Publications

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Recent Papers

  1. For a brief summary of highlight papers and topics since 1975, see http://www.public.asu.edu/~jspence/

  2. "Lightspeed". A history of the Aether. How the search for an absolute frame of reference in the Universe led to Einstein's relativity and the atom bomb.  Oxford University Press (2019). J.C.H. Spence.

  3. "High Resolution Electron Microscopy". OUP. (2017).  J.C.H. Spence.

  4. "Outrunning damage: Electrons vs X-rays - timescales and mechanisms" Structural Dynamics. 4, 044027 (2017). J.C.H.Spence.

  5. "XFELS for structure and dynamics in biology".  Spence, J.C.H. (2017). IUCrJ  4, 322 - 339


2019

  1. "Nanopatterned electron beams for temporal coherence and deterministic phase control of x-ray free-electron lasers " W.S. Graves, S.L.Y. Chang, C. Dwyer, P. Fromme, M. Holl, B.D.A. Levin, L.E. Malin, M.A. Roldan, J.L. Vincent, J.C.H. Spence  E.A. Nanni, R.K. Li, X. Shen, S. Weathersby and A. Sandhu.  Submitted to Phys Rev Accel. Beams.  Jun 5 (D-Day) 2019.  STC.

  2. "High-viscosity injector-based Pink Beam Serial Crystallography of Micro-crystals at a Synchrotron Radiation Source"  Jose  Martin-Garcia1,  Lan Zhu,  Derek  Mendez,  Ming-Yue  Lee,  Eugene  Chun,  Chufeng  Li,  Hao..Hu,  Ganesh  Subramanian,  David  Kissick,  Craig  Ogata,  Robert  Henning,  Andrii  Ishchenko,  Zachary  Dobson,  Shangji  Zhang,  Uwe  Weierstall,  John  Spence,  Petra..Fromme,  Nadia  Zatsepin,  Robert Fischetti,Vadim Cherezov and  Wei Liu.  IUCrJ.   6, 1.  (2019).  STC.

  3. Membrane Protein Megahertz Crystallography at the European XFEL

    Chris Gisriel, Jesse Coe1,2,3,4, Romain Letrun5, Cesar Luna-Chavez1,2, Natasha E. Stander1,2, Gihan K. Ketawala1,2, Stella Lisova1,6, Oleksandr N. Yefanov7, Valerio Mariani7, Thomas D. Grant8, Katerina Dörner5, Tokushi Sato5,7, Austin Echelmeier1,2, Jorvani Cruz Villarreal1,2, Mark S. Hunter9, Max O. Wiedorn7,10,11, Juraj Knoska7, Victoria Mazalova7, Shatabdi Roy-Chowdhury1,2, Jay-how Yang1,2, Alex Jones1,2, Richard Bean5, Johan Bielecki5, Yoonhee Kim5, Grant Mills5, Britta Weinhausen5, Jose Domingo Meza5, Nasser Al-Qudami5, Sasa Bajt7, Gerrit Brehm1,2, Sabine Botha1,6, Dielloul Boukelef5, Sandor Brockhauser5,12, Barry D. Bruce13,14,15, Matthew A. Coleman16, Cyril Danilevski5, Erin Discianno1, Zachary Dobson1,2, Hans Fanghor5,12, Jose M. Martin-Garcia1, Yaroslav Gevorkov7,17, Steffen Hauf5, Klaus Giewekemeyer5, Ahmad Hosseinizadeh18, Friederike Januschek5, Christopher Kupitz9,18, Luis Maia5, Maurizio Manetti5, Marc Messerschmidt1,2,5, Thomas Michelat5, Jyotirmoy Mondal13,14,15, Dominik Oberthür7, Abbas Ourmazd18, Gianpietro Previtali5, Iosifina Sarrou7, Silvan Schön7, Peter Schwander18, Megan L. Shelby16, Marcin Sikorski5, Alessandro Silenzi5, Jolanta Sztuk-Dambietz5, Janusz Szuba5, Monica Turcato5, Thomas A. White7, Krzysztof Wrona5, Chen Xu5, Mohamed H. Abdellatif7, James D. Zook1,2, John C. Spence1,6, Henry N. Chapman7,10,11, Anton Barty7, Richard A. Kirian1,6, Matthias Frank16, Alexandra Ros1,2, Marius Schmidt18, Raimund Fromme, Adrian P. Manusco, Petra Fromme and Nadia Zatsepin. PSI. Submitted  Feb 2019. Nature Comms.  STC

  4. Book review "Principles of Electron Optics". P.Hawkes and E. Kasper.  Microscopy and Microanalysis. 1, (2019). by J.C.H. Spence.

  5. "SPIND: a referenc-based auto-indexing algorithm for sparse serial crystallography data. Chufeng Li, Xuanxuan Li, Richard Kirian, John Spence, Haiguang Liu and Nadia Zatsepin. IUCrJ. 6, 72 - 84  (2019). STC.

  6. "Snapshot of an Oxygen intermediate in the catalytic reaction of cytochrome c oxidase"  :  Izumi Ishigami, Ariel Lewis-Ballester, Austin Echelmeier, Garrit F. Brehm, Nadia A. Zatsepin, Thomas D. Grant, Jesse D. Coe, Garrett Nelson, Shangli Zhang, Zachary F. Dobson, Sebastein Boutet, Raymond G. Sierra, Alexander Batyuk, Petra Fromme, Raimund Fromme, John Spence, Alexandra Ros, Syun-Ru Yeh and Denis L. Rousseau.. PNAS  (2019)  STC. PNAS published ahead of print February 11, 2019  https://doi.org/10.1073/pnas.1814526116


2018

  1. "X-ray lasers for structure and dynamics in biology" J.C.H.Spence  IUCrJ 5, 236-237 (2018)  Editorial.  STC

  2. "Supersaturation-controlled microcrystallization and visualization analysis for SFX"  Dan Bi Lee, Jong-Min Kim, Jong Hyeon Seok, Ji-Hye Lee, Jae Deok Jo, Ji Young Mun, Chelsie Conrad, Jesse Coe , Gerrett Nelson, Brenda Hogue, Thomas A. White, Nadia Zatsepin, Uwe Weierstall, Anton Barty, Henry Chapman , Petra Fromme, John Spence, Mi Sook Chung, Chang-Hyun Oh & Kyung Hyun Kim.  Scientific Reports. 8,  2541 (2018). STC.

