Curriculum Vitae

Published Research

Journal Articles

1. Weiye Zhao, Susanna F Rose, Ryan Blake, Aňze Godicelj, Amy E Cullen, Jack Stenning, Lucy Beevors, Marcel Gehrung, Sanjeev Kumar, Kamal Kishore, Ashley Sawle, Matthew Eldridge, Federico M Giorgi, Katherine S Bridge , Florian Markowetz, Andrew N Holding (2024)
   ZMIZ1 enhances ERα-dependent expression of E2F2 in breast cancer
   Journal of Molecular Endocrinology, 73, 1. [Open Access]
   
   
2. Daniele Mercatelli, Francesco Formaggio, Marco Caprini , Andrew N Holding, Federico M Giorgi (2022)
   Detection of subtype-specific breast cancer surface protein biomarkers via a novel transcriptomics approach
   Biosci Rep, 2022, [PubMed]
   
   
3. Daniele Mercatelli, Andrew N Holding, Federico M Giorgi (2021)
   Web tools to fight pandemics: the COVID-19 experience.
   Brief. Bioinformatics, bbaa261, [Open Access]
   
   
4. Ronja S Adam, Sanne M van Neerven, Cayetano Pleguezuelos-Manzano, Salvatore Simmini, Nicolas Léveillé, Nina E de Groot, Andrew N Holding, Florian Markowetz, Louis Vermeulen (2020)
   Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development.
   Cancer Cell International, 20 1, 1-15, [Open Access]
   
   
5. Andrew N. Holding*, Helen V. Cook, and Florian Markowetz (2020)
   Data generation and network reconstruction strategies for single cell transcriptomic profiles of CRISPR-mediated gene perturbations.
   BBA-GRM, 194441, [Open Access]
   
   
6. Andrew N. Holding*, Federico M. Giorgi, Amanda Donnelly, Amy E. Cullen, Sankari Nagarajan, Luke A. Selth and Florian Markowetz (2019)
   VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer
   Genome Biology, 20, 19. [Open Access]
   
   
7. Andrew N. Holding*, Amy E. Cullen and Florian Markowetz (2018)
   Genome-wide Estrogen Receptor-alpha activation is sustained, not cyclical
   eLife, 7, e40854. [PubMed]
   
   
8. Euan S. Polson, Verena B. Kuchler, Christopher Abbosh, Edith M. Ross, Ryan K. Mathew, Hester A. Beard, Bárbara da Silva, Andrew N. Holding, Stephane Ballereau, Eulashini Chuntharpursat-Bon, Jennifer Williams, Hollie B. S. Griffiths, Hao Shao, Anjana Patel, Adam J. Davies, Alastair Droop, Paul Chumas, Susan C. Short, Mihaela Lorger, Jason E. Gestwicki, Lee D. Roberts, Robin. S Bon, Simon J. Allison, Shoutian Zhu, Florian Markowetz, Heiko Wurdak (2018)
   KHS101 disrupts energy metabolism in human glioblastoma cells and reduces tumor growth in mice
   Science translational medicine, 10, 454. [PubMed]
   
   
9. Evangelia K. Papachristou, Kamal Kishore¹, Andrew N. Holding¹, … , Rasmus Siersbaek, Clive S. D’Santos and Jason S. Carroll (2018)
   A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes
   Nature Communications, 9, 2311. [PubMed]
   
   
10. Michael J. Guertin, Amy E. Cullen, Florian Markowetz and Andrew N. Holding* (2018)
    Parallel Factor ChIP Provides Essential Internal Control for Quantitative Differential ChIP-Seq
    Nucleic Acids Research. 46, 12. [PubMed]
    
    
11. Andrew N. Holding* (2015)
    XL–MS: Protein cross-linking coupled with mass spectrometry
    Methods 89. 54-63. [PubMed]
    
    
12. Jennifer Lee, ShuJing Ding, Thomas B. Walpole, Andrew N. Holding, Martin G. Montgomery, Ian M. Fearnley and John E. Walker (2015)
    Organisation of Subunits in the Membrane Domain of the Bovine F-ATPase Revealed by Covalent Cross-linking
    J. Biol. Chem. 290. 13308-20. [PubMed]
    
    
13. Andrew N Holding,* Meindert H Lamers, Elaine Stephens and J Mark Skehel (2013)
    Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples
    J Proteome Res. 12. 5923-33. [PubMed]
    
    
14. Yang Liu,¹ Hannah K Salter, ¹ Andrew N Holding, Christopher M Johnson, Elaine Stephens, Peter J Lukavsky, John Wlashaw and Simon L Bullock (2013)
    Bicaudal-D uses a parallel, homodimeric coiled coil with heterotypic registry to coordinate recruitment of cargos to dynein
    Genes Dev. 27. 1233-46. [PubMed]
    
    
15. Andrew N Holding,¹ Ana Toste Rego,¹ Helen Kent and Meindert H Lamers (2013)
    Architecture of the Pol III—clamp—exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair
    EMBO J. 32. 1334-1343. [Pubmed] [F1000Prime] - recommended as being of special significance.
    
