Publications

Mike Phuycharoen, Verena Kaestele, Thomas Williams, Lijing Lin, Tracy Hussell, John Grainger, Magnus Rattray (2026). Integration of unpaired and heterogeneous clinical flow cytometry data. iScience.

Cite DOI URL

Rufus H. Daw, Harry R. Deijnen, Magnus Rattray, John R. Grainger (2026). CellTypeAI: Automated cell identification for scRNA-seq using local generative-AI. openRxiv.

Cite DOI URL

\Robert J\ Maidstone, \A Louise\ Hunter, Mudassar Iqbal, Nicola Begley, Matthew Baxter, \Andrew S I\ Loudon, Magnus Rattray, \David W\ Ray (2026). Glucocorticoid-dependence and independence of the circadian liver transcriptome. npj Biological Timing and Sleep.

Cite DOI

Emine Beyza Çandır, Halil İbrahim Kuru, Magnus Rattray, A Ercument Cicek, Oznur Tastan (2026). One-Hot News: Drug Synergy Models Shortcut Molecular Features. Bioinformatics.

Cite DOI URL

Logan Brase, Declan R. Creamer, Yuliya Shapovalova, Mark P. Ashe, Hilary L. Ashe, Magnus Rattray (2025). Genomic foundation models reveal RNA-binding proteins regulating translation and mRNA degradation during Drosophila development. openRxiv.

Cite DOI URL

Nigel L. Hammond, Syed Murtuza Baker, Amanda McGovern, Antony Adamson, Andrew D Sharrocks, Magnus Rattray, Jill Dixon, Michael J. Dixon (2025). Decoding the Spatial and Epigenetic Logic of Early Skin Development. openRxiv.

Cite DOI URL

Charles Eldrid-Otterburn, Ellie Hawke, Kathleen Cain, Kate Meeson, Joanne Watson, Reynard Spiess, William Smith, Matthew Russell, Robyn Hoare, \John A.\ Raven, Jean-Marc Schwartz, Magnus Rattray, Leon Pybus, Alan Dickson, Andrew Pitt, Perdita Barran (2025). From Discovery to Delivery: A Rapid and Targeted Proteomics Workflow for Monitoring Chinese Hamster Ovary Biomanufacturing. Molecular & Cellular Proteomics.

Cite DOI

\Nigel L\ Hammond, \Syed Murtuza\ Baker, Sokratia Georgaka, Ali Al-Anbaki, Elliot Jokl, Kara Simpson, Rosa Sanchez-Alvarez, \Varinder S\ Athwal, Huw Purssell, \Ajith K\ Siriwardena, \Harry v M\ Spiers, \Mike J\ Dixon, \Leoma D\ Bere, \Adam P\ Jones, \Michael J\ Haley, \Kevin N\ Couper, Nicoletta Bobola, \Andrew D\ Sharrocks, \Neil A\ Hanley, Magnus Rattray, \Karen Piper\ Hanley (2025). Spatial gene regulatory networks driving cell state transitions during human liver disease. EMBO Molecular Medicine.

Cite DOI

M. Ghafoor, JE. Parkinson, T. Pham, TE. Sutherland, M. Rattray (2025). Cell–ECM Graphs: A Graph-Based Method for Joint Analysis of Cells and the Extracellular Matrix. openRxiv.

Cite DOI URL

Kate E. Meeson, Joanne Watson, Susan Rosser, Ellie Hawke, Andrew Pitt, Tessa Moses, Leon Pybus, Magnus Rattray, Alan J. Dickson, Jean‐Marc Schwartz (2025). Flux Sampling Suggests Metabolic Signatures of High Antibody‐Producing CHO Cells. Biotechnology and Bioengineering.

Cite DOI URL

Sokratia Georgaka, William Geraint Morgans, Qian Zhao, Diego Sanchez Martinez, Amin Ali, Mohamed Ghafoor, Syed Murtuza Baker, Robert G Bristow, Mudassar Iqbal, Magnus Rattray (2025). CellPie : a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization. Nucleic Acids Research.