  3. "The phase problem for two-dimensional crystals. II. Simulations". R. Arnal, Yun  Zhao,  A. Mitra, J.C.H. Spence and Rick P.Millane.  Acta. Cryst. A74. p.537.  (2018)   STC.

  4. "Direct structural and chemical characterization of photolytic intermediates of Methylcobalamin using time-resolved X-ray absorption spectroscopy." G. Subramanian, X. Zhang, G. Kodis,  Q. Kong, A. Chizmeshya, U.Weierstall,1 and J.C.H. Spence.  J. Phys Chem Letts. (2018) Submitted.  STC.

  5. "Enzyme Intermediates Captured “on-the-fly” by Mix-and-Inject Serial Crystallography".  Jose Olmos, Suraj Pandey, Jose M. Martin-Garcia, George Calvey, Andrea Katz, Juraj Knoska, Christopher Kupitz, Mark S. Hunter, Mengning Liang, Dominik Oberthuer, Oleksandr Yefanov, Max Wiedorne, Michael Heyman, Mark Holl, Kanupriya Pande, Anton Barty, Mitchell D. Miller, Stephan Stern, Shatabdi Roy- Chowdhury, Jesse Coe, Nirupa Nagaratnam, James Zook, Tyler Norwood, Ishwor Poudyal, David Xu, Jason Koglin, Matt Seaberg, Yun Zhao, Saša Bajt, Thomas Grant, Valerio Mariani, Garrett Nelson, Ganesh Subramanian, Euiyoung Bae, Raimund Fromme, Russel Fung, Peter Schwander, Matthias Frank, Thomas White, Uwe Weierstall, Nadia Zatsepin, John Spence, Petra Fromme, Henry N. Chapmane, Lois Pollack, Lee Tremblay, Abbas Ourmazd, George N. Phillip, Jr., Marius Schmidt .  BMC Biology. 16:59   (2018).  STC.

  6. "Phasing XFEL serial crystallography data". R. Kirian J. P. Chen and J.C.H.Spence. in "X-ray free electron lasers : a revolution in structural biology.". P. Fromme, M. Hunter, S. Boutet. Eds. Springer. (2018).  STC.


2017

  1. "Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography". Dan Bi Lee,, Jong-Min Kim, Jong Hyeon Seok, Ji-Hye Lee, Jae Deok Jo, Ji Young Mun, Chelsie Conrad, Jesse Coe, Gerrett Nelson, Brenda Hogue, Thomas A. White, Nadia Zatsepin, Uwe Weierstall, Anton Barty, Henry Chapman, Petra Fromme, John Spence, Mi Sook Chung, Chang-Hyun Oh, and Kyung Hyun Kim. Submitted PNAS (2017). 

  2. "The ASU Compact XFEL". W.S. Graves, J.P.J. Chen, P. Fromme, M.R. Holl, R. Kirian, L.E. Malin, K.E. Schmidt, J.C.H. Spence, M. Underhill, U. Weierstall, N.A. Zatsepin, C. Zhang, Arizona State University, Tempe, USA P.D. Brown, K.-H. Hong, D.E. Moncton, MIT, Cambridge, USA E.A. Nanni, C. Limborg-Deprey, SLAC, Menlo Park, USA .  "Free Electron Lasers" Conference. 2017.  https://www.fel2017.com

  3. "Crystal structures of phytochrome from the photomorphogenic myxobacterium Stigmatella aurantiaca determined at cryogenic and ambient temperatures" Nicole C. Woitowich, Andrei S. Halavaty, Paticia Waltz, Chris Kupitz, Joseph Valera, Gregory Tracy, Kevin D. Gallagher, Elin Claesson, Takanori Nakane, Suraj Pandey, Garrett Nelson, Rie Tanaka, Eriko Nango, Eiichi Mizohata, Shigeki Owada, Kensure Tono, Yasumasa Joti, Angela C. Nugent, Hardik Patel, Ayesha Mapara, Phu Duong, Dorina Bizhga, Svetlana E. Kovaleva, Rachael St. Peter, Cynthia N. Hernandez, Wesley B. Ozarowski, Shatabdi Roy-Showdhuri, Jay-How Yang, Petra Edlund, Heikki Takala, Janne Ihaleinen, Jennifer Scales, Tyler Norwood, Ishwor Poudyal, Petra Fromme, John Spence, Keith Moffat, Sebastian Westenhoff, Marius Schmidt & Emina A. Stojković. Sci. Adv. Submitted June 16 2017.  STC.

  4. "Serial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation"  Jose M. Martin-Garcia, Chelsie E. Conrad, Garrett Nelson, Natasha Stander, Nadia A. Zatsepin, James Zook, Lan Zhu, James Geiger, Eugene Chun, David Kissick, Mark C. Hilgart, Craig Ogata, Andrii Ishchenko, Nirupa Nagaratnam, Shatabdi Roy-Chowdhury, Jesse Coe, Ganesh Subramanian, Alexander Schaffer, Daniel James, Gihan Ketawala, Nagarajan Venugopalan, Shenglan Xu, Stephen Corcoran, Dale Ferguson, Uwe Weierstall, John C. H. Spence, Vadim Cherezov, Petra Fromme, Robert F. Fischetti, Wei Liu. IUCrJ  4, 439-454 (2017)   STC.