    
16. Andrew N Holding* and Jonathan B Spencer. (2008)
    Investigation into the mechanism of phenolic couplings during the biosynthesis of glycopeptide antibiotics
    ChemBioChem. 9. 2209-14. [Pubmed]
    
    
17. Helen M O’Hare, Fanglu Huang, Andrew Holding, Oliver W Choroba and Jonathan B Spencer. (2006)
    Conversion of hydroxyphenylpyruvate dioxygenases into hydroxymandelate synthases by directed evolution
    FEBS Lett. 580. 3445-50. [Pubmed]
    
    

¹These authors contributed equally to this work.
* Corresponding author.

Oral Presentations

1. Network Analysis of the Tissue-Specific Glucocorticoid Response
   Invited Speaker, 2024, ChatVax, Univesrity of Sheffield, UK
2. Next-generation approaches to understanding the tissue-specific regulation of the glucocorticoid response
   Invited Speaker, 2024, Chromatin and Transcription, Biochemical Society, Newcastle, UK
3. Reproducible Research
   Invited Speaker, 2024, University Medical Centre Utrecht, Center for Molecular Medicine, Utrech, NL
4. Rewiring Steroid Hormone Receptor Signalling for Better Patient Outcomes
   BBSRC Partnership Award, 2023, Keio University, Japan
5. Deciphering the Steroid Hormone Receptor Cofactor Code.
   Invited Speaker, 2023, Imperial Centre for Translational and Experimental Medicine, Imperial College London, UK
6. Next Generation Approaches to Understand the Regulation Steroid Hormone Response.
   Invited Speaker, 2023, Deparment of Biochemistry, University of Cambridge, UK
7. Machine Learning to Predict Breast Cancer Biology.
   Invited Speaker, 2022, Turing-Roche Knowledge Share Series, Online
8. Next Generation Approaches to Understand Tissue Specific Regulation of the Glucocorticoid Response.
   Invited Speaker, 2021, Biochemistry Focus Webinar: Signalling, The Biochemical Society, Online
9. How We Can Use Machine Learning to Predict Breast Cancer Biology
   Keynote Speaker, 2020, Biotechnology and Molecular Medicine PGT Conference, University of Essex, UK
10. Combining Machine Learning with ChIP-seq to Predict Transcription Factor Interactions
    2nd Nuclear Receptors Conference 2020, Nassau, Bahamas
11. Machine Learning to Predict Breast Cancer Biology
    Health and Medical Sciences Programme Seminar, 2020, Alan Turing Institute, UK
12. VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer
    Long Talk, 2019, Quantitative Genomics, Francis Crick Institute, UK
13. Reprogramming Luminal Breast Cancer: Experimental & Computational Inference of Estrogen Receptor Interactions to Derive Combinatorial Drug Targets
    Invited Speaker, 2019, EBI industry workshop on Cancer Systems Biology, EMBL-EBI, Hixton, UK
14. Reprogramming Luminal Breast Cancer: Experimental & Computational Inference of Estrogen Receptor Interactions to Derive Combinatorial Drug Targets
    Invited Speaker, 2019, AIST Tokyo Waterfront, Japan
15. Reprogramming Luminal Breast Cancer: Experimental & Computational Inference of Estrogen Receptor Interactions to Derive Combinatorial Drug Targets
    Invited Speaker, 2019, University of Birmingham, UK
16. Reprogramming Luminal Breast Cancer: Experimental & Computational Inference of Estrogen Receptor Interactions to Derive Combinatorial Drug Targets
    Invited Speaker, 2019, MRC Toxicology Unit, Leicester, UK
17. Reprogramming Luminal Breast Cancer: Experimental & Computational Inference of Estrogen Receptor Interactions to Derive Combinatorial Drug Targets
    Invited Speaker, 2018, University of Bologna, Italy
18. Integrative analysis of ER-α in breast cancer reveals a robust and sustained response to estra-2-diol
    Keynote speaker, Biosciences Symposium, 2018, Essex, UK
19. Network Dynamics of ER-α activation reveals reprogramming of GRHL2
    Applied Bioinformatics In Life Sciences, 2018, Leuven, Belgium
20. Utilising mass spectrometry for the structural and functional analysis of complex systems in medical research
    Invited speaker, 2016, University of Essex, Colchester, UK
21. Visualizing gene regulation: a combined proteomic and genomic approach for the structural analysis of steroid hormone receptor complexes
    Invited speaker, 4th International Congress on Analytical Proteomics, 2015, Lisbon, Portugal
22. Bringing Proteogenomics to the study of ER+ breast cancer
    Invited speaker, 2014, MRC Cancer Unit, Cambridge, UK
23. Interactions within the E. coli Replisome
    Mini-symposium on Biophysics, 2012, MRC Laboratory of Molecular Biology
24. Interactions within the E. coli Replisome
    Proteomics Methods Forum, 2012, Barts Cancer Institue, London, UK
    
