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  1. Analysis of XFEL serial diffraction data from individual crystalline fibrils

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    20 Oct 2017 | BioXFEL Publications | Contributor(s): David H. Wojtas, Kartik Ayyer, Mengning Liang, Estelle Mossou, Filippo Romoli, Carolin Seuring, Kenneth R. Beyerlein, Richard J. Bean, Andrew J. Morgan, Dominik Oberthuer, Holger Fleckenstein, Michael Heymann, Cornelius Gati, Oleksandr Yefanov, Miriam Barthelmess, Eirini Ornithopoulou, Lorenzo Galli, P. Lourdu Xavier, Wai Li Ling, Matthias Frank, Chun Hong Yoon, Thomas A. White, Saša Bajt, Anna Mitraki, Sebastien Boutet, Andrew Aquila, Anton Barty, V. Trevor Forsyth, Henry Chapman, Rick P. Millane

    http://dx.doi.org/10.1107/s2052252517014324 Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single …

  2. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

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    26 Sep 2016 | BioXFEL Publications | Contributor(s): Derek Mendez, Herschel Watkins, Shenglan Qiao, Kevin S. Raines, Thomas J. Lane, Gundolf Schenk, Garrett Charles Nelson, GANESH SUBRAMANIAN, Kensuke Tono, Yasumasa Joti, Makina Yabashi, Daniel Ratner, Sebastian Doniach

    During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- …

  3. Angular Momentum Decomposition

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    07 Oct 2015 | Teaching Materials | Contributor(s): Dilano Saldin

    Dr. Dilano Saldin discusses using angular momentum decomposition in the analysis of single and multi-particle imaging with XFELs.

  4. Anomalous Behavior of the Homogeneous Ice Nucleation Rate in “No-Man’s Land”

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    03 Jul 2015 | BioXFEL Publications | Contributor(s): Hartawan Laksmono, Trevor A. McQueen, Jonas A. Sellberg, N. Duane Loh, Congcong Huang, Daniel Schlesinger, Raymond G. Sierra, Christina Y. Hampton, Dennis Nordlund, Martin Beye, Andrew V. Martin, Anton Barty, M. Marvin Seibert, Marc Messerschmidt, Garth J. Williams, Sébastien Boutet, Katrin Amann-Winkel, Thomas Loerting, Lars G. M. Pettersson, Michael J. Bogan, Anders Nilsson

    http://dx.doi.org/10.1021/acs.jpclett.5b01164 Hartawan Laksmono and Trevor A. McQueen and Jonas A. Sellberg and N. Duane Loh and Congcong Huang and Daniel Schlesinger and Raymond G. Sierra and Christina Y. Hampton and Dennis Nordlund and Martin Beye and Andrew V. Martin and Anton Barty and M. …

  5. Anomalous nonlinear X-ray Compton scattering

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    31 Aug 2015 | BioXFEL Publications | Contributor(s): Matthias Fuchs, Mariano Trigo, Jian Chen, Shambhu Ghimire, Sharon Shwartz, Michael Kozina, Mason Jiang, Thomas Henighan, Crystal Bray, Georges Ndabashimiye, Philip H. Bucksbaum, Yiping Feng, Sven Herrmann, Gabriella A. Carini, Jack Pines, Philip Hart, Christopher Kenney, Serge Guillet, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, M. Marvin Seibert, Stefan Moeller, Jerome B. Hastings, David A. Reis

    http://dx.doi.org/10.1038/nphys3452 Matthias Fuchs and Mariano Trigo and Jian Chen and Shambhu Ghimire and Sharon Shwartz and Michael Kozina and Mason Jiang and Thomas Henighan and Crystal Bray and Georges Ndabashimiye and Philip H. Bucksbaum and Yiping Feng and Sven Herrmann and Gabriella A. …

  6. Anomalous Nonlinear X-ray Compton Scattering

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    14 Mar 2016 | BioXFEL Publications | Contributor(s): Matthias Fuchs

    proceedings-article http://dx.doi.org/10.1364/hilas.2016.hm3b.1 Fuchs, M., 2016. Anomalous Nonlinear X-ray Compton Scattering. High-Brightness Sources and Light-Driven Interactions. Available at: http://dx.doi.org/10.1364/hilas.2016.hm3b.1. Matthias Fuchs

  7. Apoglobin Stability Is the Major Factor Governing both Cell-free andin VivoExpression of Holomyoglobin

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    23 Jul 2015 | BioXFEL Publications | Contributor(s): Premila P. Samuel, Lucian P. Smith, George Phillips, John S. Olson

    journal-article http://dx.doi.org/10.1074/jbc.m115.672204 Samuel, P.P. et al., 2015. Apoglobin Stability Is the Major Factor Governing both Cell-free andin VivoExpression of Holomyoglobin. Journal of Biological Chemistry, 290(39), pp.23479–23495. Available at: …