  5.  "Double- flow focused liquid injector for efficient serial femtosecond crystallography" Dominik Oberthuer, Juraj Knoška, Max O. Wiedorn, Kenneth R. Beyerlein, David A. Bushnell, Elena G. Kovaleva, Michael Heymann, Lars Gumprecht, Richard A. Kirian, Anton Barty, Valerio Mariani, Aleksandra Tolstikova, Luigi Adriano, Salah Awel1, Miriam Barthelmess, Katerina Dörner, P. Lourdu Xavier, Oleksandr Yefanov, Daniel R. James, Garrett Nelson, Dingjie Wang, George Calvey, Yujie Chen, Andrea Schmidt, Michael Szczepek, Stefan Frielingsdorf, Oliver Lenz, Edward Snell, Philip J. Robinson4, Božidar Šarler, Grega Belšak, Marjan Maček, Fabian Wilde, Andrew Aquila, Sébastien Boutet, Mengning Liang, Mark S. Hunter, Patrick Scheerer, John D. Lipscomb, Uwe Weierstall, Roger D. Kornberg,John C. H. Spence, Lois Pollack, Henry N. Chapman & Saša Bajt.  Nature Scientific Reports (2017) . 7, 44628. STC

  6. "Outrunning damage:  Electrons vs X-rays - timescales and mechanisms". J.C.H.Spence. Fest. Volume for Prof. A. Zewail. Structural Dynamics. 4, 044027 (2017).  STC,ABI.

  7. "Split second reactions".  P. Fromme and J.C.H. Spence. Scientific American 316, 63-67 (2017). April 2017.

  8. "Imaging protein dynamics by XFEL". J.C.H.Spence. in "X-ray free electron lasers". Eds. U. Bergmann, Y. Yachandra and J. Yano. (2017). Roy Soc Chem. . NSF STC award 1231306  and Nadia NSF ABI 1565180

  9. "XFELS for structure and dynamics in biology".  Spence, J.C.H. (2017). IUCrJ  4, 322-339   https://doi.org/10.1107/S2052252517005760.  STC and ABI.  Hyderbad.

  10.  "Diffractive imaging for single particles and XFEL data analysis". J.C.H.Spence. in "Science of Microscopy". P. Hawkes and J.C.H.Spence Eds. Springer. (2017). STC and ABI.

  11. "Serial Crystallography at synchrotrons and free-electron lasers.  J. Standfuss and J.C.H.Spence. IUCrJ 4,  (2017).  STC. 

  12. "Coherent soft X-ray diffraction imaging of coliphage PR722 at the LCLS". Hemanth K. N. Reddy, Chun Hong Yoon, Gabriella Carini2, Maximilian Bucher, Andrew Aquila, Salah Awel, Kartik Ayyer, Anton Barty, Peter Berntsen, Johan Bielecki, Sergey Bobkov, Sebastian Carron, Henry Chapman, Benedikt Daurer, Hasan DeMirci, Tomas Ekeberg, Petra Fromme, Janos Hajdu, Max Felix Hanke, Philip Yoonhee Kim, Richard A. Kirian, Ruslan P. Kurta, Daniel S. D. Larsson, N. Duane Loh, Filipe R.N.C. Maia, Adrian Mancuso, Kerstin Mühlig, Anna Munke, Daewoong Nam, Carl Nettelblad, Abbas Ourmazd, Max Rose, Peter Schwander, Marvin Seibert, Jonas A. Sellberg, Changyong Song, John C. H. Spence, Martin Svenda, Gijs Van der Schot, Ivan A.Vartanyants, Garth J. Williams, P. Lourdu Xavier STC. Scientific Data 2017. 

  13. "X-Ray lasers in biology: Structure and Dynamics. Spence, J.C.H. Advances in Imaging and Electron Physics 200, 103 - 152. (2017). Ed P. Hawkes. Elsevier. New York. STC. and ABI.

  14. "Short wavelength free electron laser sources and science: a review". Seddon, Elaine; Clarke, Jim; Dunning, David; Masciovecchio, Claudio; Milne, Chris; Parmigiani, Fulvio; Rugg, David; Spence, John; Thompson, Neil; Ueda, Kiyoshi; Vinko, Sam; Wark, Justin; Wurth, Wilfried . Rep Prog Phys. 80,  115901 (2017).  STC. and ABI.

  15. "Atomic structure of granulovirus polyhedrin  determined from native nanocrystalline virus particles using an X-ray free-electron laser". Cornelius Gati1**, Dominik Oberthuer, Oleksandr Yefanov, Richard D. Bunker, Francesco Stellato, Elaine Chiu2, Shin-Mei Yeh, Andrew Aquila1,3, Thomas Barends4, Shibom Basu, Richard Bean, Kenneth Beyerlein, Sabine Botha, Sébastien Boutet, Daniel DePonte, R. Bruce Doak, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Daniel R. James, Christopher Kupitz, Lukas Lomb, Marc Messerschmidt, Karol Nass, Kimberley Rendek, Robert L. Shoeman,  Dingjie Wang, Uwe Weierstall, Thomas A. White, Garth J. Williams, Nadia A. Zatsepin, Petra Fromme, John Spence, Ilme Schlichting, Kenneth N. Goldie, Johannes Jehle, Peter Metcalf, Anton Barty, Henry N. Chapman. PNAS. Accepted  (2017).  STC and ABI ?

  16. "Structural enzymology using X-ray free electron lasers".  Christopher Kupitz1≠, Jose L. Olmos Jr.2≠, Mark Holl4, Lee Tremblay?, Kanupriya Pande6,7, Suraj Pandey1, Dominik Oberthür6,7, Mark Hunter8, Mengning Liang8, Andrew Aquilla8, Yujie Chen3, Andrea Katz3, George Calvey3, Jason Tenboer1, Tyler Norwood1, Ishwor Poudyal1, Valerio Mariani, Thomas Grant10, Mitchell D. Miller2, Max Wiedorn6, Juraj Knoska6, Alke Meents7, Aleksandra Tolstikova6, Andrew Morgan6, Markus Metz6, Jose Martin-Gracia4, James Zook4, Shatabdi Roy-Chowdhury4, Chelsie Conrad4, Jesse Coe4, Nirupa Nagaratnam4, Domingo Meza4, Raimund Fromme4, Matthias Frank9, Thomas White6, Anton Barty6, Sasa Bait, Oleksandr Yefanov6, Henry Chapman6, Nadia Zatsepin6, Garrett Nelson6, Uwe Weierstall5, John Spence5, Peter Schwander1, Lois Pollack3 Petra Fromme4, Abbas Ourmazd1, George N. Phillips Jr.2, Marius Schmidt1  Structural Dynamics. 4, 044003   (2017). STC.