Cite DOI URL

Inti Pagnuco, Stephen Eyre, Magnus Rattray, Andrew Morris (2025). Transferability of Single- and Cross-Tissue Transcriptome Imputation Models Across Ancestry Groups. Genetic Epidemiology.

Cite DOI

Jennifer C Love, Lauren Forbes Beadle, Catherine Sutcliffe, Magnus Rattray, Hilary L Ashe (2025). Spatially regulated mRNA decay sharpens expression patterns in the Drosophila embryo. openRxiv.

Cite DOI URL

Chenfu Shi, Danyun Zhao, Jake Butler, Antonios Frantzeskos, Stefano Rossi, James Ding, Carlo Ferrazzano, Charlotte Wynn, \Ryan Malcolm\ Hum, Ellie Richards, Muskan Gupta, Khadijah Patel, \Chuan Fu\ Yap, Darren Plant, Richard Grencis, Paul Martin, Antony Adamson, Stephen Eyre, John Bowes, Anne Barton, Pauline Ho, Magnus Rattray, Gisela Orozco (2025). Multi-omics analysis in primary T cells elucidates mechanisms behind disease-associated genetic loci. Genome Biology.

Cite DOI

Alastair Pizzey, Catherine Sutcliffe, Jennifer C. Love, Emmanuel Akabuogu, Magnus Rattray, Mark P. Ashe, Hilary L. Ashe (2025). Exploiting the SunTag system to study the developmental regulation of mRNA translation. openRxiv.

Cite DOI URL

Xiaoyu Jiang, Sokratia Georgaka, Magnus Rattray, \Mauricio A.\ Álvarez (2025). Scalable Multi-Output Gaussian Processes with Stochastic Variational Inference. Transactions on Machine Learning Research.

Cite

Charles Eldrid, Ellie Hawke, \Kathleen M.\ Cain, Kate Meeson, Joanne Watson, Reynard Spiess, William Smith, Matthew Russell, Robyn Hoare, John Raven, Jean-Marc Schwartz, Magnus Rattray, Leon Pybus, Alan Dickson, Andrew Pitt, Perdita Barran (2024). From Discovery to Delivery: A Rapid and Targeted Proteomics Workflow for Monitoring Chinese Hamster Ovary Biomanufacturing. ChemRxiv.

Cite DOI

J E Parkinson, M Ghafoor, R J Dodd, H E Tompkins, M Fergie, M Rattray, J E Allen, T E Sutherland (2024). Extracellular matrix phenotyping by imaging mass cytometry defines distinct cellular matrix environments associated with allergic airway inflammation. openRxiv.

Cite DOI URL

Cecile Le Sueur, Magnus Rattray, Mikhail Savitski (2024). GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments. PLOS Computational Biology.

Cite DOI URL

Mauro Tutino, Jenny Hankinson, Clare Murray, Lesley Lowe, Gina Kerry, Magnus Rattray, Adnan Custovic, \Sebastian L.\ Johnston, Chenfu Shi, Gisela Orozco, Stephen Eyre, Paul Martin, Angela Simpson, \John A.\ Curtin (2023). Identification of differences in CD4+ T-cell gene expression between people with asthma and healthy controls. Scientific Reports.

Cite DOI

Haoting Zhang, Carl Henrik Ek, Magnus Rattray, Marta Milo (2023). SynBa: improved estimation of drug combination synergies with uncertainty quantification. Bioinformatics.

Cite DOI URL

Lauren \Forbes Beadle\, Hongpeng Zhou, Magnus Rattray, \Hilary L.\ Ashe (2023). Modulation of transcription burst amplitude underpins dosage compensation in the Drosophila embryo. Cell Reports.

Cite DOI

Lauren Forbes Beadle, Hongpeng Zhou, Magnus Rattray, Hilary L. Ashe (2023). Modulation of transcription burst amplitude underpins dosage compensation in the Drosophila embryo. openRxiv.