  8. Applications of microfluidic mixers for time-resolved SAXS and crystallography experiments

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    11 May 2021 | BioXFEL Publications | Contributor(s): Kara Zielinski, Lois Pollack

    http://dx.doi.org/10.1107/s0108767320099663 journal-article Zielinski, K. & Pollack, L., 2020. Applications of microfluidic mixers for time-resolved SAXS and crystallography experiments. Acta Crystallographica Section A Foundations and Advances, 76(a1), pp.a33–a33. Available at: …

  9. Applications of TEM for Evaluation and Optimization of Crystal Growth

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    14 Oct 2015 | Teaching Materials | Contributor(s): Guillermo Calero

    Dr. Guillero Calero discusses using transmission electron microscopy to characterize, evaluate and subsequently optimize the growth of crystals.

  10. Approaches to time-resolved diffraction using an XFEL

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    25 Mar 2014 | BioXFEL Publications | Contributor(s): John Spence

    http://dx.doi.org/10.1039/c4fd00025k John C. H. Spence Spence, J.C.H., 2014. Approaches to time-resolved diffraction using an XFEL. Faraday Discuss., 171, pp.429–438. Available at: http://dx.doi.org/10.1039/c4fd00025k. NSF-STC Biology with X-ray Lasers (NSF-1231306) We describe several schemes …

  11. Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex

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    27 Sep 2013 | BioXFEL Publications | Contributor(s): K. Murakami, H. Elmlund, N. Kalisman, D. A. Bushnell, C. M. Adams, M. Azubel, D. Elmlund, Y. Levi-Kalisman, X. Liu, B. J. Gibbons, M. Levitt, R. D. Kornberg

    http://dx.doi.org/10.1126/science.1238724 journal-article Murakami, K. et al., 2013. Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex. Science, 342(6159), pp.1238724–1238724. Available at: http://dx.doi.org/10.1126/science.1238724. K. Murakami and H. Elmlund and N. …

  12. Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

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    23 Dec 2020 | BioXFEL Publications | Contributor(s): Filip Yabukarski, Justin T. Biel, Margaux M. Pinney, Tzanko Doukov, Alexander S. Powers, James Fraser, Daniel Herschlag

    http://dx.doi.org/10.1073/pnas.2011350117 How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes …

  13. Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography

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    02 Mar 2016 | BioXFEL Publications | Contributor(s): Christopher Barnes, Elena G. Kovaleva, Xiaofeng Fu, Hilary P. Stevenson, Aaron S. Brewster, Daniel P. DePonte, Elizabeth L. Baxter, Aina E. Cohen, Guillermo Calero

    journal-article http://dx.doi.org/10.1016/j.abb.2016.02.011 Barnes, C.O. et al., 2016. Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography. Archives of Biochemistry and Biophysics, 602, pp.61–68. Available at: …

  14. Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit

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    14 Jan 2020 | BioXFEL Publications | Contributor(s): Vanja Stojković, Alexander G Myasnikov, Iris Diane Young, Adam Frost, James Fraser, Danica Galonić Fujimori

    http://dx.doi.org/10.1093/nar/gkaa037 Abstract Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA …

  15. Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

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    27 Dec 2016 | BioXFEL Publications | Contributor(s): Yujie Chen, Joshua M. Tokuda, Traci Topping, Steve P. Meisburger, Suzette A. Pabit, Lisa M. Gloss, Lois Pollack

    http://dx.doi.org/10.1073/pnas.1611118114 journal-article Chen, Y. et al., 2016. Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. Proceedings of the National Academy of Sciences, 114(2), pp.334–339. Available at: …

  16. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

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    15 Feb 2017 | BioXFEL Publications | Contributor(s): Cornelius Gati, Dominik Oberthuer, Oleksandr Yefanov, Richard D. Bunker, Francesco Stellato, Elaine Chiu, Shin-Mei Yeh, Andrew Aquila, Shibom Basu, Richard Bean, Kenneth R. Beyerlein, Sabine Botha, Sébastien Boutet, Daniel P. DePonte, R. Bruce Doak, Raimund Fromme, Lorenzo Galli, Ingo Grotjohann, Daniel R. James, Christopher Kupitz, Lukas Lomb, Marc Messerschmidt, Karol Nass, Kimberly Rendek, Robert L. Shoeman, Dingjie Wang, Uwe Weierstall, Thomas A. White, Garth J. Williams, Nadia Zatsepin, Petra Fromme, John Spence, Kenneth N. Goldie, Johannes A. Jehle, Peter Metcalf, Anton Barty, Henry Chapman

    journal-article http://dx.doi.org/10.1073/pnas.1609243114 NSF-STC Biology with X-ray Lasers (NSF-1231306) Gati, C. et al., 2017. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. Proceedings of the National Academy of Sciences, …

