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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Future Blog Post
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Blog Post number 4
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
Portfolio item number 1
Published:
Short description of portfolio item number 1
Portfolio item number 2
Published:
Short description of portfolio item number 2
publications
Paper Title Number 1
Published in Journal 1, 2009
This paper is about the number 1. The number 2 is left for future work.
Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1).
Download Paper | Download Slides | Download Bibtex
Paper Title Number 2
Published in Journal 1, 2010
This paper is about the number 2. The number 3 is left for future work.
Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2).
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Paper Title Number 3
Published in Journal 1, 2015
This paper is about the number 3. The number 4 is left for future work.
Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3).
Download Paper | Download Slides
Alkynyl benzoxazines and dihydroquinazolines as cysteine targeting covalent warheads and their application in identification of selective irreversible kinase inhibitors
Published in Journal of the American Chemical Society, 2020
Recommended citation: Kirsten McAulay, Emily Hoyt, Morgan Thomas, Marianne Schimpl, Michael Bodnarchuk, Hilary Lewis, Derek Barratt, Deepa Bhavsar, David Robinson, Michael Deery, others, "'Alkynyl benzoxazines and dihydroquinazolines as cysteine targeting covalent warheads and their application in identification of selective irreversible kinase inhibitors.' Journal of the American Chemical Society, 2020.
Discovery of a heme-binding domain in a neuronal voltage-gated potassium channel
Published in Journal of Biological Chemistry, 2020
Recommended citation: Mark Burton, Joel Cresser-Brown, Morgan Thomas, Nicola Portolano, Jaswir Basran, Samuel Freeman, Hanna Kwon, Andrew Bottrill, Manuel Llansola-Portoles, Andrew Pascal, others, "'Discovery of a heme-binding domain in a neuronal voltage-gated potassium channel.' Journal of Biological Chemistry, 2020.
Applications of artificial intelligence in drug design: opportunities and challenges
Published in Artificial Intelligence in Drug Design, 2021
Recommended citation: Morgan Thomas, Andrew Boardman, Miguel Garcia-Ortegon, Hongbin Yang, Chris Graaf, Andreas Bender, "'Applications of artificial intelligence in drug design: opportunities and challenges.' Artificial Intelligence in Drug Design, 2021.
Comparison of structure-and ligand-based scoring functions for deep generative models: a GPCR case study
Published in Journal of cheminformatics, 2021
Recommended citation: Morgan Thomas, Robert Smith, Noel O’Boyle, Chris Graaf, Andreas Bender, "'Comparison of structure-and ligand-based scoring functions for deep generative models: a GPCR case study.' Journal of cheminformatics, 2021.
Diversity-orientated synthesis of macrocyclic heterocycles using a double SN Ar approach
Published in Organic & Biomolecular Chemistry, 2021
Recommended citation: Piotr Raubo, Rodrigo Carbajo, William McCoull, Joanna Raubo, Morgan Thomas, "'Diversity-orientated synthesis of macrocyclic heterocycles using a double SN Ar approach.' Organic & Biomolecular Chemistry, 2021.
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation
Published in Journal of cheminformatics, 2022
Recommended citation: Morgan Thomas, Noel O’Boyle, Andreas Bender, Chris De, "'Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation.' Journal of cheminformatics, 2022.
PARP inhibition is a modulator of anti-tumor immune response in BRCA-deficient tumors
Published in Oncoimmunology, 2022
Recommended citation: Anna Staniszewska, Joshua Armenia, Matthew King, Chrysiis Michaloglou, Avinash Reddy, Maneesh Singh, Maryann San, Laura Prickett, Zena Wilson, Theresa Proia, others, "'PARP inhibition is a modulator of anti-tumor immune response in BRCA-deficient tumors.' Oncoimmunology, 2022.
Re-evaluating sample efficiency in de novo molecule generation
Published in arXiv preprint arXiv:2212.01385, 2022
Recommended citation: Morgan Thomas, Noel O'Boyle, Andreas Bender, Chris De, "'Re-evaluating sample efficiency in de novo molecule generation.' arXiv preprint arXiv:2212.01385, 2022.
Integrating structure-based approaches in generative molecular design
Published in Current Opinion in Structural Biology, 2023
Recommended citation: Morgan Thomas, Andreas Bender, Chris Graaf, "'Integrating structure-based approaches in generative molecular design.' Current Opinion in Structural Biology, 2023.
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data
Published in Journal of Cheminformatics, 2023
Recommended citation: Koichi Handa, Morgan Thomas, Michiharu Kageyama, Takeshi Iijima, Andreas Bender, "'On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data.' Journal of Cheminformatics, 2023.
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery
Published in Journal of Chemical Information and Modeling, 2024
Recommended citation: Albert Bou, Morgan Thomas, Sebastian Dittert, Carles Navarro, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, others, "'ACEGEN: Reinforcement learning of generative chemical agents for drug discovery.' Journal of Chemical Information and Modeling, 2024.
Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential
Published in Journal of Chemical Information and Modeling, 2024
Recommended citation: Sonja Peter, Lydia Siragusa, Morgan Thomas, Tommaso Palomba, Simon Cross, Noel O’Boyle, D{\'a}vid Bajusz, György Ferenczy, György Keserű, Giovanni Bottegoni, others, "'Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential.' Journal of Chemical Information and Modeling, 2024.
Modern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learning
Published in , 2024
Recommended citation: Morgan Thomas, Pierre Matricon, Robert Gillespie, Maja Napi{\'o}rkowska, Hannah Neale, Jonathan Mason, Jason Brown, Charlotte Fieldhouse, Nigel Swain, Tian Geng, others, "'Modern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learning.' , 2024.
MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design
Published in Journal of Cheminformatics, 2024
Recommended citation: Morgan Thomas, Noel O’Boyle, Andreas Bender, Chris De, "'MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design.' Journal of Cheminformatics, 2024.
PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models
Published in Journal of Cheminformatics, 2024
Recommended citation: Morgan Thomas, Mazen Ahmad, Gary Tresadern, Gianni De, "'PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models.' Journal of Cheminformatics, 2024.
Paper Title Number 4
Published in GitHub Journal of Bugs, 2024
This paper is about fixing template issue #693.
Recommended citation: Your Name, You. (2024). "Paper Title Number 3." GitHub Journal of Bugs. 1(3).
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REINFORCE-ING Chemical Language Models in Drug Design
Published in arXiv preprint arXiv:2501.15971, 2025
Recommended citation: Morgan Thomas, Albert Bou, Gianni De, "'REINFORCE-ING Chemical Language Models in Drug Design.' arXiv preprint arXiv:2501.15971, 2025.
Test-Time Training Scaling for Chemical Exploration in Drug Design
Published in arXiv preprint arXiv:2501.19153, 2025
Recommended citation: Morgan Thomas, Albert Bou, Gianni De, "'Test-Time Training Scaling for Chemical Exploration in Drug Design.' arXiv preprint arXiv:2501.19153, 2025.
talks
Identifying Novel Nanomolar A2A Receptor Ligands by Combining Docking and Reinforcement Learning
Published:
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.