Matter & Antimatter - ATomic Laboratory

AI-Driven Immunology

by Adriana Tomic | 25 April 2024 | Editorials, Upcoming events | 0 Comments

Contribute to AI-Driven Immunology Special Collection in Oxford Open Immunology Are you at the forefront of AI, computational science, or biomedicine? Atomic Lab invites you to submit your pioneering research to our upcoming Special Collection on AI-Driven Immunology,...

Systems Viral Immunology: Data driven approaches to decipher viral-host interplay

by Adriana Tomic | 20 June 2023 | Editorials | 0 Comments

This Systems Viral Immunology Topic, led by Adriana Tomic in Frontiers in Virology, explores how systems-level approaches can help identify essential pathways in host immune responses to viral infections. By understanding these mechanisms, we can potentially develop...

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

by Adriana Tomic | 26 July 2022 | Publications | 0 Comments

The COVID-19 Multi-omic Blood Atlas (COMBAT) has identified blood hallmarks of COVID-19 involving particular immune cell populations and their development, components of innate and adaptive immunity, and connectivity with the inflammatory response. A...

Obesity Differs from Diabetes Mellitus in Antibody and T Cell Responses Post COVID-19 Recovery.
Ali M, Longet S, Neale I, Rongkard P, Chowdhury FUH, Hill J, Brown A, Laidlaw S, Tipton T, Hoque A, Hassan N, Hackstein CP, Adele S, Akther HD, Abraham P, Paul S, Rahman MM, Alam MM, Parvin S, Hoque Mollah F, Hoque MM, Moore SC, Biswas SK, Turtle L, de Silva TI, Ogbe A, Frater J, Barnes E, Tomic A, Carroll MW, Klenerman P, Kronsteiner B, Chowdhury FR, Dunachie SJ. Clin Exp Immunol. 2024 Apr 20:uxae030. doi: 10.1093/cei/uxae030. Online ahead of print. PMID: 38642547

2023

Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history.
Hornsby H, Nicols AR, Longet S, Liu C, Tomic A, Angyal A, Kronsteiner B, Tyerman JK, Tipton T, Zhang P, Gallis M, Supasa P, Selvaraj M, Abraham P, Neale I, Ali M, Barratt NA, Nell JM, Gustafsson L, Strickland S, Grouneva I, Rostron T, Moore SC, Hering LM, Dobson SL, Bibi S, Mongkolsapaya J, Lambe T, Wootton D, Hall V, Hopkins S, Dong T, Barnes E, Screaton G; PITCH Consortium; Richter A, Turtle L, Rowland-Jones SL, Carroll M, Duncan CJA, Klenerman P, Dunachie SJ, Payne RP, de Silva TI. Nat Commun. 2023 Aug 21;14(1):5065. doi: 10.1038/s41467-023-40592-4. PMID: 37604803
CD4+ and CD8+ T cells and antibodies are associated with protection against Delta vaccine breakthrough infection: a nested case-control study within the PITCH study.
Neale I, Ali M, Kronsteiner B, Longet S, Abraham P, Deeks AS, Brown A, Moore SC, Stafford L, Dobson SL, Plowright M, Newman TAH, Wu MY; Crick COVID Immunity Pipeline; Carr EJ, Beale R, Otter AD, Hopkins S, Hall V, Tomic A, Payne RP, Barnes E, Richter A, Duncan CJA, Turtle L, de Silva TI, Carroll M, Lambe T, Klenerman P, Dunachie S; PITCH Consortium. mBio. 2023 Oct 31;14(5):e0121223. doi: 10.1128/mbio.01212-23. Epub 2023 Sep 1. PMID: 37655880
Obesity Differs from Diabetes Mellitus in Antibody and T Cell Responses Post COVID-19 Recovery
Mohammad Ali, Stephanie Longet, Isabel Neale, Patpong Rongkard, Forhad Uddin Hassan Chowdhury, Jennifer Hill, Anthony Brown, Stephen Laidlaw, Tom Tipton, Ashraful Hoque, Nazia Hassan, Carl-Philipp Hackstein, Sandra Adele, Hossain Delowar Akther, Priyanka Abraham, Shrebash Paul, Md Matiur Rahman, Md Masum Alam, Shamima Parvin, Forhadul Hoque Mollah, Md Mozammel Hoque, Shona C Moore, Subrata K Biswas, Lance Turtle, Thushan I de Silva, Ane Ogbe, John Frater, Eleanor Barnes, Adriana Tomic, Miles W Carroll, Paul Klenerman, Barbara Kronsteiner, Fazle Rabbi Chowdhury, Susanna J Dunachie
medRxiv 2023.06.14.23291375; doi: https://doi.org/10.1101/2023.06.14.23291375