  17. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

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    19 Dec 2017 | BioXFEL Publications | Contributor(s): Cornelius Gati, Dominik Oberthuer, Oleksandr Yefanov, Richard D. Bunker, Peter Metcalf, Anton Barty, Henry Chapman

    http://dx.doi.org/10.1107/s0108767317097124 journal-article Gati, C. et al., 2017. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a292–a293. Available at: …

  18. Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED

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    13 Feb 2017 | BioXFEL Publications | Contributor(s): M Jason De La Cruz, Johan Hattne, Dan Shi, Paul Seidler, Jose Rodriguez, Francis E Reyes, Michael R Sawaya, Duilio Cascio, Simon C Weiss, Sun Kyung Kim, Cynthia S Hinck, Andrew P Hinck, Guillermo Calero, David Eisenberg, Tamir Gonen

    journal-article http://dx.doi.org/10.1038/nmeth.4178 NSF-STC Biology with X-ray Lasers (NSF-1231306) De la Cruz, M.J. et al., 2017. Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. Nature Methods, 14(4), pp.399–402. Available at: …

  19. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye–Semiconductor Interface

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    25 Jul 2014 | BioXFEL Publications | Contributor(s): Katrin R. Siefermann, Chaitanya D. Pemmaraju, Stefan Neppl, Andrey Shavorskiy, Amy A. Cordones, Josh Vura-Weis, Daniel S. Slaughter, Felix P. Sturm, Fabian Weise, Hendrik Bluhm, Matthew L. Strader, Hana Cho, Ming-Fu Lin, Camila Bacellar, Champak Khurmi, Jinghua Guo, Giacomo Coslovich, Joseph S. Robinson, Robert A. Kaindl, Robert W Schoenlein, Ali Belkacem, Daniel M. Neumark, Stephen R. Leone, Dennis Nordlund, Hirohito Ogasawara, Oleg Krupin, Joshua J. Turner, William F. Schlotter, Michael R. Holmes, Marc Messerschmidt, Michael P. Minitti, Sheraz Gul, Jin Z. Zhang, Nils Huse, David Prendergast, Oliver Gessner

    http://dx.doi.org/10.1021/jz501264x journal-article Siefermann, K.R. et al., 2014. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye–Semiconductor Interface. The Journal of Physical Chemistry Letters, 5(15), pp.2753–2759. Available at: http://dx.doi.org/10.1021/jz501264x. Katrin …

  20. Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

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    11 Oct 2023 | BioXFEL Publications | Contributor(s): Weiwei He, Josue San Emeterio, Michael T Woodside, Serdal Kirmizialtin, Lois Pollack

    http://dx.doi.org/10.1093/nar/gkad809 Abstract SARS-CoV-2 depends on −1 programmed ribosomal frameshifting (−1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating −1 PRF is thus an attractive drug target. However, the structural models of this …

  21. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

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    10 Apr 2013 | BioXFEL Publications | Contributor(s): Yingssu Tsai, Scott E. McPhillips, Ana González, Timothy M. McPhillips, Daniel Zinn, Aina E. Cohen, Michael D. Feese, David Bushnell, Theresa Tiefenbrunn, C. David Stout, Bertram Ludaescher, Britt Hedman, Keith O. Hodgson, S. Michael Soltis

    journal-article http://dx.doi.org/10.1107/s0907444913001984 Tsai, Y. et al., 2013. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. Acta Crystallographica Section D Biological Crystallography, 69(5), pp.796–803. Available at: …

  22. Automated identification of functional dynamic contact networks from X-ray crystallography

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    05 Aug 2013 | BioXFEL Publications | Contributor(s): Henry Van Den Bedem, Gira Bhabha, Kun Yang, Peter E Wright, James Fraser

    http://dx.doi.org/10.1038/nmeth.2592 journal-article Van den Bedem, H. et al., 2013. Automated identification of functional dynamic contact networks from X-ray crystallography. Nature Methods, 10(9), pp.896–902. Available at: http://dx.doi.org/10.1038/nmeth.2592. Henry van den Bedem and Gira …

