Professor Alice Pyne (she/her)

MSci, MRes, EngD

School of Chemical, Materials and Biological Engineering

Professor of Biophysics

UKRI Future Leaders Fellow

Head shot of Alice Pyne (young white woman with dark hair)
Profile picture of Head shot of Alice Pyne (young white woman with dark hair)
a.l.pyne@sheffield.ac.uk
+44 114 222 5969
Sir Robert Hadfield Building

Full contact details

Professor Alice Pyne
School of Chemical, Materials and Biological Engineering
Sir Robert Hadfield Building
Mappin Street
Sheffield
S1 3JD
Profile

I am a Professor of Biophysics and UKRI Future Leaders Fellow at the University of Sheffield. Following my undergraduate degree in Physics at Bristol and my EngD in Biophysics at UCL, I was awarded EPSRC and MRC fellowships to establish my independent research group at UCL. I moved to Sheffield in 2019 as a Lecturer, where I established the Henry Royce Nanocharacterisation Laboratory

My research focusses on developing high-resolution Atomic Force Microscopy (AFM) imaging methods for structural characterisation of biomolecules in solution. I have pioneered single-molecule imaging studies of the DNA double helix, including unique time-resolved imaging at the atomic scale, showing DNA molecules twisting and dancing in ways that had not previously been imaged. I have a keen interest in bioimage analysis, and have developed an automated image analysis pipeline, , that combines AFM image correction, molecule identification, and tracing into a single tool.

Qualifications
  • EngD Biophysics, University College London & the National Physical Laboratory, High Resolution Atomic Force Microscopy of Functional Biological Molecules (2015)
  • MRes (Hons) Distinction, UCL, Molecular Modelling and Materials Science (2011)
  • MSci (Hons) Physics, University of Bristol (2009)
Research interests

My research is highly interdisciplinary, working closely with industry to engineer new high-resolution Atomic Force Microscopy (AFM) technologies which enable us to understand the fundamental properties of biological molecules at the nanoscale. These technologies have enabled us to perform unique time-resolved imaging of DNA at the sub-molecular scale. Beyond hardware, I am spearheading the development of an open-source, automated AFM image analysis pipeline, TopoStats, which is becoming the fields gold standard, for which I was awarded the 2023 Royal Microscopy Societys AFM & SPM award. Our current research impact spans fundamental biological understanding to therapeutic development. 

Key research interests:

  • Atomic Force Microscopy
  • Open-source image analysis pipelines
  • Structure and Function of nucleic acids
  • Materials surface characterisation at the nanoscale
Publications

