CV

Nadia Zatsepin

Professional experience

• 2024 - current: Associate Professor and ARC Future Fellow, Department of Physics and Astronomy, Swinburne University of Technology, Melbourne, Australia.

• 2024: Principal Research Fellow and Associate Professor,  Department of Mathematical and Physical Sciences, La Trobe University, Melbourne, Australia

• 2019 - 2022: Senior Research Fellow, Department of Chemistry and Physics, School of Molecular Sciences, La Trobe University, Melbourne, Australia. 

• 2015 - 2019: Assistant Research Professor, Department of Physics, Arizona State University, USA.

Affiliated with the Center for Biological Physics and Biodesign Center for Applied Structural Discovery at Arizona State University and the National Science Foundation BioXFEL Science and Technology Center.

• 2013– 2015: Assistant Research Scientist, Department of Physics, Arizona State University, USA.

• 2011 – 2013: Postdoctoral Scholar, Department of Physics, Arizona State University, USA. Supervised by Prof. John C. H. Spence.

Research summary

Publications: 62 refereed journal papers; over 8800 citations; h-index = 35 (Google Scholar,  April 2024).  Journals include Nature, Science, Cell, Nature Methods, Nature Communications, Nature Structural and Molecular Biology, Journal of the American Chemical Society, Proceedings of the National Academy of Sciences, an invited review article in Current Opinions in Structural Biology (2019), an invited book chapter on serial crystallography with XFELs (2018, Royal Soc. Chemistry), 3 refereed conference proceedings. Click here for full list of publications.

Research focus:  My overarching research goal is to enable molecular movies with atomic resolution and ultrafast time resolution. We focus on the development and application of serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs), and serial crystallography with synchrotron and novel compact X-ray light sources. We work on novel algorithms/software, radiation damage and de novo phasing to obtain room-temperature structures of macromolecules, and to study their dynamics. One main target is a bacterial protein, disulphide bond-forming enzyme A, to aid in novel drug development to combat global antimicrobial resistance . 

Highlights and impact: Principal investigator on 4, and co-PI or collaborator on over 110 XFEL experiments. Corresponding senior author on the first membrane protein structure determination from a megahertz XFEL (Nature Communications 2019). Established a robust technique for high-resolution structure determination of G protein-coupled receptors and other membrane proteins from microcrystals at room-temperature: SFX in lipidic cubic phase (e.g. Fenalti, Zatsepin et al. Nature Struct. Mol. Biol. 2015). First SFX studies of ligand-binding activated reactions, observing large conformational changes in crystallo (Nature 2017), and real-time enzyme catalysis in microcrystals. First SFX studies observing femtosecond-scale dynamics of light-activated reactions with atomic resolution (Science 2014, 2015). Demonstrated proof-of-concept room-temperature serial microcrystallography at five microfocus synchrotron beamlines . 

Lead role: Over 2014-2019: Led serial crystallography data analysis in the National Science Foundation Science and Technology Center for Biology with X-ray Lasers (BioXFEL), a 10-year multi-US university consortium for the application and development of biological imaging with XFELs. 

Grants

I have been awarded over $3.2M  AUD  in research grants since 2015 as principal or co-principal investigator. (assuming 1 USD ~ 1.5 AUD). 

1. Zatsepin, N. A. Developing serial crystallography for room temperature structure & dynamics. ARC Future Fellowship. Australia. 

2. Zatsepin, R. Kirian, K. Schmidt, J. Spence, U. Weierstall, ABI Innovation: New Algorithms for Biological X-ray Free Electron Laser Data, NSF Division of Biological Infrastructure, Advances in Bioinformatics (08/2016 – 07/2019) www.nsf.gov/awardsearch/showAward?AWD_ID=1565180. $761,649.

3. Brown, P. Fromme, N. Zatsepin, R. Kirian and T. Grant. Light-Induced Protein Quake of Visual Rhodopsin Investigated by Femtosecond Time-Resolved X-Ray Scattering. NSF MCB 1817862 (07/2018 – 06/2021). $800,000.

4. N. Zatsepin and J. Lovell, Serial Femtosecond Crystallography of Nanocrystalline Drug Release Using XFELs. BioXFEL Collaboration Grant from NSF BioXFEL STC, 2016. $35,000.