  23. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

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    27 Apr 2016 | BioXFEL Publications | Contributor(s): Ray Yu-Ruei Wang, Yifan Song, Benjamin Barad, Yifan Cheng, James Fraser, Frank DiMaio

    http://dx.doi.org/10.1101/050286 Cryo-EM has revealed many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5 Angstrom), providing biological phenomena with molecular descriptions. However, at these resolutions accurately positioning individual atoms remains …

  24. AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy

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    28 Feb 2016 | BioXFEL Publications | Contributor(s): F.X. Kärtner, F. Ahr, A.-L. Calendron, H. Çankaya, S. Carbajo, G. Chang, G. Cirmi, K. Dörner, U. Dorda, A. Fallahi, A. Hartin, M. Hemmer, R. Hobbs, Y. Hua, W.R. Huang, R. Letrun, N. Matlis, V. Mazalova, O.D. Mücke, E. Nanni, W. Putnam, K. Ravi, F. Reichert, I. Sarrou, X. Wu, A. Yahaghi, H. Ye, L. Zapata, D. Zhang, C. Zhou, R.J.D. Miller, K.K. Berggren, H. Graafsma, A. Meents, R.W. Assmann, H.N. Chapman, P. Fromme

    http://dx.doi.org/10.1016/j.nima.2016.02.080 F.X. Kärtner and F. Ahr and A.-L. Calendron and H. Çankaya and S. Carbajo and G. Chang and G. Cirmi and K. Dörner and U. Dorda and A. Fallahi and A. Hartin and M. Hemmer and R. Hobbs and Y. Hua and W.R. Huang and R. Letrun and N. Matlis and V. …

  25. Bacterial expression, correct membrane targeting and functional folding of the HIV-1 membrane protein Vpu using a periplasmic signal peptide

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    22 Feb 2017 | BioXFEL Publications | Contributor(s): Arpan Deb, William A. Johnson, Alexander P. Kline, Boston J. Scott, Lydia R. Meador, Dustin Srinivas, Jose M. Martin-Garcia, Katerina Dörner, Chad R. Borges, Rajeev Misra, Brenda Hogue, Petra Fromme, Tsafrir S. Mor

    http://dx.doi.org/10.1371/journal.pone.0172529 journal-article Deb, A. et al., 2017. Bacterial expression, correct membrane targeting and functional folding of the HIV-1 membrane protein Vpu using a periplasmic signal peptide M. Schindler, ed. PLOS ONE, 12(2), p.e0172529. Available at: …

  26. Bacterial phytochromes: More than meets the light

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    21 Jan 2011 | BioXFEL Publications | Contributor(s): Michele E. Auldridge, Katrina T. Forest

    http://dx.doi.org/10.3109/10409238.2010.546389 journal-article Auldridge, M.E. & Forest, K.T., 2011. Bacterial phytochromes: More than meets the light. Critical Reviews in Biochemistry and Molecular Biology, 46(1), pp.67–88. Available at: http://dx.doi.org/10.3109/10409238.2010.546389. Michele …

  27. Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

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    26 Jun 2015 | BioXFEL Publications | Contributor(s): Wenting Wu, Przemyslaw Nogly, Jan Rheinberger, Leonhard M. Kick, Cornelius Gati, Garrett Charles Nelson, Xavier Deupi, Jörg Standfuss, Gebhard F.X. Schertler, Valérie Panneels

    Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the …

  28. Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway

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    29 Aug 2018 | BioXFEL Publications | Contributor(s): Thibault Annaval, Lu Han, Jeffrey D. Rudolf, Guangbo Xie, Dong Yang, Chin-Yuan Chang, Ming Ma, Ivana Crnovcic, Mitchell Miller, Jayashree Soman, Weijun Xu, George Phillips, Ben Shen

    http://dx.doi.org/10.1021/acschembio.8b00673 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Annaval, T. et al., 2018. Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway. ACS Chemical Biology, …

  29. Biochemical and Structural Studies of the Carminomycin 4-O-Methyltransferase DnrK

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    27 Feb 2024 | BioXFEL Publications | Contributor(s): Elnaz Jalali, Fengbin Wang, Brooke R. Overbay, Mitchell Miller, Khaled A. Shaaban, Larissa V. Ponomareva, Qing Ye, Hoda Saghaeiannejad-Esfahani, Minakshi Bhardwaj, Andrew D. Steele, Christiana N. Teijaro, Ben Shen, Steven G. Van Lanen, Qing-Bai She, S. Randal Voss, George Phillips, Jon S. Thorson

    http://dx.doi.org/10.1021/acs.jnatprod.3c00947 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Jalali, E., Wang, F., Overbay, B. R., Miller, M. D., Shaaban, K. A., Ponomareva, L. V., Ye, Q., Saghaeiannejad-Esfahani, H., Bhardwaj, M., Steele, A. D., Teijaro, C. N., Shen, B., Van …