  17. "Time-resolved structures of a riboswitch RNA by diffusion-delay-diffraction using XFEL". J.R. Stagno, Y. Bhandari, C. Conrad, Y. Liu, Monalisa Swain, G. Nelson, C. Li, D.R. Wendel, T. White, A. Barty, R.A. Tuckey, P. Y, U. Weierstall, N. Zatsepin, P. Fromme, X. Ji, J.C.H. Spence, Y.-X. Wang.  Nature, 541, p.242. 2017  STC 1231306. 

  18. "Merging single-shot  XFEL diffraction data from inorganic particles: a new approach to size and orientation determination"  Xuanxuan Li, John. C. H. Spence, Brenda G. Hogue, Haiguang Liu.  IUCrJ  4, 1 (2017)   NSF STC 1231306. 


2016

  1. "Ondrej Krivanek's early scientific research".  J.C.H. Spence. Ultramic. 180,  8-13  (2016). STC.

  2. " Diffraction data of core-shell nanoparticles from X-ray Free Electron Laser".  X. Li….J. Spence….Haiguang Liu.   Science Data. (2016).  STC.

  3. "Imaging enzyme kinetics at atomic resolution". J.C.H. Spence and E. Lattman.  IUCrJ , 3. 228 – 229 (2016). Commentary on "Serial crystallography captures enzyme catalysis in copper nitrite reductase" by Horrell S et al. IUCrJ.  (2016).

  4. "The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography".   Petra Edlund, Heikki Takala, Elin Claesson, Léocadie Henry, Robert Dods, Heli Lehtivuori, Matthijs Panman, Kanupriya Pande, Thomas White, Takanori Nakane, Oskar Berntsson, Emil Gustavsson, Petra Båth, Vaibhav Modi, Shatabdi Roy-Chowdhury, James Zook, Peter Berntsen, Suraj Pandey, Ishwor Poudyal, Jason Tenboer, Christopher Kupitz, Anton Barty, Petra Fromme, Jake D. Koralek, Tomoyuki Tanaka, John Spence, Mengning Liang, Mark S. Hunter, Sebastien Boutet Eriko Nango, Keith Moffat, Gerrit Groenhof, Janne Ihalainen, Emina A. Stojković, Marius Schmidt, and Sebastian Westenhoff   Scientific Reports 6:35279 (2016).      STC.

  5. “Measurements of transmitted electron beam extinction through silicon crystal membranes”.  E. A. Nanni†, C. Limborg, W. S. Graves, R. Kirian, J. Spence, U. Weierstall.  IPAC16  (2016).  STC1231306.

  6. “X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex”. X. E. Zhou…..J. Spence, E. Xu   Scientific Data. 3, UNSP 160021 (2016). STC 1231306

  7. “Native Phasing of X-ray Free Electron Laser data for a G protein-coupled receptor”. Alexander Batyuk, Lorenzo Galli, Andrii Ishchenko, Gye Won Han3, Cornelius Gati2, Petr Popov4, Ming-Yue Lee3, Thomas A. White2, Anton Barty2, Andy Aquila5, Mark S. Hunter5, Mengning Liang5, Sébastien Boutet5, Mengchen Pu6, Zhi-jie Liu6,7, Garrett Nelson8, Daniel James8, Chufeng Li8, Yun Zhao8, John C.H. Spence8, Wei Liu9, Petra Fromme9, Vsevolod Katritch10, Uwe Weierstall8, Raymond C. Stevens3,10, Vadim Cherezov,  (Adenosine receptor).  Science Advances. Accepted Aug 1,   2016. STC 1231306

  8. "XFEL Data analysis for structural biology".  H. Liu and J.C.H. Spence. Quantitative Biology 4,   pp.159 - 176   (2016). STC 1231306.  doi:10.1007/s40484-016-0076-z.

  9. "Sub-millisecond switching of a liquid jet using a 2D Laval profile in a composite microfluidic gas dynamic virtual nozzle". G. Nelson, R. B. Doak, U. Weierstall and J. C. H. Spence. Experiments in fluids. Submitted.  (2016)  STC 1231306.

  10. "Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein" . Kanupriya Pande, Christopher D. M. Hutchison, Gerrit Groenhof, Andy Aquila, Josef S. Robinson, Jason Tenboer, Shibom Basu, Sébastien Boutet, Daniel P. DePonte, Mengning Liang, Thomas A. White, Nadia A. Zatsepin, Oleksandr Yefanov, Dmitry Morozov, Dominik Oberthuer, Cornelius Gati, Ganesh Subramanian, Daniel James, Yun Zhao, Jake Koralek, Jennifer Brayshaw, Christopher Kupitz, Chelsie Conrad, Shatabdi Roy-Chowdhury, Jesse D. Coe, Markus Metz, Paulraj Lourdu Xavier, Thomas D. Grant, Jason E. Koglin, Gihan Ketawala, Raimund Fromme, Vukica Šrajer, Robert Henning, John C. H. Spence, Abbas Ourmazd, Peter Schwander, Uwe Weierstall, Matthias Frank, Petra Fromme, Anton Barty, Henry N. Chapman, Keith Moffat, Jasper J. van Thor, Marius Schmidt . Science. Vol 352, issue 6286, p. 725 .  STC. (2016).

  11. "3D-printed Gas Dynamic Virtual Nozzles for X-ray Laser Sample Delivery". G. Nelson,a M. Heymann,b R. A. Kirian,a U. Weierstall,a N. Zatsepin,a T. Faragó,c T. Baumbach,c F. Niesler,d B. Zimmerd and J. C. H. Spence.. Optics Express 24, 11515  (2016).. NSF STC 1231306.