I was also a co-author on three large research centre grants as a senior investigator named in the grant:

-  NSF Science and Technology Center for Biology with X-ray Lasers, a consortium of eight US universities for the application and development of biological imaging with XFELs, awarded $25M USD for 2013 - 2018 ((PI: John C. H. Spence, ASU);

-  NSF BioXFEL STC renewal proposal, awarded $22.5M USD for 2018 - 2023 (PI: John C. H. Spence, ASU)

-  NSF Mid-scale Research Infrastructure-1 proposal for the design of a Compact X-ray Free-electron Laser at Arizona State University awarded $4.8M USD in 2019 (PI: William S. Graves, ASU).

Highlighted Publications

Click here for full list of publications.

(Updated May 2023)

1.     *** Gisriel, C., Coe, J., (74 more co-authors), Fromme, P., Zatsepin, N.A. (2019). Membrane protein megahertz crystallography at the European XFEL. Nature Commun. 10, 1–11.

Significance: World’s first structure determination of a large membrane protein (Photosystem I, key to photosynthesis in plants and some bacteria), using the world’s first ultra-high repetition rate X-ray laser. This was one of the largest membrane protein complexes ever studied with XFELs and the culmination of over a decade of technique and algorithm development. CrystFEL and DatView (see 6 and 8 below) were critical to this work.

2. Clabbers, M.T.B., Holmes, S., (14 more co-authors),  Zatsepin, N.A., Abbey, B., Sierecki, E., Gambin, Y., Stacey, K.J., Darmanin, C., Kobe, B., Xu, H., Ve, T. (2021) Nature Commun. 12, 1-14.

Significance: High-resolution structure determination comparing serial femtosecond crystallography and micro-electron diffraction from nano-scale crystals of the MyD88 TIR domain. MyD88 is involved in innate immune responses leading to pro-inflammatory cytokine production.

3. Tenboer, J., Basu, S., Zatsepin, N.A., (32 more co-authors), Schmidt, M. (2014). Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science 346, 1242–1246.

Significance: The first molecular movie snapshots from an X-ray free-electron laser: studies of light-triggered dynamics of biomolecules with atomic resolution, which we then extended to femtosecond time resolution (i.e .the timescale of the initial photon capture) in Pande, et al. (2015). Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 352, 725-729.

4.  Stagno, J.R., Liu, Y., Bhandari, Y.R., (30 more co-authors), Zatsepin, N.A., Chapman, H.N., Spence, J.C.H., Woodson, S.A., Wang, Y.-X., (2017). Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 541, 242–246.

Significance: In this world-first 'mix-and-inject' SFX experiment, we demonstrated that SFX can be used for structure determination during cyclic and non-cyclic reactions initiated by ligand binding, showing that, in some microcrystals, very large conformational changes are possible without loss of crystallinity.

5. Fenalti, G., Zatsepin, N.A., (32 more co-authors), Stevens, R.C., Cherezov, V., (2015). Structural basis for bifunctional peptide recognition at human δ-opioid receptor. Nat. Struct. Mol. Biol. 22, 265–268.

Significance: We determined a high-resolution, room-temperature structure of an opioid receptor involved in pain signalling with a bound peptide known to attenuate opioid side effects, providing a structural basis for (a) opioid receptor specificity and function, and (b) design of more effective, less addictive opioid-based drugs.

6.      ***   Stander, N., Fromme, P., Zatsepin, N.A., (2019). DatView: a graphical user interface for visualizing and querying large data sets in serial femtosecond crystallography. J. Appl. Cryst. 52, 1440–1448.

Significance: Python tool for multi-dimensional dataset exploration, which enables otherwise inaccessible feedback for data collection and facilitates data subset optimisation with an easy-to-use interface.

7. ***   Li, C., Li, X., Kirian, R., Spence, J.C.H., Liu, H., Zatsepin, N.A., (2019). SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data. IUCrJ. 6, 1, 72-84.

Significance: Robust new algorithm and open source software facilitating indexing snapshot serial crystallography patterns with > 4 Bragg spots, such as from small unit cells or weak patterns from crystals with larger unit cells. SPIND enabled the analysis of previously intractable data from ultrafast electronic damage studies.

8. White, T.A., Barty, A., Stellato, F., Holton, J.M., Kirian, R.A., Zatsepin, N.A., Chapman, H.N., (2013). Crystallographic data processing for free-electron laser sources. Acta Cryst. D 69, 1231–1240.

Significance: Description of data processing pipeline for XFEL serial crystallography: Cheetah (data reduction) and CrystFEL (indexing and merging); CrystFEL is the most widely used serial snapshot crystallography SFX analysis software worldwide, used for structure determination in 242 published papers (excluding reviews).