2022

Tomic A, Skelly DT, Ogbe A, O’Connor D, Pace M, Adland E, Alexander F, Ali M, Allott K, Azim Ansari M, Belij-Rammerstorfer S, Bibi S, Blackwell L, Brown A, Brown H, Cavell B, Clutterbuck EA, de Silva T, Eyre D, Lumley S, Flaxman A, Grist J, Hackstein CP, Halkerston R, Harding AC, Hill J, James T, Jay C, Johnson SA, Kronsteiner B, Lie Y, Linder A, Longet S, Marinou S, Matthews PC, Mellors J, Petropoulos C, Rongkard P, Sedik C, Silva-Reyes L, Smith H, Stockdale L, Taylor S, Thomas S, Tipoe T, Turtle L, Vieira VA, Wrin T, Pollard AJ, Lambe T, Conlon CP, Jeffery K, Travis S, Goulder P, Frater J, Mentzer AJ, Stafford L, Carroll MW, James WS, Klenerman P, Barnes E, Dold C, Dunachie SJ. Divergent trajectories of antiviral memory after SARS-CoV-2 infection. Nat Commun. 2022 Mar 10;13(1):1251. doi: 10.1038/s41467-022-28898-1. PubMed PMID: 35273178; PubMed Central PMCID: PMC8913789.

COMBAT consortium. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell. 2022 Mar 3;185(5):916-938.e58. doi: 10.1016/j.cell.2022.01.012. Epub 2022 Jan 21. PubMed PMID: 35216673; PubMed Central PMCID: PMC8776501.

Kotanidis CP, Xie C, Alexander D, Rodrigues JCL, Burnham K, Mentzer A, O’Connor D, Knight J, Siddique M, Lockstone H, Thomas S, Kotronias R, Oikonomou EK, Badi I, Lyasheva M, Shirodaria C, Lumley SF, Constantinides B, Sanderson N, Rodger G, Chau KK, Lodge A, Tsakok M, Gleeson F, Adlam D, Rao P, Indrajeet D, Deshpande A, Bajaj A, Hudson BJ, Srivastava V, Farid S, Krasopoulos G, Sayeed R, Ho LP, Neubauer S, Newby DE, Channon KM, Deanfield J, Antoniades C; COMBAT Consortium; ORFAN investigators. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19. Lancet Digit Health. 2022 Oct;4(10):e705-e716. doi: 10.1016/S2589-7500(22)00132-7. Epub 2022 Aug 26.

Kim Y, Zheng X, Eschke K, Chaudhry MZ, Bertoglio F, Tomić A, Krmpotić A, Hoffmann M, Bar-On Y, Boehme J, Bruder D, Ebensen T, Brunotte L, Ludwig S, Messerle M, Guzman C, Mandelboim O, Hust M, Pöhlmann S, Jonjić S, Čičin-Šain L. MCMV-based vaccine vectors expressing full-length viral proteins provide long-term humoral immune protection upon a single-shot vaccination. Cell Mol Immunol. 2022 Feb;19(2):234-244. doi: 10.1038/s41423-021-00814-5. Epub 2022 Jan 7.

2021

Ramasamy MN, Minassian AM, Ewer KJ, Flaxman AL, Folegatti PM, Owens DR, Voysey M, Aley PK, Angus B, Babbage G, Belij-Rammerstorfer S, Berry L, Bibi S, Bittaye M, Cathie K, Chappell H, Charlton S, Cicconi P, Clutterbuck EA, Colin-Jones R, Dold C, Emary KRW, Fedosyuk S, Fuskova M, Gbesemete D, Green C, Hallis B, Hou MM, Jenkin D, Joe CCD, Kelly EJ, Kerridge S, Lawrie AM, Lelliott A, Lwin MN, Makinson R, Marchevsky NG, Mujadidi Y, Munro APS, Pacurar M, Plested E, Rand J, Rawlinson T, Rhead S, Robinson H, Ritchie AJ, Ross-Russell AL, Saich S, Singh N, Smith CC, Snape MD, Song R, Tarrant R, Themistocleous Y, Thomas KM, Villafana TL, Warren SC, Watson MEE, Douglas AD, Hill AVS, Lambe T, Gilbert SC, Faust SN, Pollard AJ and COVID vaccine group. Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial. Lancet. 2021 Dec 19;396(10267):1979-1993. doi: 10.1016/S0140-6736(20)32466-1.