  12. "Macromolecular diffractive imaging using imperfect crystals"  Kartik Ayyer, Oleksandr Yefanov, Dominik Oberthür, Shatabdi Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse Coe, Chelsie E. Conrad, Raimund Fromme, Katerina Dorner, Matthias Frank, Daniel James, Christopher Kupitz, Markus Metz, Garrett Nelson, Xavier Lourdu Paulraj, Kenneth Beyerlein, Marius Schmidt, Iosifina Sarrou, John C. H. Spence, Uwe Weierstall, Thomas A. White, Jayhow Yang, Nadia A. Zatsepin, Yun Zhao, Mengning Liang, Andrew Aquila, Mark Hunter, Joseph S. Robinson, Jason E. Koglin, Sebastien Boutet, Petra Fromme, Anton Barty, and Henry N. Chapman. Nature, p. 202, Vol 530,  (2016).  NSF STC 1231306.

  13. "Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography" by Przemyslaw Nogly, Valerie Panneels, Garrett Nelson, Cornelius Gati, Tetsunari Kimura, Christopher Milne, Despina Milathianaki, Minoru Kubo, Wenting Wu, Chelsie Conrad, Jesse Coe, Richard Bean, Yun Zhao, Petra Bath, Robert Dods, Rajiv Harimoorthy, Kenneth Beyerlein, Jan Rheinberger, Daniel James, Daniel DePonte, Chufeng Li, Leonardo Sala, Garth Williams, Mark Hunter, Jason Koglin, Peter Berntsen, Eriko Nango, So Iwata, Henry Chapman, Petra Fromme, Matthias Frank, Rafael Abela, Sébastien Boutet, Anton Barty, Thomas White, Uwe Weierstall, John Spence, Richard Neutze, Gebhard Schertler, and Joerg Standfuss . Nature Communications.  7  (2016). NSF STC 1231306.


2015

  1. “Image reconstruction in serial femtosecond nanocrystallography using x-ray free-electron lasers”   J.P.J. Chen, R.A. Kirian, K.R. Beyerlein, R.J. Bean, A.J. Morgan, O.M. Yefanov, R.D. Arnal, D.H. Wojtas, P.J. Bones, H.N. Chapman, J.C.H. Spence and R.P. Millane.  Image reconstruction in serial femtosecond nanocrystallography using x-ray free-electron lasers.  In “Image Reconstruction from Incomplete Data VIII,” P.J. Bones, M.A. Fiddy and R.P. Millane (Eds.), Proc. SPIE, Vol. 9600, 960002, 2015. STC 1231306

  2. "The LCLS Single Particle Imaging Road Map"  A. Aquila, A. Barty, C. Bostedt, S. Boutet, G. Carini, D. dePonte, P. Drell, S. Doniach, K. H. Downing, T. Earnest, H. Elmlund, V. Elser, M. Gu ̈hr, J. Hajdu, J. Hastings, S. P. Hau-Riege, Z. Huang, E. E. Lattman, F. R. N. C. Maia, S. Marchesini, A. Ourmazd, C. Pellegrini, R. Santra, 19 I. Schlichting, C. Schroer, J. C. H. Spence, I. A. Vartanyants, S. Wakatsuki, W. I. Weis, and G. J. Williams. Structural Dynamics. 2, 041701 (2015)  doi = "http://dx.doi.org/10.1063/1.4918726 STC 1231306.

  3. "Surface Microscopy with low energy electrons", by E. Bauer.  Book Review. "Microscopy and Microanalysis (2015) 21(3):788 – 789.  J.C.H. Spence.

  4. "Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography." Zhang, Haitao, Hamiyet Unal, Cornelius Gati, Gye Won Han, Wei Liu, Nadia A. Zatsepin, Daniel James et al. " Cell 16 No 4, p.833-844. (2015).  NSF STC 1231306.

  5. "Serial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase" 
    Raimund Fromme, Andrii Ishchenko, Markus Metz, Shatabdi Roy Chowdhury, Shibom Basu, Sebastien Boutet, Petra Fromme, Thomas White, Anton Barty, John Spence, Uwe Weierstall, Wei Liu and Vadim Cherezov. IUCrJ (2015) 2, No 5. 545-551 NSF STC 1231306.

  6. A. Aquila et al., " The linac coherent light source single particle imaging road map" Structural Dynamics 2, 041701 (2015)   doi = "http://dx.doi.org/10.1063/1.4918726

  7. "X-ray lasers and serial crystallography". J.C.H. Spence. IUCrJ (2015). STC award 1231306.  Spence, J. (2015). IUCrJ 2, doi:10.1107/S2052252515008027.

  8. "Hollow cone illumination for fast TEM, and outrunning damage with electrons".
    J.C.H.Spence, G. Subrumanian and P. Musumeci.  J.Phys B. (AMO). 48, 214003. (2015) NSF STC award 1231306. (2015) .

  9. "Serial femtosecond x-ray diffraction of enveloped virus micro-crystals".  Robert M. Lawrence1, Chelsie 3, Nadia A. Zatsepin4, Tom D. Grant5, Haiguang Liu6, Daniel James4, Garrett Nelson4, Ganesh Subramanian4, Andrew Aquila7, Mark Hunter7, Jesse Coe3, John C.H. Spence1,4, Uwe Weierstall1,4, Wei Liu8, Petra Fromme1,3, Vadim Cherezov8, Edward Snell5, Brenda G. Hogue.  Structural Dynamics. NSF STC award 1231306. (2015) .