Cite DOI URL

Polly Downton, Fabio Sanna, Robert Maidstone, Toryn Poolman, Edward Hayter, Suzanna Dickson, James Early, Antony Adamson, David Spiller, Devin Simpkins, Matthew Baxter, Roman Fischer, Magnus Rattray, Andrew Loudon, Julie Gibbs, David Bechtold, David Ray (2022). Chronic inflammatory arthritis drives systemic changes in circadian energy metabolism. PNAS.

Cite DOI

\Muhammad Zaki Hidayatullah\ Fadlullah, \Wen Hao\ Neo, Michael Lie-a-Ling, Roshana Thambyrajah, Rahima Patel, Renaud Mevel, Irène Aksoy, Nam \Do Khoa\, Pierre Savatier, Laura Fontenille, \Syed Murtuza\ Baker, Magnus Rattray, Valerie Kouskoff, Georges Lacaud (2022). Murine AGM single-cell profiling identifies a continuum of hemogenic endothelium differentiation marked by ACE. Blood.

Cite DOI

Eteri Regis, Sara Fontanella, Lijing Lin, Rebecca Howard, Sadia Haider, \John A.\ Curtin, \Michael R.\ Edwards, Magnus Rattray, Angela Simpson, Adnan Custovic, \Sebastian L.\ Johnston (2021). Sex differences in innate anti-viral immune responses to respiratory viruses and in their clinical outcomes in a birth cohort study. Scientific Reports.

Cite DOI

Jonathan R Bowles, Caroline Hoppe, Hilary L Ashe, Magnus Rattray (2021). Scalable inference of transcriptional kinetic parameters from MS2 time series data. Bioinformatics.

Cite DOI URL

Chenfu Shi, Helen Ray-Jones, James Ding, Kate Duffus, Yao Fu, \Vasanthi Priyadarshini\ Gaddi, Oliver Gough, Jenny Hankinson, Paul Martin, Amanda McGovern, Annie Yarwood, Patrick Gaffney, Steve Eyre, Magnus Rattray, \Richard B\ Warren, Gisela Orozco (2021). Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits. The Journal of Investigative Dermatology.

Cite DOI

Nuha BinTayyash, Sokratia Georgaka, S T John, Sumon Ahmed, Alexis Boukouvalas, James Hensman, Magnus Rattray (2021). Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments. Bioinformatics.

Cite DOI URL

Joshua Burton, Cerys S Manning, Magnus Rattray, Nancy Papalopulu, Jochen Kursawe (2021). Inferring kinetic parameters of oscillatory gene regulation from single cell time series data. Cold Spring Harbor Laboratory.

Cite DOI URL

\Coronavirus Immune Response, \ Clinical Outcomes (CIRCO) Collaborative Group, T Williams, V Kästele, E Mann, S Knight, M Menon, C Jagger, S Khan, J Konkel, T Shaw, M Rattray, L Pearmain, A Horsley, A Ustianowski, I Prise, T Hussell (2021). P058 Persistence of neutrophil abnormalities in COVID-19 convalescence. Rheumatology.

Cite DOI

Laure Bridoux, Peyman Zarrineh, Joshua Mallen, Mike Phuycharoen, Victor Latorre, Frank Ladam, Marta Losa, \Syed Murtuza\ Baker, Charles Sagerstrom, \Kimberly A\ Mace, Magnus Rattray, Nicoletta Bobola (2020). HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation. PLoS Genetics.

Cite DOI

Sam Humphrey, Alastair Kerr, Magnus Rattray, Caroline Dive, Crispin Miller (2020). A model of k-mer surprisal to quantify local sequence information content surrounding splice regions. PeerJ.

Cite DOI

Eteri Regis, Sara Fontanella, Lijing Lin, Rebecca Howard, Sadia Haider, John a Curtin, Michael R Edwards, Magnus Rattray, Angela Simpson, Adnan Custovic, Sebastian L Johnston (2020). Sex differences in innate anti-viral immune responses to respiratory viruses. Cold Spring Harbor Laboratory.

