID

B Chen, B Julg, S Mohandas, SB Bradfute - Elife, 2023 - elifesciences.org
The COVID-19 global pandemic caused by the severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) infection has infected hundreds of millions of individuals …

SARS-CoV-2 pathogenesis

MM Lamers, BL Haagmans - Nature reviews microbiology, 2022 - nature.com
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has
caused a devastating pandemic. Although most people infected with SARS-CoV-2 develop …

Dictionary learning for integrative, multimodal and scalable single-cell analysis

Y Hao, T Stuart, MH Kowalski, S Choudhary… - Nature …, 2024 - nature.com
Map** single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

Impact of the Human Cell Atlas on medicine

JE Rood, A Maartens, A Hupalowska, SA Teichmann… - Nature medicine, 2022 - nature.com
Single-cell atlases promise to provide a 'missing link'between genes, diseases and
therapies. By identifying the specific cell types, states, programs and contexts where disease …

Pathological sequelae of long-haul COVID

S Mehandru, M Merad - Nature immunology, 2022 - nature.com
The world continues to contend with successive waves of coronavirus disease 2019 (COVID-
19), fueled by the emergence of viral variants. At the same time, persistent, prolonged and …

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities

S Müller-Dott, E Tsirvouli, M Vazquez… - Nucleic Acids …, 2023 - academic.oup.com
Gene regulation plays a critical role in the cellular processes that underlie human health and
disease. The regulatory relationship between transcription factors (TFs), key regulators of …