  10. "Structural basis for bifunctional peptide recognition at human δ-opioid receptor"
               Gustavo Fenalti1,16, Nadia A Zatsepin2, Cecilia Betti3,4, Patrick Giguere5–7, Gye Won Han1,16, Andrii Ishchenko1,16, Wei Liu1,16, Karel Guillemyn3,4, Haitao Zhang1,16, Daniel James2, Dingjie Wang2, Uwe Weierstall2, John C H Spence2, Sébastien Boutet8, Marc Messerschmidt8,16, Garth J Williams8, Cornelius Gati9, Oleksandr M Yefanov9, Thomas A White9, Dominik Oberthuer9,10, Markus Metz9,11, Chun Hong Yoon9,12, Anton Barty9, Henry N Chapman9,11, Shibom Basu13,14, Jesse Coe13,14, Chelsie E Conrad13,14, Raimund Fromme13,14, Petra Fromme13,14, Dirk Tourwé3,4, Peter W Schiller15, Bryan L Roth5–7, Steven Ballet3,4, Vsevolod Katritch1,16, Raymond C Stevens1,16 & Vadim Cherezov.  Nature Struct and Mol Biol. . 22, 265 (2015) NSF STC award 1231306 (2015) doi:10.1038/nsmb.2965

  11. "Microfluidic sorting of protein nanocrystals by size for XFEL diffraction" Bahige G. Abdallah, Nadia A. Zatsepin, Shatabdi Roy-Chowdhury,  Jesse Coe, Chelsie E. Conrad, Katerina Dörner, Raymond G. Sierra, Hilary P. Stevenson, Fernanda Camacho-Alanis, Thomas D. Grant, Garrett Nelson, Daniel R. James, Guillermo Calero, Rebekka M. Wachter, John C. H. Spence, Uwe Weierstall, Petra Fromme, Alexandra Ros.. Structural Dynamics. 2(4)  p. 041720   (2015).  NSF STC award 1231306

  12.  "Electronic damage from S atoms in a native protein crystal induced by an intense X-ray free-electron laser".  L. Galli, S-K. Son, S. Bajt, T.R.M. Barends, A. Barty, R. Bean, K. Beyerlein, C. Caleman, B. Doak, H. Fleckenstein, C. Gati, B. Hunt, R. Kirian,  M. Liang, M.H. Nanao, K. Nass, D. Oberthür, L. Redecke R. Shoeman, F. Stellato, C.H. Yoon, T.A. White, O. Yefanov, I. Schlichting, J. Spence, and H.N. Chapman. Structural Dynamics, 2, 041703 (2015)  Puerto Rico issue 2015. NSF STC award 1231306

  13. "A novel inert crystal delivery medium for serial femtosecond crystallography" 
    Chelsie E. Conrad, Daniel James, Dingjie Wang, Alex Schaffer, Shatabdi Roy-Chowdhury, Shibom Basu, Nadia A. Zatsepin, Andrew Aquila4,6, Jesse Coe, Mark S. Hunter, Christopher Kupitz, Garrett Nelson, Ganesh Subramanian, Yun Zhao, James Zook, Sébastien Boutet, Vadim Cherezov, John C. H. Spence, Raimund Fromme, Uwe Weierstall, Petra Fromme.   IUCrJ  IUCrJ  2 (4) 421 - 430 (2015). Accepted.  STC NSF 1231306  Donaic  NIH RO1 GM097463-04 

  14.   "Monte-Carlo, Two-color and Goniometer-based XFEL structure factor measurements compared for time-resolved diffraction". Chufeng Li, Kevin Schmidt, and John C Spence. Structural Dynamics.  2, No 4,  041714 (2015)   Special BioXFEL Issue STC NSF 1231306.

  15. "Introduction to the theory and practice of space-group determination"  Uri Shmueli, Howard D. Flack and John C. H. Spence. Symmetry. (2015). Submitted.
    Longer version accepted by ITA6 (Int Tables).  Short version accepted by Brief Teaching edition of ITA6

  16.  " Lipidic cubic phase serial millisecond crystallography using synchrotron radiation" 
    Przemyslaw Nogly, Daniel James,Thomas White, Nadja Zatsepin, Anastasya Shilova, Garret Nelson, Michael Heymann, Kathrin Jäger, Markus Metz, Michael Heymann, Wenting Wu, Petra Baath, Valerie Panneels, Vadim Cherezov, Henry Chapman, Richard Neutze, John Spence, Gebhard Schertler, Isabel Moraes, Manfred Burghammer*, Jörg Standfuss*, Uwe Weierstall. IUCrJ  doi:10.1107/S2052252514026487, 2 (2015). STC award 1231306 and Donaic  NIH award 02597

  17.  "Crystal structure of rhodopsin bound to arrestin determined by femtosecond X-ray laser " Yanyong Kang1*, X. Edward Zhou1*, Xiang Gao1*, Yuanzheng He1*, Wei Liu2, Andrii Ishchenko3,4, Anton Barty5, Thomas A. White5, Oleksandr Yefanov5, Gye Won Han3,4, Qingping Xu6, Parker W. de Waal1, Jiyuan Ke1, M. H. Eileen Tan1,7, Chenghai Zhang1, Arne Moeller8, Graham M. West9, Ned Van Eps10, Lydia N. Caro11, Sergey A. Vishnivetskiy12, Regina J. Lee12, Kelly M. Suino-Powell1, Xin Gu1, Kuntal Pal1, Jinming Ma1, Xiaoyong Zhi1, Sébastien Boutet12, Garth J. Williams12, Marc Messerschmidt12, Cornelius Gati5, Nadia A. Zatsepin2,13, Dingjie Wang2,13, Daniel James2,13, Shibom Basu2,13, Shatabdi Roy-Chowdhury2,13, Chelsie Conrad2, Jesse Coe2, Haiguang Liu2, Stella Lisova2, Christopher Kupitz2, Ingo Grotjohann2, Raimund Fromme2, Yi Jiang14, Minjia Tan14, Huaiyu Yang14, Jun Li7, Meitian Wang15, Zhong Zheng3, Dianfan Li16, Yingming Zhao14,17, Jörg Standfuss18, Kay Diederichs19, Yuhui Dong20, Clinton S Potter8, Bridget Carragher8, Martin Caffrey16, Hualiang Jiang14, Henry N. Chapman5,21, John C. H. Spence2,13, Petra Fromme2, Uwe Weierstall2,13, Oliver P. Ernst11,22, Vsevolod Katritch3,4, Vsevolod V. Gurevich12, Patrick R. Griffin9, Wayne L. Hubbell10, Raymond C. Stevens3,4,23, Vadim Cherezov3,4,23, Karsten Melcher1, and H. Eric Xu. . NSF STC award 1231306. Nature, 523 (7562) 561 – 567  (2015).  