  30. Biochemical Characterization and Crystal Structures of a Fungal Family 3  -Glucosidase, Cel3A from Hypocrea jecorina

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    27 Aug 2014 | BioXFEL Publications | Contributor(s): Saeid Karkehabadi, Kate E. Helmich, Thijs Kaper, Henrik Hansson, Nils-Egil Mikkelsen, Mikael Gudmundsson, Kathleen Piens, Meredith Fujdala, Goutami Banerjee, John S. Scott-Craig, Jonathan D. Walton, George Phillips, Mats Sandgren

    http://dx.doi.org/10.1074/jbc.m114.587766 journal-article Karkehabadi, S. et al., 2014. Biochemical Characterization and Crystal Structures of a Fungal Family 3  -Glucosidase, Cel3A from Hypocrea jecorina. Journal of Biological Chemistry, 289(45), pp.31624–31637. Available at: …

  31. Biological function investigated by time-resolved structure determination

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    21 Feb 2023 | BioXFEL Publications | Contributor(s): Marius Schmidt

    http://dx.doi.org/10.1063/4.0000177 Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the …

  32. Biological Networks across Scales—The Theoretical and Empirical Foundations for Time-Varying Complex Networks that Connect Structure and Function across Levels of Biological Organization

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    21 May 2021 | BioXFEL Publications | Contributor(s): Paul Bogdan, Gustavo Caetano-Anollés, Anna Jolles, Hyunju Kim, James Morris, Cheryl A Murphy, Catherine Royer, Edward Snell, Adam Steinbrenner, Nicholas Strausfeld

    http://dx.doi.org/10.1093/icb/icab069 Abstract Many biological systems across scales of size and complexity exhibit a time-varying complex network structure that emerges and self-organizes as a result of interactions with the environment. Network interactions optimize some intrinsic …

  33. Biological Small Angle Scattering

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    20 Sep 2018 | BioXFEL Publications | Contributor(s): Eaton E Lattman, Thomas D. Grant, Edward Snell

    http://dx.doi.org/10.1093/oso/9780199670871.001.0001 The technique of small angle solution scattering has been revolutionized in the last two decades. Exponential increases in computing power, parallel algorithm development, and the development of synchrotron, free-electron X-ray sources, and …

  34. Biomechanical Analysis of Retrograde Superior Ramus Screw Fixation Constructs

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    08 Oct 2020 | BioXFEL Publications | Contributor(s): Justin F. Lucas, Milton L. Chip Routt, Jonathan G. Eastman

    http://dx.doi.org/10.1097/bot.0000000000001951 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Justin F. Lucas and Milton L. Chip Routt and Jonathan G. Eastman

  35. Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes

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    26 Aug 2020 | BioXFEL Publications | Contributor(s): Rafael Maldonado-Hernandez, Orestes Quesada, José A. Lasalde-Dominicci

    http://dx.doi.org/10.1016/j.dib.2020.106230 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Maldonado-Hernández, R., Quesada, O. & Lasalde-Dominicci, J.A., 2020. Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes. Data …

  36. Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The “Undoing” of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network

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    15 Jan 2019 | BioXFEL Publications | Contributor(s): Shenshen Hu, Adam R. Offenbacher, Erin M. Thompson, Christine L. Gee, Jarett Wilcoxen, Cody A. M. Carr, Daniil M. Prigozhin, Vanessa Yang, Tom Alber, R. David Britt, James Fraser, Judith P. Klinman

    http://dx.doi.org/10.1021/jacs.8b10992 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Hu, S. et al., 2019. Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The “Undoing” of Precise Substrate Positioning Relative to Metal Cofactor and an …

  37. Biophysical Characterization of a Vaccine Candidate against HIV-1: The Transmembrane and Membrane Proximal Domains of HIV-1 gp41 as a Maltose Binding Protein Fusion

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    21 Aug 2015 | BioXFEL Publications | Contributor(s): Zhen Gong, Jose M. Martin-Garcia, Sasha M. Daskalova, Felicia M. Craciunescu, Lusheng Song, Katerina Dörner, Debra T. Hansen, Jay-How Yang, Joshua LaBaer, Brenda Hogue, Tsafrir S. Mor, Petra Fromme

    http://dx.doi.org/10.1371/journal.pone.0136507 Zhen Gong and Jose M. Martin-Garcia and Sasha M. Daskalova and Felicia M. Craciunescu and Lusheng Song and Katerina Dörner and Debra T. Hansen and Jay-How Yang and Joshua LaBaer and Brenda G. Hogue and Tsafrir S. Mor and Petra Fromme Gong, Z. et al., …

