Dr Alice Pyne

MSci, MRes, EngD

School of Chemical, Materials and Biological Engineering

Senior Lecturer in Soft Matter & Polymers

UKRI Future Leaders Fellow

Dr Alice Pyne
Profile picture of Dr Alice Pyne
a.l.pyne@sheffield.ac.uk
+44 114 222 5969

Full contact details

Dr Alice Pyne
School of Chemical, Materials and Biological Engineering
Sir Robert Hadfield Building
Mappin Street
葫芦影业
S1 3JD
Profile

I am a Senior Lecturer and UKRI Future Leaders Fellow at the University of 葫芦影业. 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 葫芦影业 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 鈥渄ancing鈥 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 field鈥檚 鈥済old standard鈥, for which I was awarded the 2023 Royal Microscopy Society鈥檚 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

  • Smith QM, Aramayo RJ, Rollins DE, Pyne ALB, Morris KL & Rueda DS (2024) . Biophysical Journal, 123(3), 320a-320a. RIS download Bibtex download
  • Newton MD, Lewis JS, Anand R, Holmes EP, Pyne ALB & Boulton SJ (2023) . Biophysical Journal, 122(3), 9a-10a. RIS download Bibtex download
  • Haynes PJ, Main KHS, Akpinar B & Pyne ALB (2022) . Methods Mol Biol, 2476, 43-62. RIS download Bibtex download
  • Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA & Pyne ALB (2021) . APL Bioengineering, 5. RIS download Bibtex download
  • 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. RIS download Bibtex download
  • Beton JG, Moorehead R, Helfmann L, Gray R, Hoogenboom BW, Joseph AP, Topf M & Pyne ALB (2021) . Methods. RIS download Bibtex download
  • Hammond K, Benn G, Bennett I, Parsons ES, Ryadnov MG, Hoogenboom BW & Pyne ALB (2021) , 225-235. RIS download Bibtex download
  • Bennett I, Pyne ALB & McKendry RA (2020) . ACS Sensors, 5(10), 3133-3139. RIS download Bibtex download
  • Benn G, Pyne ALB, Ryadnov MG & Hoogenboom BW (2019) . The Analyst, 144(23), 6944-6952. RIS download Bibtex download
  • 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), ---. RIS download Bibtex download
  • Akpinar B, Haynes PJ, Bell NAW, Brunner K, Pyne ALB & Hoogenboom BW (2019) . Nanoscale, 11(42), 20072-20080. RIS download Bibtex download
  • 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). RIS download Bibtex download
  • 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). RIS download Bibtex download
  • 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). RIS download Bibtex download
  • Burns JR, Lamarre B, Pyne ALB, Noble JE & Ryadnov MG (2018) . ACS Synthetic Biology, 7(3), 767-773. RIS download Bibtex download
  • Heesterbeek DAC, Bardoel BW, Bennett I, Pyne A, Berends ETM, Ruyken M, Hoogenboom B & Rooijakkers SHM (2017) . Molecular Immunology, 89, 154-154. RIS download Bibtex download
  • 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. RIS download Bibtex download
  • 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. RIS download Bibtex download
  • 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. RIS download Bibtex download
  • Pyne A, Thompson R, Leung C, Roy D & Hoogenboom BW (2014) . Small, 10(16), 3257-3261. RIS download Bibtex download
  • 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. RIS download Bibtex download
  • Leung C, Bestembayeva A, Thorogate R, Stinson J, Pyne A, Marcovich C, Yang J, Drechsler U, Despont M, Jankowski T , Tsch枚pe M et al (2012) . Nano Letters, 12(7), 3846-3850. RIS download Bibtex download
  • 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. RIS download Bibtex download
  • Benn G, Bortolini C, Roberts DM, Pyne ALB, Holden S & Hoogenboom BW () . The EMBO Journal. RIS download Bibtex download
  • Diggines B, Whittle S, Yadav I, Holmes EP, Rollins DE, Catley TE, Doyle PS & Pyne A () . Physical Chemistry Chemical Physics. RIS download Bibtex download
  • Bennett ID, Burns JR, Ryadnov MG, Howorka S & Pyne ALB () . Small. RIS download Bibtex download
  • dos Santos 脕, Rollins DE, Hari-Gupta Y, McArthur H, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Lambert D , Brown I et al () . Nature Communications, 14(1). RIS download Bibtex download
  • Klejevskaja B, Pyne ALB, Reynolds M, Shivalingam A, Thorogate R, Hoogenboom BW, Ying L & Vilar R () . Chemical Communications, 52(84), 12454-12457. RIS download Bibtex download

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 RIS download Bibtex download
  • Pyne ALB & Hoogenboom BW (2016) , Methods in Molecular Biology (pp. 47-60). Springer New York RIS download Bibtex download
  • 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 RIS download Bibtex download

Conference proceedings papers

  • 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) RIS download Bibtex download
  • 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) RIS download Bibtex download
  • 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) RIS download Bibtex download
  • 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) RIS download Bibtex download

Software / Code

  • Beton J, Pyne A, Joseph AP & Topf M . RIS download Bibtex download

Datasets

  • J P, H K & Pyne A . RIS download Bibtex download
  • J P, H K & Pyne A . RIS download Bibtex download
  • J P, H K & Pyne A . RIS download Bibtex download
  • J P, H K & Pyne A . RIS download Bibtex download
  • J P, H K & Pyne A . RIS download Bibtex download
  • J P, H K & Pyne A . RIS download Bibtex download

Other

  • Pyne A () . RIS download Bibtex download

Preprints

  • Diggines B, Whittle S, Yadav I, Holmes EP, Rollins DE, Catley TE, Doyle PS & Pyne ALB (2024) , Cold Spring Harbor Laboratory. RIS download Bibtex download
  • Gamill MC, Holmes EP, Provan JI, Wiggins L, Ruskov谩 R, Whittle S, Catley TE, Main KHS, Shephard N, Bryant HE , Ra膷ko D et al (2024) , Cold Spring Harbor Laboratory. RIS download Bibtex download
  • Benn G, Bortolini C, Roberts DM, Pyne ALB, Holden S & Hoogenboom BW (2023) , Cold Spring Harbor Laboratory. RIS download Bibtex download
  • 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) , bioRxiv. RIS download Bibtex download
  • dos Santos 脕, Rollins DE, Hari-Gupta Y, Reed HCW, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Brown I , Howland K et al () , Cold Spring Harbor Laboratory. RIS download Bibtex download
  • Beton JG, Moorehead R, Helfmann L, Gray R, Hoogenboom BW, Joseph AP, Topf M & Pyne ALB () . RIS download Bibtex download
  • 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 () . RIS download Bibtex download
  • Benn G, Pyne ALB, Ryadnov MG & Hoogenboom BW () . RIS download Bibtex download
  • Akpinar B, Bell NAW, Pyne ALB & Hoogenboom BW () . RIS download Bibtex download
  • Bennett I, Pyne A & McKendry R () . RIS download Bibtex download
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-Topoiomerase 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