Cite DOI URL

Elizabeth R. Mann, Madhvi Menon, Sean Blandin Knight, Joanne E. Konkel, Christopher Jagger, Tovah N. Shaw, Siddharth Krishnan, Magnus Rattray, Andrew Ustianowski, Nawar Diar Bakerly, Paul Dark, Graham M. Lord, Angela Simpson, Timothy Felton, Ling-Pei Ho, Marc Feldmann, John R. Grainger, Tracy Hussell, And (2020). Longitudinal immune profiling reveals key myeloid signatures associated with COVID-19. Science Immunology.

Cite DOI URL

Chenfu Shi, Magnus Rattray, Anne Barton, John Bowes, Gisela Orozco (2020). Using functional genomics to advance the understanding of psoriatic arthritis. Rheumatology.

Cite DOI URL

Luisa Cutillo, Alexis Boukouvalas, Elli Marinopoulou, Nancy Papalopulu, Magnus Rattray (2020). OscoNet: inferring oscillatory gene networks. BMC Bioinformatics.

Cite DOI

Caroline Hoppe, \Jonathan R.\ Bowles, \Thomas G.\ Minchington, Catherine Sutcliffe, Priyanka Upadhyai, Magnus Rattray, \Hilary L.\ Ashe (2020). Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo. Developmental cell.

Cite DOI

\Respiratory TRC\, CIRCO, \Elizabeth R.\ Mann, Madhvi Menon, \Sean Blandin\ Knight, \Joanne E.\ Konkel, Christopher Jagger, \Tovah N.\ Shaw, Siddharth Krishnan, Magnus Rattray, Andrew Ustianowski, \Nawar Diar\ Bakerly, Paul Dark, Graham Lord, Angela Simpson, Timothy Felton, \Ling Pei\ Ho, Marc Feldmann, \John R.\ Grainger, Tracy Hussell, Rohan Ahmed, \Halima Ali\ Shuwa, Miriam Avery, Katharine Birchall, Oliver Brand, Alistair Chenery, Christine Chew, Richard Clark, Emma Connolly, Hannah Durrington, Helen Francis, Miriam Franklin, \Kathryn J.\ Gray, Seamus Grundy, Mudassar Iqbal, Saba Khan, Sylvia Lui, Lesley Lowe, \Flora A.\ McClure, David Morgan, \Syed Murtuza\ Baker, Laurence Pearmain, Barbora Salcman, \Nicholas A.\ Scott, Seema Sharma, Elizabeth Shepley, Simon Stephan, Ruth Stephens, Thomas Williams, Lisa Willmore, Mehwish Younas, Jane Davies (2020). Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis. medRxiv.

Cite DOI

Stephen Kershaw, David Morgan, James Boyd, David Spiller, Gareth Kitchen, Egor Zindy, Mudassar Iqbal, Magnus Rattray, \Christopher M.\ Sanderson, Andrew Brass, Claus Jorgensen, Tracy Hussell, Laura Matthews, David Ray (2020). Glucocorticoids rapidly inhibit cell migration through a novel, non-transcriptional HDAC6 pathway. Journal of Cell Science.

Cite DOI

Mike Phuycharoen, Peyman Zarrineh, Laure Bridoux, Shilu Amin, Marta Losa, Ke Chen, Nicoletta Bobola, Magnus Rattray (2020). Uncovering tissue-specific binding features from differential deep learning. Nucleic Acids Res.

Cite DOI

Caroline Hoppe, Jonathan R Bowles, Thomas G Minchington, Catherine Sutcliffe, Priyanka Upadhyai, Magnus Rattray, Hilary L Ashe (2019). Modulation of the promoter activation rate dictates the transcriptional response to graded BMP signaling levels in the Drosophila embryo. Cold Spring Harbor Laboratory.

Cite DOI URL

Magnus Rattray, Sumon Ahmed, Alexis Boukouvalas (2019). Modelling gene expression dynamics with Gaussian process inference. Handbook of Statistical Genomics.

Cite DOI