Barrett JR, Belij-Rammerstorfer S, Dold C, Ewer KJ, Folegatti PM, Gilbride C, Halkerston R, Hill J, Jenkin D, Stockdale L, Verheul MK, Aley PK, Angus B, Bellamy D, Berrie E, Bibi S, Bittaye M, Carroll MW, Cavell B, Clutterbuck EA, Edwards N, Flaxman A, Fuskova M, Gorringe A, Hallis B, Kerridge S, Lawrie AM, Linder A, Liu X, Madhavan M, Makinson R, Mellors J, Minassian A, Moore M, Mujadidi Y, Plested E, Poulton I, Ramasamy MN, Robinson H, Rollier CS, Song R, Snape MD, Tarrant R, Taylor S, Thomas KM, Voysey M, Watson MEE, Wright D, Douglas AD, Green CM, Hill AVS, Lambe T, Gilbert S, Pollard AJ. Author Correction: Phase 1/2 trial of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 with a booster dose induces multifunctional antibody responses. Nat Med. 2021 Jun;27(6):1113. doi: 10.1038/s41591-021-01372-z. PubMed PMID: 33958800; PubMed Central PMCID: PMC8101331.

Ewer KJ, Barrett JR, Belij-Rammerstorfer S, Sharpe H, Makinson R, Morter R, Flaxman A, Wright D, Bellamy D, Bittaye M, Dold C, Provine NM, Aboagye J, Fowler J, Silk SE, Alderson J, Aley PK, Angus B, Berrie E, Bibi S, Cicconi P, Clutterbuck EA, Chelysheva I, Folegatti PM, Fuskova M, Green CM, Jenkin D, Kerridge S, Lawrie A, Minassian AM, Moore M, Mujadidi Y, Plested E, Poulton I, Ramasamy MN, Robinson H, Song R, Snape MD, Tarrant R, Voysey M, Watson MEE, Douglas AD, Hill AVS, Gilbert SC, Pollard AJ, Lambe T. Author Correction: T cell and antibody responses induced by a single dose of ChAdOx1 nCoV-19 (AZD1222) vaccine in a phase 1/2 clinical trial. Nat Med. 2021 Jun;27(6):1116. doi: 10.1038/s41591-021-01363-0. PubMed PMID: 34021278.

Tomic A, Pollard AJ, Davis MM. Systems Immunology: Revealing Influenza Immunological Imprint. Viruses. 2021 May 20;13(5). doi: 10.3390/v13050948. Review. PubMed PMID: 34065617; PubMed Central PMCID: PMC8160800.

Voysey M, Costa Clemens SA, Madhi SA, Weckx LY, Folegatti PM, Aley PK, Angus B, Baillie VL, Barnabas SL, Bhorat QE, Bibi S, Briner C, Cicconi P, Clutterbuck EA, Collins AM, Cutland CL, Darton TC, Dheda K, Dold C, Duncan CJA, Emary KRW, Ewer KJ, Flaxman A, Fairlie L, Faust SN, Feng S, Ferreira DM, Finn A, Galiza E, Goodman AL, Green CM, Green CA, Greenland M, Hill C, Hill HC, Hirsch I, Izu A, Jenkin D, Joe CCD, Kerridge S, Koen A, Kwatra G, Lazarus R, Libri V, Lillie PJ, Marchevsky NG, Marshall RP, Mendes AVA, Milan EP, Minassian AM, McGregor A, Mujadidi YF, Nana A, Padayachee SD, Phillips DJ, Pittella A, Plested E, Pollock KM, Ramasamy MN, Ritchie AJ, Robinson H, Schwarzbold AV, Smith A, Song R, Snape MD, Sprinz E, Sutherland RK, Thomson EC, Török ME, Toshner M, Turner DPJ, Vekemans J, Villafana TL, White T, Williams CJ, Douglas AD, Hill AVS, Lambe T, Gilbert SC, Pollard AJ. Single-dose administration and the influence of the timing of the booster dose on immunogenicity and efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine: a pooled analysis of four randomised trials. Lancet. 2021 Mar 6;397(10277):881-891. doi: 10.1016/S0140-6736(21)00432-3. Epub 2021 Feb 19. PubMed PMID: 33617777; PubMed Central PMCID: PMC7894131.