2014

  1. "Trace phase detection and strain characterization from serial X-ray free-electron laser crystallography of a Pr0.5Ca0.5MnO3 powder"  Kenneth R. Beyerlein, Christian Jooss, Anton Barty, Richard Bean, Sébastien Boutet, Sarnjeet S. Dhesi, R. Bruce Doak, Michael Först, Lorenzo Galli, Richard A. Kirian, Joseph Kozak, Michael Lang, Roman Mankowsky, Marc Messerschmidt, John C. H. Spence, Dingjie Wang, Uwe Weierstall, Thomas A. White, Garth J. Williams, Oleksandr Yefanov, Nadia A. Zatsepin, Andrea Cavalleri, and Henry N. Chapman. Powder Diffraction. p. 1- 6. Nov (2014)  STC NSF 1231306.

  2. "Approaches to time-resolved diffraction using an XFEL". J.C.H.Spence. Faraday Discussions. Vol 171, p 429 - 434 (2014)  STC NSF 1231306.

  3. "The indexing ambiguity in serial femtosecond 58 crystallography (SFX) resolved using an expectation maximization algorithm " Haiguang Liu and John C.H. Spence IUCrJ.  1, 393 - 401 (2014)  STC NSF 1231306. 

  4.  "Double focusing mixing jet for XFEL Study of Chemical Kinetics". D. Wang, U. Weierstall, L. Pollack and John Spence. J. Synch. Rad. 21, 1364 - 1366 (2014). STC NSF 1231306.

  5. "The birth of a new field".   J.C.H.Spence and H.N.Chapman. Phil. Trans. R. Soc. B 369, p. 20130309 (2014)

  6. "Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Jason Tenboer, Shibom Basu, Nadia Zatsepin, Kanupriya Pande, Despina Milathianaki, Matthias  Frank, Mark Hunter, Sébastien Boutet, Garth J.Williams, Jason E. Koglin, Dominik Oberthuer, Michael Heymann Christopher Kupitz, Chelsie Conrad, Jesse Coe, Shatabdi Roy-Chowdhury, Uwe Weierstall, Daniel James, Dingjie Wang, Thomas Grant, Anton Barty, Oleksandr Yefanov, Jennifer Scales, Cornelius Gati, Carolin Seuring, Vukica Srajer, Robert Henning, Peter Schwander, Raimund Fromme, Abbas Ourmazd, Keith Moffat, Jasper J. Van Thor, John C. H. Spence, Petra Fromme, Henry N. Chapman, Marius Schmidt, Science  346,  1242 - 1246  (2014). STC award  1231306

  7. "Three-dimensional structure from a single diffraction pattern of non-periodic molecules aligned along a single axis" D. Starodub, J.C.H Spence, D.K.Saldin. (2014). IUCrJ  STC award. Submitted. sept 2014.

  8. "X-ray lasers and crystallography". J.C.H.Spence (2014). IUCrJ 1, doi:10.1107/S2052252514009567.

  9. "Serial Time-resolved crystallography of Photosystem II using a femtosecond 
    X-ray laser". Christopher Kupitz, Shibom Basu, Ingo Grotjohann, Raimund Fromme, Nadia A. Zatsepin, Kimberly N. Rendek, Mark Hunter, Robert L. Shoeman, Thomas A. White, Dingjie Wang, Daniel James, Jay-How Yang, Danielle E. Cobb, Brenda Reeder,  Raymond G. Sierra, Haiguang Liu , Anton Barty, Andrew L. Aquila, Daniel Deponte, Richard A. Kirian, Sadia Bari, Jesse J. Bergkamp, Kenneth R. Beyerlein, Michael J. Bogan, Carl Caleman, Tzu-Chiao Chao, Chelsie E. Conrad, Katherine M.  Davis, Holger Fleckenstein, Lorenzo Galli, Stefan P. Hau-Riege, Stephan Kassemeyer, Hartawan Laksmono, Mengning Liang, Lukas Lomb, Stefano Marchesini, Andrew M.  Martin, Marc Messerschmidt, Despina Milathianaki, Karol Nass, Alexandra Ros, Shatabdi Roy-Chowdhury, Kevin Schmidt, Marvin Seibert, Jan Steinbrener, Francesco Stellato, Lifen Yan, ‎Chunhong Yoon, Thomas A. Moore, Ana L. Moore, Yulia Pushkar, Garth J. Williams, Sébastien Boutet,  R. Bruce Doak, Uwe Weierstall, Matthias Frank, Henry N. Chapman, John C.H. Spence   and Petra Fromme.  Nature (Letter).  Nature 513, 261–265 (11 September 2014). Received 26 November 2013 Accepted 04 May 2014 Published online 09 July 2014.  doi:10.1038/nature13453.  STC award 1231306.      Kern paper was  Rec;d 20 Feb, Accepted june, Pubd 9 july.

  10. "Solving Protein Nanocrystals by Cryo-EM diffraction: Multiple Scattering artifacts". Ganesh Subramanian, Shibom Basu, Haiguang Liu, J. M. Zuo and John. C. H. Spence. Ultramicroscopy.  148, p.87 (2014). .  STC award 1231306.

  11. "7 ̊A resolution in protein 2D-crystal X-ray diffraction at LCLS"  Bill Pedrini, Ching-Ju Tsai, Guido Capitani, Celestino Padeste, Mark S. Hunter, Nadia A. Zatsepin, Anton Barty, W. Henry Benner, Sebastian Boutet, Geoffrey K. Feld , Stephan P. Hau-Riege , Richard A. Kirian, Christopher Kupitz, Marc Messerschmitt, John I. Ogren, Tommaso Pardini , Brent Segelke , Garth J. Williams , John C. H. Spence, Rafael Abela1, Matthew Coleman, James E. Evans, Gebhard Schertler, Matthias Frank, and Xiao-Dan Li. Phil. Trans. R. Soc. B 2014 369, 20130500   (2014).  STC award 1231306.