  38. Biostructural Science Inspired by Next-Generation X-Ray Sources

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    06 Mar 2015 | BioXFEL Publications | Contributor(s): Sol M. Gruner, Eaton E Lattman

    http://dx.doi.org/10.1146/annurev-biophys-060414-033813 Sol M. Gruner and Eaton E. Lattman Gruner, S.M. & Lattman, E.E., 2015. Biostructural Science Inspired by Next-Generation X-Ray Sources. Annual Review of Biophysics, 44(1), pp.33–51. Available at: …

  39. BioXFEL Annual Report 2014

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    04 Jun 2014 | Downloads | Contributor(s): Jill Szczesek

    BioXFEL will create a diverse and inclusive community of scholars who will transform our ability to visualize the building blocks of life at a molecular scale, advancing from today's static pictures to recording detailed motions. These "movies" will lead to deeper understanding and to the …

  40. BioXFEL Expert Panel Discussion

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    29 Aug 2014 | Teaching Materials

    Expert Panel Discussion including: Anton Barty, Michael Rossman, James Holton, Tom White, Wolfgang Brehm, Oliver Zeldin, John Spence, Karol Nass, Nick Sauter, Aaron Brewster, Johan Hattne

  41. BioXFEL Graduate Student Cross-Training Scholarship

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    11 Nov 2015 | Teaching Materials

    BioXFEL is committed to providing our students with opportunities to diversify their skill sets and integrate themselves into our highly multidisciplinary Center. In addition to the workshops, conferences and online courses, we will now be offering our students the opportunity to train in another …

  42. BioXFEL Lecture Series

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    13 Nov 2014 | Courses

    The BioXFEL Lecture Series is an online colloquium featuring lectures on various topics related to XFEL science in biology. Prominent experts in their respective fields, lecturers will present a broad range of materials from an introduction to XFEL radiation to more advanced topics of time-resolved …

  43. BioXFEL Logos

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    25 Jul 2018 | Downloads | Contributor(s): Sean Kilcullen

    Three BioXFEL logos in PNG format

  44. BioXFEL Poster Template

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    23 Jul 2018 | Downloads

    Please use this template for all BioXFEL-related posters. This version has been updated to reflect the current requirements for the 2019 Annual conference.

  45. BioXFEL PowerPoint Template

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    24 Jul 2018 | Downloads

    A PowerPoint template to be used for all BioXFEL presentations.

  46. BioXFEL Scholar Application Form

    0.0 out of 5 stars 

    10 Nov 2015 | Teaching Materials

    …

  47. BioXFEL Science Graphic

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    25 Apr 2014 | Downloads | Contributor(s): Edward J Sobczak

    …

  48. BioXFEL Strategic Plan 2013-2018

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    28 May 2014 | Downloads | Contributor(s): Jill Szczesek

    We present a strategic plan for the operation of BioXFEL, a National Science Foundation Science and Technology Center, Biology with X-ray Lasers. The plan is the organic product of a meeting facilitated by Giant Leap at Arizona State University in February 2014, and covers the period 2013 – 2018.

  49. Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography

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    31 Jan 2024 | BioXFEL Publications | Contributor(s): Marius Schmidt, Emina Stojkovic

    http://dx.doi.org/10.1063/4.0000233 Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales. Originally a synchrotron-based method, TRX is enabled by the development of TR Laue crystallography (TRLX). TR serial …

  50. Breaking the Boundary between Solution X-Ray Scattering and Molecular Dynamics Simulations of Structured Nucleic Acids

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    12 Feb 2021 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Weiwei He, Lois Pollack, Serdal Kirmizialtin

    http://dx.doi.org/10.1016/j.bpj.2020.11.1995 journal-article Chen, Y.-L. et al., 2021. Breaking the Boundary between Solution X-Ray Scattering and Molecular Dynamics Simulations of Structured Nucleic Acids. Biophysical Journal, 120(3), p.315a. Available at: …

  51. Breaking the Radiation Damage Limit with Cryo-SAXS

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    08 Jan 2013 | BioXFEL Publications | Contributor(s): Steve P. Meisburger, Matthew Warkentin, Huimin Chen, Jesse B. Hopkins, Richard E. Gillilan, Lois Pollack, Robert E. Thorne

    http://dx.doi.org/10.1016/j.bpj.2012.11.3817 journal-article Meisburger, S.P. et al., 2013. Breaking the Radiation Damage Limit with Cryo-SAXS. Biophysical Journal, 104(1), pp.227–236. Available at: http://dx.doi.org/10.1016/j.bpj.2012.11.3817. Steve P. Meisburger and Matthew Warkentin and …