9. Zatsepin, N.A., Li, C., Colasurd, P., Nannenga, B.L., (2019). The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals. Curr. Op. Struct. Bio. 52, 1-8.

Significance: Invited review article. A concise comparison of two powerful, emerging techniques for high-resolution structure determination from macromolecular nano/microcrystals, SFX (using XFELs) or micro-electron diffraction (using transmission electron microscopes), emphasizing the techniques' complementary nature.

10.   *** Zatsepin, N. (2018). Crystallography with X-ray free electron lasers. In K. Beis and G. Evans (Eds.), Protein crystallography challenges and practical solutions (pp. 181–224).  Cambridge, UK: Royal Society of Chemistry.

Significance: Invited book chapter: Historical overview of serial femtosecond crystallography, new sample delivery technologies, the unique challenges and opportunities in SFX data collection and analysis, and a review of time-resolved pump-probe and mix-and-inject SFX results and ab initio phasing of SFX data to date.

Invited Talks

1. Molecular movies with X-ray lasers. Seminar, Department of Physics and Astronomy, Swinburne University, Melbourne, Australia, Jan 2024.

2. Molecular movies with X-ray lasers. Seminar, Research School of Chemistry, Australian National University, Canberra, Australia, Nov 2023.

3. XFEL Serial femtosecond crystallography data analysis. Advances in macromolecule microcrystallography: innovations in production, detection, handling and data collection of microcrystals Workshop at IUCr 2023 Congress, Melbourne, Australia, Aug 2023.

4. Molecular movies with x-ray lasers. Monash University, Physics of Imaging Seminar, Australia, Aug 2023.

5. Serial femtosecond crystallography for membrane proteins in LCP and future serial crystallography at MX3, Group seminar, Monash University, Australia, Nov 2021 

6. Perspectives on protein crystallography with a compact XFEL, Australian Compact Light Source Workshop, ANSTO, Australia, June 2021.

7. XFEL Crystallography: Imaging Molecular Reactions. Big Science Workflows and Orchestration Workshop, Monash University, Australia, August 2020.

8. Time-resolved serial femtosecond crystallography with X-ray free-electron lasers. Monash Physics Colloquium, Australia, August 2020.

9. Membrane protein megahertz crystallography at the European XFEL. European XFEL Users’ Meeting, Hamburg, Germany, Feb 2020.

10. Time-resolved serial femtosecond crystallography at X-ray free-electron lasers. ARC Centre of Excellence for Advanced Molecular Imaging Annual Summit, Torquay, Australia, Nov 2019.

11. Capturing enzyme catalysis in action by mix-and-inject serial crystallography. Infection & Immunity Forum Seminar, La Trobe Institute of Molecular Sciences, Melbourne, Australia, Oct 2019.

12. Development of native SAD phasing in serial millisecond crystallography. ARC Centre of Excellence for Advanced Molecular Imaging Physics Symposium, Melbourne University, Australia, July 2019.

13. Data sharing and optimizing data quality in injector-based serial millisecond crystallography, at the Transactions Symposium on "Data Best Practices", American Crystallographic Association Annual Meeting, KY, USA, July 2019.

14. Low-dose serial crystallography. CXFEL Workshop #2: Research opportunities for structure and dynamics in biology, Arizona State University, AZ, USA, April 2018. 

15. High-resolution room-temperature serial microcrystallography at synchrotrons with a high viscosity medium injector and snapshot serial crystallography analysis. NSLS II, Brookhaven National Lab, NY, USA, 2018.

16. BioXFEL: using X-ray lasers to study the ultra-small and ultra-fast in biology. Keynote speaker at Conference for Undergraduate Women in Physics, Arizona State University, AZ, USA, January 2018.

17. Time-resolved serial femtosecond crystallography at XFELs. National Cancer Institute, National Institutes of Health, Frederick, MD, USA, 2017.

18. Serial millisecond protein crystallography using synchrotron radiation: Opportunities and Challenges, Seminar, Synchrotron SOLEIL, Paris, France, August 2017.

19. Serial millisecond crystallography at the Advanced Photon Source, CHESS User Meeting workshop Advances in Serial Synchrotron Crystallography, Cornell University, NY, USA, June 2017.

20. X-ray free-electron laser applications in biology, Asia Oceania Forum for Synchrotron Radiation School, Melbourne, Australia, 2017.

21. Between and beyond Bragg reflections: Macromolecular diffractive imaging from crystals & finite crystal phasing at XFELs, Understanding Biology Through Structure, Santa Fe, NM, USA, 2017.

