Matt Raybould

You can view my publications on Google Scholar or ResearchGate.

Alternatively, below is an updated list of preprints (papers currently in peer review with a journal, but not yet accepted), peer-reviewed papers, invited articles, and book chapters. *Shared authorship.

Preprints

• Quast, N.P.; Abanades, B.; Guloglu, B.; Karuppiah, V.; Harper, S.; Raybould, M.I.J., Deane, C.M. (2024) T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity. bioRxiv. 10.1101/2024.05.20.594940.

  [Link to Preprint]

Peer-Reviewed Papers

1. Raybould, M.I.J.* and Greenshields-Watson, A.*; Agarwal, P.; Aguilar-Sanjuan, B.; Olsen, T.H.; Turnbull, O.M.; Deane, C.M. (2024) The Observed T cell receptor Space database enables paired-chain repertoire mining, coherence analysis and language modelling. Cell Rep. (Accepted)

   [Link to Preprint; Database]

2. Fischer, K.; Lulla, A.* and So, T.* and Pereyra-Gerber, P.* and Raybould, M.I.J.* and Kohler, T.N.* and Yam-Puc, J.C.*; Kaminski, T.S.; Hughes, R.; Leiss-Maier, F.; Brear, P.; Matheson, N.J.; Deane, C.M.; Hyvonen, M.; Thaventhiran, J.; Hollfelder, F. (2024) Microfluidics-enabled fluorescence-activated cell sorting of single pathogen-specific antibody secreting cells for the rapid discovery of monoclonal antibodies. Nat Biotechnol. doi: 10.1038/s41587-024-02346-5

   [Link to Paper]

3. Gordon, G.; Raybould, M.I.J.; Wong, A.; Deane, C.M. (2024) Prospects for the computational humanization of antibodies and nanobodies. Front Immunol. 15:1399438

   [Link to Review]

4. Theorell, J.; Harrison, R.; Williams, R.; Raybould, M.I.J.; Zhao, M.; Fox, H.; Fower, A.; Miller, G.; Wu, Z.; Browne, E.; Mgbachi, V.; Sun, B.; Mopuri, R.; Li, Y.; Waters, P.; Deane, C.M.; Handel, A.; Makuch, M.; Irani, S.R. (2024) Ultra-high frequencies of peripherally matured LGI1 & CASPR2-reactive B cells characterise the cerebrospinal fluid in autoimmune encephalitis. PNAS. 121(7):e2311049121

   [Link to Paper]

5. Raybould, M.I.J.; Turnbull, O.M.; Suter, A.; Guloglu, B.; Deane, C.M. (2024) Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling. Commun Biol. 7:62.

   [Link to Paper]

6. Abanades, B.* and Olsen, T.H.*; Raybould, M.I.J.; Aguilar-Sanjuan, B.; Wong, W-K.; Georges, G.; Bujotzek, A.; Deane, C.M. (2024) The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures. Nucleic Acids Res. 52(D1):D545-D551.

   [Link to Paper; Database]

7. Spoendlin, F.C.; Abanades, B.; Raybould, M.I.J.; Wong W-K.; Georges, G.; Deane, C.M. (2023) Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope. Front Mol Biosci. 10:1237621.

   [Link to Paper]

8. Raybould, M.I.J.; Nissley, D.A.; Kumar, S.; Deane, C.M. (2023) Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies. Front Immunol. 13:1080596.

   [Link to Paper; Datasets]

9. Schneider, C.; Raybould, M.I.J.; Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372.

   [Link to Paper; SAbDab-Nano]

10. Robinson, S.A.* and Raybould, M.I.J.*; Schneider, C.; Wong, W-K.; Marks, C.; Deane, C.M. (2021) Epitope Profiling using Computational Structural Modelling Demonstrated on Coronavirus-Binding Antibodies. PLoS Comput Biol. 17(12):e1009675.

    [Link to Paper; Code]

11. Raybould, M.I.J.; Rees, A.R.; Deane, C.M. (2021) Current Strategies for Detecting Functional Convergence across B-cell Receptor Repertoires. MAbs. 13(1):1996732.

    [Link to Review]

12. Raybould, M.I.J.; Marks, C.; Kovaltsuk, A.; Lewis, A.P.; Shi, J. & Deane, C.M. (2021) Public Baseline and Shared Response Structures Support the Theory of Antibody Repertoire Functional Commonality. PLoS Comput Biol. 17(3):e1008781.

    [Links to Paper; Datasets]

13. Raybould, M.I.J.; Kovaltsuk, A.; Marks, C. & Deane, C.M. (2021) CoV-AbDab: the Coronavirus Antibody Database. Bioinformatics. 37(5):734-735.

    [Links to Paper; Database]

14. Galson, J.D.; Schaetzle, S.; Bashford-Rogers, R.J.M.; Raybould, M.I.J.; Kovaltsuk, A.; Kilpatrick, G.J.; Minter, R.; Finch, D.K.; Dias, J.; James, L.; Thomas, G.; Lee, W.-Y.J.; Betley, J.; Cavlan, O.; Leech, A.; Deane, C.M.; Seoane, J.; Caldas, C.; Pennington, D.; Pfeffer, P.; Osbourn, J. (2020) Deep Sequencing of B cell Receptor Repertoires from COVID-19 Patients Reveals Strong Convergent Immune Signatures. Front Immunol. 11:605170.