Journal articles

  • Holleman E, Catley TE, Sereiva T, Hartono SR, Pyne ALB & Ch矇din F (2025) . Proceedings of the National Academy of Sciences, 122(38).
  • O'Carroll S, Slator C, de Paiva REF, 壅翌腦瞳ome C, Searle B, Kk S, Whittle S, Catley TE, Scoditti S, Mnich K , Peterson EJ et al (2025) . Nucleic acids research, 53(13).
  • Holmes EP, Gamill MC, Provan JI, Wiggins L, Ruskov獺 R, Whittle S, Catley TE, Main KHS, Shephard N, Bryant HE , Gilhooly NS et al (2025) . Nature Communications, 16(1).
  • Poole S, Aning OA, McKee V, Catley T, Nielsen AY, Thisgaard H, Johansson P, Menounou G, Hennessy J, Slator C , Gibney A et al (2025) . Nucleic Acids Research, 53(1).
  • Benn G, Bortolini C, Roberts DM, Pyne ALB, Holden S & Hoogenboom BW (2024) . The EMBO Journal, 43(23), 6152-6160.
  • Diggines B, Whittle S, Yadav I, Holmes EP, Rollins DE, Catley TE, Doyle PS & Pyne A (2024) . Physical Chemistry Chemical Physics, 26(40), 25798-25807.
  • Bennett ID, Burns JR, Ryadnov MG, Howorka S & Pyne ALB (2024) . Small, 20(35).
  • Smith QM, Aramayo RJ, Rollins DE, Pyne ALB, Morris KL & Rueda DS (2024) . Biophysical Journal, 123(3), 320a-320a.
  • dos Santos A, Rollins DE, Hari-Gupta Y, Reed HCW, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Lambert D , Brown I et al (2023) . Nature Communications, 14.
  • Newton MD, Lewis JS, Anand R, Holmes EP, Pyne ALB & Boulton SJ (2023) . Biophysical Journal, 122(3), 9a-10a.
  • Haynes PJ, Main KHS, Akpinar B & Pyne ALB (2022) , 43-62.
  • Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA & Pyne ALB (2021) . APL Bioengineering, 5.
  • Pyne ALB, Noy A, Main KHS, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW , Bates AD et al (2021) . Nature Communications, 12.
  • Beton JG, Moorehead R, Helfmann L, Gray R, Hoogenboom BW, Joseph AP, Topf M & Pyne ALB (2021) . Methods, 193, 68-79.
  • Hammond K, Benn G, Bennett I, Parsons ES, Ryadnov MG, Hoogenboom BW & Pyne ALB (2021) , 225-235.
  • Bennett I, Pyne ALB & McKendry RA (2020) . ACS Sensors, 5(10), 3133-3139.
  • Benn G, Pyne ALB, Ryadnov MG & Hoogenboom BW (2019) . The Analyst, 144(23), 6944-6952.
  • Parsons ES, Stanley GJ, Pyne ALB, Hodel AW, Nievergelt AP, Menny A, Yon AR, Rowley A, Richter RP, Fantner GE , Bubeck D et al (2019) . Nature Communications, 10(1), ---.
  • Akpinar B, Haynes PJ, Bell NAW, Brunner K, Pyne ALB & Hoogenboom BW (2019) . Nanoscale, 11(42), 20072-20080.
  • Heesterbeek DAC, Bardoel BW, Parsons ES, Bennett I, Ruyken M, Doorduijn DJ, Gorham RD, Berends ETM, Pyne ALB, Hoogenboom BW & Rooijakkers SHM (2019) . The EMBO Journal, 38(4).
  • Pfeil M-P, Pyne ALB, Losasso V, Ravi J, Lamarre B, Faruqui N, Alkassem H, Hammond K, Judge PJ, Winn M , Martyna GJ et al (2018) . Scientific Reports, 8(1).
  • Pfeil M-P, Pyne ALB, Losasso V, Ravi J, Lamarre B, Faruqui N, Alkassem H, Hammond K, Judge PJ, Winn M , Martyna GJ et al (2018) . Scientific Reports, 8(1), 17266.
  • Burns JR, Lamarre B, Pyne ALB, Noble JE & Ryadnov MG (2018) . ACS Synthetic Biology, 7(3), 767-773.
  • Heesterbeek DAC, Bardoel BW, Bennett I, Pyne A, Berends ETM, Ruyken M, Hoogenboom B & Rooijakkers SHM (2017) . Molecular Immunology, 89, 154-154.
  • Pyne A, Pfeil M-P, Bennett I, Ravi J, Iavicoli P, Lamarre B, Roethke A, Ray S, Jiang H, Bella A , Reisinger B et al (2017) . Chemical Science, 8(2), 1105-1115.
  • Messager L, Burns JR, Kim J, Cecchin D, Hindley J, Pyne ALB, Gaitzsch J, Battaglia G & Howorka S (2016) . Angewandte Chemie, 128(37), 11272-11275.
  • Messager L, Burns JR, Kim J, Cecchin D, Hindley J, Pyne ALB, Gaitzsch J, Battaglia G & Howorka S (2016) . ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 55(37), 11106-11109.
  • Pyne A, Thompson R, Leung C, Roy D & Hoogenboom BW (2014) . Small, 10(16), 3257-3261.
  • Rakowska PD, Jiang H, Ray S, Pyne A, Lamarre B, Carr M, Judge PJ, Ravi J, M. Gerling UI, Koksch B , Martyna GJ et al (2013) . Proceedings of the National Academy of Sciences, 110(22), 8918-8923.
  • Leung C, Bestembayeva A, Thorogate R, Stinson J, Pyne A, Marcovich C, Yang J, Drechsler U, Despont M, Jankowski T , Tsch繹pe M et al (2012) . Nano Letters, 12(7), 3846-3850.
  • Pyne A, Marks W, M. Picco L, G. Dunton P, Ulcinas A, E. Barbour M, B. Jones S, Gimzewski J & J. Miles M (2009) . Archives of Histology and Cytology, 72(4/5), 209-215.
  • Klejevskaja B, Pyne ALB, Reynolds M, Shivalingam A, Thorogate R, Hoogenboom BW, Ying L & Vilar R () . Chemical Communications, 52(84), 12454-12457.
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Book chapters

  • Tor Y, Gehring K, Fabris D, Egli M, Korostelev AA, Craggs TD, Pyne A, Gagnon KT, Watts JK, Cheatham III TE & Richards NGJ (2022) , Nucleic Acids in Chemistry and Biology (pp. E1-E50). The Royal Society of Chemistry
  • Pyne ALB & Hoogenboom BW (2016) , Methods in Molecular Biology (pp. 47-60). Springer New York
  • Egli M, Flavell A, Pyle AM, Wilson WD, Haq SI, Luisi B, Fisher J, Laughton C, Allen S, Engels J , Grasby JA et al (2006) In Blackburn GM, Gait MJ, Loakes D & Williams DM (Ed.) The Royal Society of Chemistry
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Conference proceedings