  52. Bringing diffuse X-ray scattering into focus

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    15 Feb 2018 | BioXFEL Publications | Contributor(s): Michael E Wall, Alexander M Wolff, James Fraser

    http://dx.doi.org/10.1016/j.sbi.2018.01.009 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Wall, M.E., Wolff, A.M. & Fraser, J.S., 2018. Bringing diffuse X-ray scattering into focus. Current Opinion in Structural Biology, 50, pp.109–116. Available at: …

  53. C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

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    26 Jan 2021 | BioXFEL Publications | Contributor(s): Iosifina Sarrou, Christian G. Feiler, Sven Falke, Nolan Peard, Oleksandr Yefanov, Henry Chapman

    http://dx.doi.org/10.1107/s2059798320016071 The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a …

  54. CAMP@FLASH: an end-station for imaging, electron- and ion-spectroscopy, and pump–probe experiments at the FLASH free-electron laser

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    02 Aug 2018 | BioXFEL Publications | Contributor(s): Benjamin Erk, Jan P. Müller, Cédric Bomme, Rebecca Boll, Günter Brenner, Henry Chapman, Jonathan Correa, Stefan Düsterer, Siarhei Dziarzhytski, Stefan Eisebitt, Heinz Graafsma, Sören Grunewald, Lars Gumprecht, Robert Hartmann, Günter Hauser, Barbara Keitel, Clemens Von Korff Schmising, Marion Kuhlmann, Bastian Manschwetus, Laurent Mercadier, Erland Müller, Christopher Passow, Elke Plönjes, Daniel Ramm, Dimitrios Rompotis, Artem Rudenko, Daniela Rupp, Mario Sauppe, Frank Siewert, Dieter Schlosser, Lothar Strüder, Angad Swiderski, Simone Techert, Kai Tiedtke, Thomas Tilp, Rolf Treusch, Ilme Schlichting, Joachim Ullrich, Robert Moshammer, Thomas Möller, Daniel Rolles

    http://dx.doi.org/10.1107/s1600577518008585 The non-monochromatic beamline BL1 at the FLASH free-electron laser facility at DESY was upgraded with new transport and focusing optics, and a new permanent end-station, CAMP, was installed. This multi-purpose instrument is optimized for electron- and …

  55. Carbamate Insecticides Target Human Melatonin Receptors

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    27 Dec 2016 | BioXFEL Publications | Contributor(s): Marina Popovska-Gorevski, Margarita L. Dubocovich, Rajendram V. Rajnarayanan

    http://dx.doi.org/10.1021/acs.chemrestox.6b00301 journal-article Popovska-Gorevski, M., Dubocovich, M.L. & Rajnarayanan, R.V., 2017. Carbamate Insecticides Target Human Melatonin Receptors. Chemical Research in Toxicology, 30(2), pp.574–582. Available at: …

  56. Carbon nanotube dielectrophoresis: Theory and applications

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    31 May 2020 | BioXFEL Publications | Contributor(s): Mohammad Towshif Rabbani, Mukul Sonker, Alexandra Ros

    http://dx.doi.org/10.1002/elps.202000049 journal-article Rabbani, M.T., Sonker, M. & Ros, A., 2020. Carbon nanotube dielectrophoresis: Theory and applications. ELECTROPHORESIS. Available at: http://dx.doi.org/10.1002/elps.202000049. Mohammad Towshif Rabbani and Mukul Sonker and Alexandra Ros

  57. Career Trends: Exploring Careers Beyond the Bench

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    20 Jan 2015 | Publications

    Last month, the U.S. National Science Foundation (NSF) released a report* with some grim news that confirmed what is painfully obvious to recent Ph.D. graduates in science, technology, engineering, and mathematics (STEM) fields: Unemployment for this cohort is on the rise (at 2.4% in 2010, up …

  58. Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

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    19 Dec 2021 | BioXFEL Publications | Contributor(s): Omur Guven, Mehmet Gul, Esra Ayan, J Austin Johnson, Baris Cakilkaya, Gozde Usta, Fatma Betul Ertem, Nurettin Tokay, Busra Yuksel, Oktay Gocenler, Cengizhan Buyukdag, Sabine Botha, Gihan Kaushylal Ketawala, Zhen Su, Brandon Hayes, Frederic Poitevin, Alexander Batyuk, Chun Hong Yoon, Christopher Kupitz, Serdar Durdagi, Raymond G. Sierra, Hasan Demirci

    http://dx.doi.org/10.3390/cryst11121579 Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial …

