[HTML][HTML] A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

DJ Ahern, Z Ai, M Ainsworth, C Allan, A Allcock… - Cell, 2022 - cell.com
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete
description of specific immune biomarkers. We present here a comprehensive multi-omic …

Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history

H Hornsby, AR Nicols, S Longet, C Liu, A Tomic… - Nature …, 2023 - nature.com
Pronounced immune escape by the SARS-CoV-2 Omicron variant has resulted in many
individuals possessing hybrid immunity, generated through a combination of vaccination …

The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires

M Pavlović, L Scheffer, K Motwani, C Kanduri… - Nature Machine …, 2021 - nature.com
Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as
they record past and ongoing adaptive immune responses. The capacity of machine …

A spatially resolved single-cell lung atlas integrated with clinical and blood signatures distinguishes COVID-19 disease trajectories

J Da Silva Filho, V Herder, MP Gibbins… - Science Translational …, 2024 - science.org
COVID-19 is characterized by a broad range of symptoms and disease trajectories.
Understanding the correlation between clinical biomarkers and lung pathology during acute …

Robustness and reproducibility for AI learning in biomedical sciences: RENOIR

A Barberis, HJWL Aerts, FM Buffa - Scientific Reports, 2024 - nature.com
Artificial intelligence (AI) techniques are increasingly applied across various domains,
favoured by the growing acquisition and public availability of large, complex datasets …

[HTML][HTML] Systems immunology: revealing influenza immunological imprint

A Tomic, AJ Pollard, MM Davis - Viruses, 2021 - mdpi.com
Understanding protective influenza immunity and identifying immune correlates of protection
poses a major challenge and requires an appreciation of the immune system in all of its …

Divergent trajectories of antiviral memory after SARS-CoV-2 infection

A Tomic, DT Skelly, A Ogbe, D O'Connor… - Nature …, 2022 - nature.com
The trajectories of acquired immunity to severe acute respiratory syndrome coronavirus 2
infection are not fully understood. We present a detailed longitudinal cohort study of UK …

ProPythia: A Python package for protein classification based on machine and deep learning

AM Sequeira, D Lousa, M Rocha - Neurocomputing, 2022 - Elsevier
The field of protein data mining has been growing rapidly in the last years. To characterize
proteins and determine their function from their amino acid sequences are challenging and …

Evaluating the immune response in treatment-naive hospitalised patients with influenza and COVID-19

J Legebeke, J Lord, R Penrice-Randal… - Frontiers in …, 2022 - frontiersin.org
The worldwide COVID-19 pandemic has claimed millions of lives and has had a profound
effect on global life. Understanding the body's immune response to SARS-CoV-2 infection is …

Disease trajectories in hospitalized COVID-19 patients are predicted by clinical and peripheral blood signatures representing distinct lung pathologies

J Da Silva Filho, V Herder, MP Gibbins, MF dos Reis… - MedRxiv, 2023 - medrxiv.org
Linking clinical biomarkers and lung pathology still is necessary to understand COVID-19
pathogenesis and the basis of progression to lethal outcomes. Resolving these knowledge …