25. Cross-linking in mass spectrometry
    Proteomics Methods Forum, 2010, Department of Biochemistry, University of Cambridge
    
26. Cross-linking in mass spectrometry
    Mini-symposium on Biophysics, 2010, MRC Laboratory of Molecular Biology
    

Poster Presentations

1. Genome-wide Estrogen Receptor-a activation is sustained, not cyclical
   A. N. Holding, A. E. Cullen, F. Markowetz,
   Hormone-Dependent Cancers, Gordon Research Conference, 2019, Newry, ME, USA.
2. Parallel Factor ChIP Provides Essential Internal Control for Quantitative Differential ChIP-seq
   M. J. Guertin, A. E. Cullen, F. Markowetz, A. N. Holding,
   EMBO Nuclear Receptors and Biological Networks, 2018, Kolymbari, Crete, Greece.
3. Network Dynamics of ER-α activation reveals reprogramming of GRHL2
   A. N. Holding, F. Giorgi, A. Donnelly, A. E. Cullen, L. A. Selth, F. Markowetz,
   Applied Bioinformatics in Life Sciences, 2018, Leuven, Belgium
4. Parallel Factor ChIP Provides Essential Internal Control for Quantitative Differential ChIP-seq
   M. J. Guertin, A. E. Cullen, F. Markowetz, A. N. Holding,
   Cambridge Cancer Centre Symposium, 2017, Cambridge, UK.
5. ChIP-MS/TMT: a quantative proteomic analysis of steroid hormone receptor activation.
   A. N. Holding, F. Markowetz
   64th ASMS Conference on Mass Spectrometry and Allied Topics, 2016, San Antonio, Texas, USA
6. Visualising gene regulation: A combined proteomic and genomic approach for the analysis of steroid hormone receptor complexes.
   A. N. Holding, J. C. Carroll, F. Markowetz
   29th Annual Symposium of the Protein Society, Barcelona, Spain
7. Visualising gene regulation: A combined proteomic and genomic approach for the analysis of steroid hormone receptor complexes.
   A. N. Holding, J. C. Carroll, F. Markowetz
   Cambridge Cancer Centre Symposium, 2015, Cambridge, UK.
8. Hekate – Software suite for the mass spectrometric analysis & three-dimensional visualization of cross-linked protein samples.
   A. N. Holding, Y. Liu, H. K. Salter, M. L. Lamers, S. L. Bullock, M. J. Skehel
   Postdoctoral Career Development Day, Cancer Research UK, 2014,London, UK
9. Resolving interactions involved in binding of the dynein co-factor Bicaudal-D (BicD) to Rab6
   Andrew N Holding, Elaine Stephens.
   60th ASMS Conference on Mass Spectrometry and Allied Topics, 2012, Vancouver Convention Centre, Vancouver, BC, Canada.
   
10. Development of arginine and guanine specific isotopically-labelled linkers for the characterisation of binding interactions by mass spectrometry
    Andrew N Holding, Elaine Stephens.
    59th ASMS Conference on Mass Spectrometry and Allied Topics, 2011, Colorado Convention Center, Denver, CO, USA.
    
11. Sdo1/Efl1 interaction site mapped by photocrosslinking
    Andrew N Holding, Nicholas Basse, Alan Warren, Elaine Stephens.
    Memorial symposium for Dr. Jonathan Spencer, 2010, University of Cambridge.
    
12. Investigation into the mechanism of phenolic couplings during the biosynthesis of glycopeptide antibiotics
    Andrew N Holding, Jonathan B Spencer.
    Zing Conference in Natural Products, 2009, Antigua.