22. Serial femtosecond x-ray crystallography of carbon monoxide-bound Cytochrome c Oxidase. 4th Annual BioXFEL International Conference, Las Vegas, NV, USA, January 2017.

23. Serial femtosecond crystallography at LCLS: the first 5 years. 5th International Symposium on Diffraction Structural Biology, Oak Ridge National Laboratory, Oak Ridge, TN, USA, August 2016.

24. Making the most out of XFELs. Gordon Research Conference on Diffraction Methods in Biology, Lewiston, ME, USA, July 2016. 

25. Serial femtosecond crystallography with XFELs: Data Analysis and Research Highlights. SwissFEL Seminar, Paul Scherrer Institute, Switzerland, 2016.

26. Highlights in data analysis developments. BioXFEL NSF Site visit, Buffalo, NY, USA, 2016. 

27. Serial femtosecond crystallography using XFELs. Physics Seminar, La Trobe University, Australia, 2015. 

28. Serial femtosecond crystallography using XFELs. Physics Seminar, Monash University, Australia, 2015. 

29. Association of BioXFEL Young Scientists workshop. BioXFEL STC 2nd Annual International Conference, Ponce, Puerto Rico, USA, 2015.

30. Software tools for the analysis of serial crystallography data. IUCr 2014 Workshop on Crystallography at XFEL Sources. Montréal, Canada, 2014.

31. Serial femtosecond protein nano-crystallography using a free-electron laser. Dept. of Physics Colloquium, U. Wisconsin-Milwaukee, WI, USA, 2013. 

32. Serial femtosecond nano-crystallography data analysis. Workshop on Dynamic Structural Photo-crystallography in Chemistry & Materials Science, University at Buffalo, SUNY, New York, USA, 2013.

33. High-resolution diffraction from membrane protein nanocrystals using serial femtosecond crystallography. Gordon Research Conference on Diffraction Methods in Structural Biology. Invited as speaker from poster session. Lewiston, ME, USA, July 2012.

34. Development of a new in situ x-ray diffraction technique for characterising embedded nanoparticles. Seminar at Paul Scherrer Institute, Switzerland, 2009.

35. Advances in real time X-ray diffraction in-situ nanoscopy. X-ray Micro & Nanoprobes, Palinuro, Italy, 2009.

36. Toward in situ X-ray diffraction imaging at the nanometer scale. SPIE Optics and Photonics: NanoScience and Engineering, San Diego, CA, USA, 2008.

Conferences and workshops

• 2024 (upcoming) Invited speaker, Serial crystallography theory and statistics/data quality, EMBO Practical Course on Time-resolved macromolecular serial crystallography, Grenoble, France.

• 2023  Organiser and speaker, Recent breakthroughs and developments in sample delivery methods for X-ray serial crystallography. Upcoming satellite workshop of IUCr 2023, La Trobe University, Australia

• 2023  Organiser, Novel Data Methods for Crystallography, upcoming 1.5 day workshop at the Software Fayre at IUCr 2023, Melbourne, Australia.

• 2023  Committee Member of International Program for IUCr 2023 (August 2023): The 26th Congress and General Assembly of the International Union of Crystallography, Melbourne, Australia.

• 2019            Advisor for Workshop on Macromolecular Serial Crystallography using the LCP Jet Injector at NSLS-II & CFN Users’ Meeting, NY.  Dr. Chufeng Li and Dr. Sabine Botha from the Zatsepin lab presented. 

• 2019            Chair of the BioXFEL 6th Annual International Meeting, San Diego, CA.

• 2018            Organizer of the New Opportunities at the European XFEL Workshop at the BioXFEL 5th Annual International Conference, New   Orleans, LA, USA.

• 2018            Chair of conference session on New Measurement and Analysis Strategies at the BioXFEL 5th Annual International Conference, New Orleans, LA, USA.

• 2016            Organizer and instructor at the 2016 ACA Serial Crystallography Data Analysis Workshop, an international computational workshop held at the American Crystallographic Association Annual Meeting, Denver, CO, USA.

• 2015            Chair of conference session Advances in multi-crystal approaches and serial crystallography at the Annual Meeting of the American Crystallographic Association, Philadelphia, PA, USA.

• 2015            Organizer and instructor at Serial crystallography data analysis with Cheetah and CrystFEL: concepts and tutorials, a sold-out, international computational workshop at ACA Annual Meeting, Philadelphia, PA, USA.