  12. "X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser. J.Kupper, S.Stern,L.Holmegaard,F.Filsinger,A.Rouze,D.Rolles,A.Rudenko, P.Johnsson, A.V. Martin, M. Adolph, A.Aquila, Sash Bajt, A.Barty, C.Bostedt, J. Bozek, C.Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B.Erk, L.Foucar,T. Gorkhover, LarsGumprecht,A.Hartmann,R.Hartmann, Gunter Hauser, P.Holl, A. Homke, N.Kimmel, F. Krasniqi, Kai-Uwe Kuhnel, J.Maurer, M. Messerschmidt, R.Moshammer,C. Reich, B.Rudek,R.Santra,I. Schlichting, C.Schmidt,S. Schorb,J. Schulz,H. Soltau, L.Struder, J.Thøgersen, M. Vrakking,G.Weidenspointner, T.A.White, C.Wunderer, G. Meijer, J.C.H.Spence, J.Ullrich, H.Stapelfeldt, and H. N. Chapman.   Phys Rev Letts 112, 083002 (2014)  NSF STC award 1231306.

  13. "Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells". Haiguang Liu, Nadia A. Zatsepin and John C. H. Spence. IUCrJ 1, 19-27 (2014). NSF STC award 1231306. HFSP. NSF MCB1021557

  14. "Coherent Convergent-Beam Time-resolved X-ray Diffraction". John C.H. Spence, Nadia A. Zatsepin and Chufeng Li. Phil. Trans. R. Soc. B 2014 369, 20130325
     NIH Grant number GM095583 (Petra). NSF 1231306 (STC).

  15. "A protein quake in photosynthesis".  David Arnlund, Linda C. Johansson, Anton Barty, Garth Williams, Gerrit Groenhoff, Cecilia Wikstrand, Jan Davidsson, Despina Milathianaki, Erik Malmerberg, Daniel P. DePonte, Robert L. Shoeman, Dingjie Wang, Daniel James, Gergely Katona, Sebastian Westenhoff, Thomas A. White, Andrew Aquila, Sadia Bari, Peter Berntsen, Mike Bogan, Tim Brandt van Driel, R. Bruce Doak, Matthias Frank, Raimund Fromme, Ingo Grotjohann, Robert Henning, Mark S. Hunter, Richard A. Kirian, Irina Koshelev, Christopher Kupitz, Mengning Liang, Andrew V. Martin, Martin Meedom Nielsen, Marc Messerschmidt, Lars Redecke, M. Marvin Seibert, Jennie Sjöhamn, Kasper Skov Kjær, Francesco Stellato, Uwe Weierstall, Nadia Zatsepin, John C. H. Spence, Petra Fromme, Ilme Schlichting, Sebastian Boutet, Henry N. Chapman, Richard Neutze.  Nature Methods. 11, 923- 926 (2014); doi:10.1038/NMeth.3067.  NSF MCB1021557, and STC acknowledgment.

  16. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.  Uwe Weierstall, Daniel James, Dingjie Wang, Wei Liu, John C.H. Spence, R. Bruce Doak, Garrett Nelson, Petra Fromme, Raimund Fromme, Ingo Grotjohann, Christopher Kupitz, Nadia A. Zatsepin, Shibom Basu, Daniel Wacker, Chong Wang, Sébastien Boutet, Marc Messerschmidt, Garth J. Williams, Jason E.Koglin, M. Marvin Seibert,  Cornelius Gati, Robert L. Shoeman, Anton Barty, Henry N. Chapman, Richard A. Kirian Kenneth R. Beyerlein, Raymond C. Stevens , Dianfan Li, Syed T.A. Shah, Nicole Howe, Martin Caffrey, Vadim Cherezov Nature Communications 5, p. 3309 (2014)   DOI: 10.1038/ (2014).  NSF MCB1021557. STC 1231306.

  17. Direct phasing in femtosecond nanocrystallography.  II. Phase Retrieval. Joe P J Chen, J.C.H.Spence and R. P. Millane. Acta A70, 154 - 161   (2014) NSF MCB1021557 (JCHS), STC 1231306. 

  18. Direct phasing in femtosecond nanocrystallography. I. Diffraction Characteristics. Joe P J Chen, J.C.H.Spence and R. P. Millane. Acta A70, 143-153  (2014).  NSF MCB1021557, STC 1231306.

  19. "Femtosecond X-ray diffraction from two-dimensional protein crystals". Matthias Frank, David B. Carlson, Mark S. Hunter, Garth J. Williams, Marc Messerschmidt, Nadia A. Zatsepin, Anton Barty, W. Henry Benner, Kaiqin Chu2, Alexander Graf1, Stefan P. Hau-Riege1, Richard A. Kirian, Celestino Padeste, Tommaso Pardini, Bill Pedrini, Brent Segelke, M. Marvin Seibert, John C. H. Spence, Ching-Ju Tsai, Stephen M. Lane, Xiao-Dan Li, Gebhard Schertler, Sébastien Boutet, Matthew Coleman and James E. Evans. IUCRJ. 1, 95-100 (2014).   . doi:10.1107/S2052252514001444 . NSF MCB1021557. STC grant 1231306. 

  20. "Time-resolved spectra from millivolt EELS data".  Chufeng Li, Ganesh Subramanian and   John C.H. Spence. Microscopy and Microanalysis, 20, 837 (2014). (Proc Edge). STC 1231306.

  21. Three dimensional analysis of serial femtosecond crystallographic data. Phil Trans. (2013). Oleksandr Yefanov, Cornelius Gati, Richard Kirian, Thomas A White, John C H Spence, Henry Chapman and Anton Barty.  STC award 1231306. Phil. Trans. R. Soc. B 369, p. 20130xxx (2014)