Barrett JR, Belij-Rammerstorfer S, Dold C, Ewer KJ, Folegatti PM, Gilbride C, Halkerston R, Hill J, Jenkin D, Stockdale L, Verheul MK, Aley PK, Angus B, Bellamy D, Berrie E, Bibi S, Bittaye M, Carroll MW, Cavell B, Clutterbuck EA, Edwards N, Flaxman A, Fuskova M, Gorringe A, Hallis B, Kerridge S, Lawrie AM, Linder A, Liu X, Madhavan M, Makinson R, Mellors J, Minassian A, Moore M, Mujadidi Y, Plested E, Poulton I, Ramasamy MN, Robinson H, Rollier CS, Song R, Snape MD, Tarrant R, Taylor S, Thomas KM, Voysey M, Watson MEE, Wright D, Douglas AD, Green CM, Hill AVS, Lambe T, Gilbert S, Pollard AJ. Phase 1/2 trial of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 with a booster dose induces multifunctional antibody responses. Nat Med. 2021 Feb;27(2):279-288. doi: 10.1038/s41591-020-01179-4. Epub 2020 Dec 17. PubMed PMID: 33335322.

Ewer KJ, Barrett JR, Belij-Rammerstorfer S, Sharpe H, Makinson R, Morter R, Flaxman A, Wright D, Bellamy D, Bittaye M, Dold C, Provine NM, Aboagye J, Fowler J, Silk SE, Alderson J, Aley PK, Angus B, Berrie E, Bibi S, Cicconi P, Clutterbuck EA, Chelysheva I, Folegatti PM, Fuskova M, Green CM, Jenkin D, Kerridge S, Lawrie A, Minassian AM, Moore M, Mujadidi Y, Plested E, Poulton I, Ramasamy MN, Robinson H, Song R, Snape MD, Tarrant R, Voysey M, Watson MEE, Douglas AD, Hill AVS, Gilbert SC, Pollard AJ, Lambe T. T cell and antibody responses induced by a single dose of ChAdOx1 nCoV-19 (AZD1222) vaccine in a phase 1/2 clinical trial. Nat Med. 2021 Feb;27(2):270-278. doi: 10.1038/s41591-020-01194-5. Epub 2020 Dec 17. PubMed PMID: 33335323.

Voysey M, Clemens SAC, Madhi SA, Weckx LY, Folegatti PM, Aley PK, Angus B, Baillie VL, Barnabas SL, Bhorat QE, Bibi S, Briner C, Cicconi P, Collins AM, Colin-Jones R, Cutland CL, Darton TC, Dheda K, Duncan CJA, Emary KRW, Ewer KJ, Fairlie L, Faust SN, Feng S, Ferreira DM, Finn A, Goodman AL, Green CM, Green CA, Heath PT, Hill C, Hill H, Hirsch I, Hodgson SHC, Izu A, Jackson S, Jenkin D, Joe CCD, Kerridge S, Koen A, Kwatra G, Lazarus R, Lawrie AM, Lelliott A, Libri V, Lillie PJ, Mallory R, Mendes AVA, Milan EP, Minassian AM, McGregor A, Morrison H, Mujadidi YF, Nana A, O’Reilly PJ, Padayachee SD, Pittella A, Plested E, Pollock KM, Ramasamy MN, Rhead S, Schwarzbold AV, Singh N, Smith A, Song R, Snape MD, Sprinz E, Sutherland RK, Tarrant R, Thomson EC, Török ME, Toshner M, Turner DPJ, Vekemans J, Villafana TL, Watson MEE, Williams CJ, Douglas AD, Hill AVS, Lambe T, Gilbert SC, Pollard AJ. Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. Lancet. 2021 Jan 9;397(10269):99-111. doi: 10.1016/S0140-6736(20)32661-1.