  • Ravi J, Pfeil MP & Pyne AL (2019) Probing antimicrobial mechanisms for effective strategies to overcome resistance. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 48 (pp S223-S223)
  • Pyne ALB, Hoogenboom BW, Vilar R & Maxwell A (2017) Visualisation of DNA conformational changes in situ at nanometre resolution. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S369-S369)
  • Yon AR, Pyne ALB, Kwakwa K, Lowe AR, Williams WA & Hoogenboom BW (2017) A combinatorial single-molecule study of ligand-gated ion channels and monoclonal antibodies. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S371-S371)
  • Pyne ALB, Pfeil M-P, Bennett I, Ravi J, Lamarre B, Hoogenboom BW & Ryadnov MG (2017) Investigating the mechanism of action of a novel antimicrobial peptide on live E. coli cells. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S389-S389)
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Software, code or databases

  • Beton J, Pyne A, Joseph AP & Topf M .
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Datasets

  • J. Haynes P, H. S. Main K & L Pyne A (2020) .
  • J. Haynes P, H. S. Main K & L Pyne A (2020) .
  • J. Haynes P, H. S. Main K & L Pyne A (2020) .
  • J. Haynes P, H. S. Main K & L Pyne A (2020) .
  • J. Haynes P, H. S. Main K & L Pyne A (2020) .
  • J. Haynes P, H. S. Main K & L Pyne A (2020) .
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Other

  • Pyne A () .
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Preprints

  • Millan-Solsona R, Checa M, Brown S, Bible A, Srijanto B, Wiggins L, Madugula S, Pyne A, Morrell-Falvey J, Retterer S , Vasudevan R et al (2025) , Springer Science and Business Media LLC.
  • Velasco-Berrelleza V, Catley TE, Rollins DE, Pyne ALB & Noy A (2025) , Cold Spring Harbor Laboratory.
  • Mosley SR, Lapa N, Namdar A, Catley TE, Meier-Stephenson F, Mowat C, Gao P, Sun X, Meier-Stephenson V, Pyne ALB & Baker K (2025) , Cold Spring Harbor Laboratory.
  • Holleman E, Catley TE, Sereiva T, Hartono SR, Pyne ALB & Ch矇din F (2025) , Cold Spring Harbor Laboratory.
  • Diggines B, Whittle S, Yadav I, Holmes EP, Rollins DE, Catley TE, Doyle PS & Pyne ALB (2024) , Cold Spring Harbor Laboratory.
  • Holmes EP, Gamill MC, Provan JI, Wiggins L, Ruskov獺 R, Whittle S, Catley TE, Main KHS, Shephard N, Bryant HE , Gilhooly NS et al (2024) , Cold Spring Harbor Laboratory.
  • Benn G, Bortolini C, Roberts DM, Pyne ALB, Holden S & Hoogenboom BW (2023) , Cold Spring Harbor Laboratory.
  • dos Santos , Rollins DE, Hari-Gupta Y, Reed HCW, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Brown I , Howland K et al (2022) , Cold Spring Harbor Laboratory.
  • Beton JG, Moorehead R, Helfmann L, Gray R, Hoogenboom BW, Joseph AP, Topf M & Pyne ALB (2020) , Cold Spring Harbor Laboratory.
  • Pyne ALB, Noy A, Main K, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW , Bates AD et al (2019) , Cold Spring Harbor Laboratory.
  • Benn G, Pyne ALB, Ryadnov MG & Hoogenboom BW (2019) , Cold Spring Harbor Laboratory.
  • Akpinar B, Bell NAW, Pyne ALB & Hoogenboom BW (2019) , Cold Spring Harbor Laboratory.
  • Bennett I, Pyne A & McKendry R (2019) , Cold Spring Harbor Laboratory.
  • Parsons ES, Stanley GJ, Pyne ALB, Hodel AW, Nievergelt AP, Menny A, Yon AR, Rowley A, Richter RP, Fantner GE , Bubeck D et al (2018) , Cold Spring Harbor Laboratory.
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Research group

PhD Students:

  • Daniel Rollins (AFM analysis of supercoiled DNA interactions)
  • Mingxue Du (TopoStats: Automating AFM analysis of DNA & protein interactions)
  • Libby Holmes (Complex DNA structures in cancer)
  • Max Gamil (Deep probabilistic models for analysing complex DNA structures)

PhD Students (UCL):

Kavit Main (Single molecule insights into DNA-Topoisomerase interactions) 

Professional activities and memberships
  • Fellow of the Royal Microscopy Society
  • Committee member of the British Biophysical Society
  • Committee member of the Royal Microscopy Society - vice chair of the Data Analysis in Microscopy (DAIM) subgroup

Links