• 2014            Organizer and presenter at the Conference for BioXFEL Students and Postdocs at the SSRL/LCLS Annual Users’ Meeting and Workshops, Palo Alto, CA, USA.

• 2014            Organizer and speaker at the Two-day workshop on Bio-XFEL data analysis. Lawrence Berkeley National Lab, Berkeley, CA, USA.

• 2013            Instructor of workshop session on Computer exercises: Introduction to serial femtosecond crystallography data analysis with CrystFEL, Dynamic Structural Photocrystallography in Chemistry & Materials Science, University at Buffalo, SUNY, NY, USA.

• 2013            Instructor at Nanocrystal data analysis workshop, CFEL, DESY, Hamburg, Germany.

• 2014            Attendee of APS data collection workshop and CCP4 school, From data collection to structure refinement and beyond. APS, Argonne National Laboratory, IL, USA.

• 2013            Chair of conference session and presenter for Updates on Photosystem I and II at the 4th Imager          Retreat, Koenigstein, Germany.          

Outreach

• 2024 (Upcoming) Speaker at Girls in Physics Breakfast (VicPhysics), Bendigo 2024. https://www.vicphysics.org/events/girls/ 

• 2024 Interviewee on Triple R 102.7FM Melbourne Independent Radio show, Einstein a Go-Go https://www.rrr.org.au/explore/programs/einstein-a-go-go/episodes/28351-einstein-a-go-go-25-february-2024   

• 2023        Mentor for year 11 students through the Alumni Mentor Matching Program, Kilvington Grammar School, Ormond, Australia

• 2023        Interviewee subject for high school student project focusing on the professional use of advanced maths (female year 11 student in Tennessee, USA).

• 2019        Invited lecture at girls’ school on "The role of mathematics in science" for grade 9 mathematics class, Presbyterian Ladies' College, Melbourne, Australia.

• 2018         Local organizing committee member for American Physical Society Conference for   Undergraduate Women in Physics held at Arizona State University (for the southwest region).

• 2016        Grand Award Judge for Intel Science and Engineering Fair Physics & Astronomy (high school)

• 2015        Interviewed for a documentary by the American Institute of Physics, highlighting biology with XFELs. Trailer: https://youtu.be/AsSEDgjeFcE

• 2014        Interviewed for the BioXFEL promotional video. “Center for Biology with X-ray free electron lasers – Understanding Molecular Machines”, by WebsEdge Science https://youtu.be/ellwt1n_CbI

• 2012         Poster judge at Graduate Student Research Poster Exhibit in Chemistry & Biochemistry, Arizona      State University.

• 2011        Science representative at ASU Origins Project outreach event 'The Matter of Origins', bridging physics and modern dance, held at Arizona State University Gammage Auditorium.

• 2008        Intern at Catalyst, Australian Broadcasting Corporation. Researched science news and developed publicly accessible stories from formal scientific publications. Two of my story ideas led to televised research stories on Catalyst.

• 2004 – 2007  Siemens Science Week Instructor for year 10 students. Led interactive sessions on the physics and mathematics of soap film and optimization at this annual event at Monash University..

• 2005        TV segment presenter on “Totally Wild” (Network TEN, Australia). Guest TV segment on the mathematics of soap film and bubbles on a children’s weekly science show on national television. This invitation arose from the popularity of my Siemens Science Week activity at Monash Uni.

Awards

• 2022 ARC Future Fellowship (2023-2027)

• Science journal’s 2012 ‘Breakthrough of the Year Runner Up’, First protein structure from an X-ray laser, for X-ray laser crystallography: Redecke et al. Science 2013 339 (6116) 227 – 2302012.

• Ultrafast X-ray Summer School, SLAC Nat. Accel. Lab. XFEL proposal poster prize, 2012

• Australian Postgraduate Award, 2006 - 2009

• SPIE Scholarship in Optical Science and Engineering, 2008

• J.L. William Honours scholarship, Monash University, 2005

Skills

• High performance computing, batch processing, big data management/curation (>100 experiments)

• Crystallography software, including CrystFEL, MOSFLM, Phenix, CCP4, PyMOL.

• Proficient with Unix, BASH scripts, git; familiar with Python, MATLAB, IDL, C.

Languages

• English, Russian (fluent) - no, it doesn't make me Russian. I'm Ukrainian and, like any sane and moral person, obviously against the horrendous Russian war.

• Ukrainian, French, Spanish (beginner)

Music

• Classical piano - Associate in Music, Australia (AMusA), 1999

• Jazz and folk gigs