Tomic A, Tomic I, Waldron L, Geistlinger L, Kuhn M, Spreng RL, Dahora LC, Seaton KE, Tomaras G, Hill J, Duggal NA, Pollock RD, Lazarus NR, Harridge SDR, Lord JM, Khatri P, Pollard AJ, Davis MM. SIMON: Open-Source Knowledge Discovery Platform. Patterns (N Y). 2021 Jan 8;2(1):100178. doi: 10.1016/j.patter.2020.100178. eCollection 2021 Jan 8. PubMed PMID: 33511368; PubMed Central PMCID: PMC7815964.

2020

O’Connor D, Pinto MV, Sheerin D, Tomic A, Drury RE, Channon-Wells S, Galal U, Dold C, Robinson H, Kerridge S, Plested E, Hughes H, Stockdale L, Sadarangani M, Snape MD, Rollier CS, Levin M, Pollard AJ. Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine. Mol Syst Biol. 2020 Nov;16(11):e9888. doi: 10.15252/msb.20209888. PubMed PMID: 33210468; PubMed Central PMCID: PMC7674973.

2019

Tomic A, Tomic I, Dekker CL, Maecker HT, Davis MM. The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system. Sci Data. 2019 Oct 21;6(1):214. doi: 10.1038/s41597-019-0213-4. PubMed PMID: 31636302; PubMed Central PMCID: PMC6803714.

Tomic A, Tomic I, Rosenberg-Hasson Y, Dekker CL, Maecker HT, Davis MM. SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses. J Immunol. 2019 Aug 1;203(3):749-759. doi: 10.4049/jimmunol.1900033. Epub 2019 Jun 14. PubMed PMID: 31201239; PubMed Central PMCID: PMC6643048.

2018

Hammer Q, Rückert T, Borst EM, Dunst J, Haubner A, Durek P, Heinrich F, Gasparoni G, Babic M, Tomic A, Pietra G, Nienen M, Blau IW, Hofmann J, Na IK, Prinz I, Koenecke C, Hemmati P, Babel N, Arnold R, Walter J, Thurley K, Mashreghi MF, Messerle M, Romagnani C. Peptide-specific recognition of human cytomegalovirus strains controls adaptive natural killer cells. Nat Immunol. 2018 May;19(5):453-463. doi: 10.1038/s41590-018-0082-6. Epub 2018 Apr 9. PubMed PMID: 29632329.

2016

Tomić A, Varanasi PR, Golemac M, Malić S, Riese P, Borst EM, Mischak-Weissinger E, Guzmán CA, Krmpotić A, Jonjić S, Messerle M. Activation of Innate and Adaptive Immunity by a Recombinant Human Cytomegalovirus Strain Expressing an NKG2D Ligand. PLoS Pathog. 2016 Dec;12(12):e1006015. doi: 10.1371/journal.ppat.1006015. eCollection 2016 Dec. PubMed PMID: 27907183; PubMed Central PMCID: PMC5131914.

Lenac Rovis T, Kucan Brlic P, Kaynan N, Juranic Lisnic V, Brizic I, Jordan S, Tomic A, Kvestak D, Babic M, Tsukerman P, Colonna M, Koszinowski U, Messerle M, Mandelboim O, Krmpotic A, Jonjic S. Inflammatory monocytes and NK cells play a crucial role in DNAM-1-dependent control of cytomegalovirus infection. J Exp Med. 2016 Aug 22;213(9):1835-50. doi: 10.1084/jem.20151899. Epub 2016 Aug 8. PubMed PMID: 27503073; PubMed Central PMCID: PMC4995080.

2014

Zarama A, Pérez-Carmona N, Farré D, Tomic A, Borst EM, Messerle M, Jonjic S, Engel P, Angulo A. Cytomegalovirus m154 hinders CD48 cell-surface expression and promotes viral escape from host natural killer cell control. PLoS Pathog. 2014 Mar;10(3):e1004000. doi: 10.1371/journal.ppat.1004000. eCollection 2014 Mar. PubMed PMID: 24626474; PubMed Central PMCID: PMC3953435.

2013

Trsan T, Busche A, Abram M, Wensveen FM, Lemmermann NA, Arapovic M, Babic M, Tomic A, Golemac M, Brinkmann MM, Jäger W, Oxenius A, Polic B, Krmpotic A, Messerle M, Jonjic S. Superior induction and maintenance of protective CD8 T cells in mice infected with mouse cytomegalovirus vector expressing RAE-1γ. Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16550-5. doi: 10.1073/pnas.1310215110. Epub 2013 Sep 19. PubMed PMID: 24052528; PubMed Central PMCID: PMC3799388.