    [Link to Paper]

15. Kovaltsuk, A.; Raybould, M.I.J.; Wong, W-K.; Marks, C.; Kelm, S.; Snowden, J.; Trück, J. & Deane, C.M. (2020) Structural Diversity of B-cell Receptor Repertoires along the B-cell Differentiation Axis in Humans and Mice. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1007636.

    [Link to Paper; Code]

16. Raybould, M.I.J.; Marks, C.; Lewis, A.P.; Shi, J.; Bujotzek, A.; Taddese, B. & Deane, C.M. (2020) Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res. 48(1):D383-D388.

    [Links to Paper; Database]

17. Krawczyk, K.; Raybould, M.I.J.; Kovaltsuk, A.; Deane, C.M. (2019) Looking for Therapeutic Antibodies in Next-Generation Sequencing Repositories. MAbs. 11(7):1197-1205.

    [Link to Paper]

18. Raybould, M.I.J.* and Wong, W-K.*; Deane, C.M. (2019) Antibody-Antigen Complex Modelling in the Era of Immunoglobulin Repertoire Sequencing. Mol Syst Des Eng. 4(4):679-688.

    [Link to Review]

19. Raybould, M.I.J.; Marks, C.; Krawczyk, K.; Taddese, B.; Nowak, J.; Lewis, A.P.; Bujotzek, A.; Shi, J.; Deane, C.M. (2019) Five Computational Developability Guidelines for Therapeutic Antibody Profiling. PNAS. 116(10):4025-4030.

    [Links to Paper; Web Application]

Invited Articles

1. Raybould, M.I.J.; Deane C.M. (2019) Structural Information to Aid in silico Therapeutic Antibody Design from Next-Generation Sequencing Repertoires. Am Pharm Rev. 22(5):30-35.

   [Link to Article]

Book Chapters

1. Nissley, D.A.; Raybould, M.I.J.; Deane, C.M.; Kumar, S. (2024) Use of Molecular Simulations to Understand Structural Dynamics of Antibodies. Chapter in: Biopharmaceutical Informatics: Learning to discover developable molecules. [In Press]
2. Raybould, M.I.J.; Deane C.M. (2022) The Therapeutic Antibody Profiler for Computational Developability Assessment. Chapter in: Therapeutic Antibodies (Methods in Molecular Biology). vol 2313, pp. 115-125.

   [Link to Chapter]

Upcoming:

The Antibody Series, Madeira (Portugal), 4th-6th September. Talk title: "An ecosystem of tools for computational antibody design, including the second-generation Therapeutic Antibody Profiler".

Discngine Meetup 2024, Virtual, 8th October. Panellist.

2024

• Oxford Cancer Immuno-Oncology Network Annual Symposium, Oxford UK. Talk title: "Applying OPIG's computational tools and databases to characterise cancer-associated adaptive immune receptors".
• Antibody Engineering and Therapeutics Europe, London UK. Talk title: "The Second-Generation Therapeutic Antibody Profiler for Computational Developability Triaging and Rational Design".
• Molecular Graphics and Modelling Society: Adaptive Immune Receptors 2024, Oxford UK. Co-organiser.
• Gordon Research Seminar/Conference on Biotherapeutics and Vaccines Development (Galveston TX, USA). Talk and Poster: "Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling".

2023

• Oxford Immunology Symposium. Lightning Talk & Poster: "Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies".
• Keystone Symposium. Joint meetings: Multispecific Immune Cell Engagers for Cancer Immunotherapy" & "Next Generation Antibody Therapeutics: From Discovery to Patient" (Banff AB, Canada).
  Talk & Poster: "Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies".

2022

• Antibody Society Webinar (Virtual). Community engagement talk.
  "How Structure Prediction Can Enhance Antibody Repertoire Sequence Analysis"
• PEGS (Boston MA, USA). Invited talks.
  "Understanding TCR-pMHC Binding Guides TCR Mimetic Antibody Design" and "How structure-based machine learning can drive the development of biotherapeutics"

2021

• NeurIPS, Learning Meaningful Representations of Life track (Virtual). Invited talk.
  "Applications of machine learning for antibody drug discovery"
• European Antibody Congress (Basel, Switzerland). Invited talk.
  "Epitope profiling of coronavirus-binding antibodies using computational structural modelling"
• RSC Antibody Workshop, CICAG (Virtual). Community engagement talk.
  "The OPIG Antibody Modeling Tools"
• Meeting Minds Global (Virtual). Outreach talk.
  "How a database of coronavirus-binding antibodies (CoV-AbDab) can help us control SARS-CoV-2"
• CASSS Higher Order Structure (Virtual). Invited talk.
  "Five computational developability guidelines for therapeutic antibody profiling"

2020

• BioDataScience101 (Virtual). Invited talk.
  "Antibody sequence analysis to better understand SARS-CoV-2 infection"
• European Antibody Congress (Virtual). Invited talk.
  "Public Baseline and Shared Response Structures and their Application for Screening Library Design"
• Intelligent Systems in Molecular Biology (Virtual). Accepted talks.
  "CoV-AbDab: the Coronavirus Antibody Database"
  "Evidence for Antibody Functional Convergence through Public Baseline and Shared Response Structures"

2018

• Intelligent Systems in Molecular Biology (Chicago IL, USA). Poster.
  "The Therapeutic Antibody Profiler; Five Computational Developability Guidelines"