  59. Casimir torque between birefringent plates with metamaterials

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    26 Jun 2013 | BioXFEL Publications | Contributor(s): Xiang Chen, John Spence

    journal-article http://dx.doi.org/10.1002/pssa.201329144 Chen, X. & Spence, J.C.H., 2013. Casimir torque between birefringent plates with metamaterials. physica status solidi (a), p.n/a–n/a. Available at: http://dx.doi.org/10.1002/pssa.201329144. Xiang Chen and John C. H. Spence

  60. CASS and SFX SAD Tutorial

    0.0 out of 5 stars 

    03 Sep 2014 | Teaching Materials

    Karol Nass (MPI) Extraction of diffraction images of the lysozyme Gadolinium derivative (Barends et al. Science 2013) from the raw LCLS format to HDF5 format. Integration of CrystFEL analysis with CASS start-up scripts. Ab initio SAD phasing of SFX data.

  61. cctbx.xfel Tutorial

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    03 Sep 2014 | Teaching Materials

    Nick Sauter (LBNL) Aaron Brewster (LBNL) Oliver Zeldin (Stanford)

  62. Cell-free production of a functional oligomeric form of aChlamydiamajor outer-membrane protein (MOMP) for vaccine development

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    24 Jul 2017 | BioXFEL Publications | Contributor(s): Wei He, Martina Felderman, Angela C. Evans, Jia Geng, David Homan, Feliza Bourguet, Nicholas O. Fischer, Yuanpei Li, Kit S. Lam, Aleksandr Noy, Li Xing, R. Holland Cheng, Amy Rasley, Craig D. Blanchette, Kurt Kamrud, Nathaniel Wang, Heather Gouvis, Todd C. Peterson, Bolyn Hubby, Matthew Coleman

    http://dx.doi.org/10.1074/jbc.m117.784561 journal-article He, W. et al., 2017. Cell-free production of a functional oligomeric form of aChlamydiamajor outer-membrane protein (MOMP) for vaccine development. Journal of Biological Chemistry, 292(36), pp.15121–15132. Available at: …

  63. Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

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    09 Dec 2015 | BioXFEL Publications | Contributor(s): K. R. Beyerlein, L. Adriano, M. Heymann, R. Kirian, J. Knoška, F. Wilde, H. N. Chapman, S. Bajt

    http://dx.doi.org/10.1063/1.4936843 K. R. Beyerlein and L. Adriano and M. Heymann and R. Kirian and J. Knoška and F. Wilde and H. N. Chapman and S. Bajt Beyerlein, K.R. et al., 2015. Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery. Review of Scientific …

  64. Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering

    0.0 out of 5 stars 

    15 Sep 2022 | BioXFEL Publications | Contributor(s): Kara Zielinski, Andrea Katz, George Douglas Calvey, Suzette Pabit, Josue San Emeterio, Lois Pollack

    http://dx.doi.org/10.1107/s2053273322099715 journal-article Zielinski, K., Katz, A., Calvey, G., Pabit, S., San Emeterio, J., & Pollack, L. (2022). Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering. …

  65. Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering

    0.0 out of 5 stars 

    02 May 2023 | BioXFEL Publications | Contributor(s): Kara Zielinski, Andrea Katz, George Douglas Calvey, Suzette A. Pabit, Shawn K. Milano, Cody Aplin, Josue San Emeterio, Richard A. Cerione, Lois Pollack

    http://dx.doi.org/10.1107/s2052252523003482 Advances in time-resolved structural techniques, mainly in macromolecular crystallography and small-angle X-ray scattering (SAXS), allow for a detailed view of the dynamics of biological macromolecules and reactions between binding partners. Of particular …

  66. Chapter 2. Delivery of GPCR Crystals for Serial Femtosecond Crystallography

    0.0 out of 5 stars 

    19 Jun 2018 | BioXFEL Publications | Contributor(s): E. E. Abola, U. Weierstall, W. Liu, V. Cherezov

    http://dx.doi.org/10.1039/9781788010504-00028 book-chapter Abola, E.E. et al., Chapter 2. Delivery of GPCR Crystals for Serial Femtosecond Crystallography. Chemical Biology, pp.28–53. Available at: http://dx.doi.org/10.1039/9781788010504-00028. E. E. Abola and U. Weierstall and W. Liu and V. …

  67. Chapter 8. Crystallography with X-ray Free Electron Lasers

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    19 Jun 2018 | BioXFEL Publications | Contributor(s): N. A. Zatsepin

    http://dx.doi.org/10.1039/9781788010504-00181 book-chapter NSF-STC Biology with X-ray Lasers (NSF-1231306) Zatsepin, N.A., Chapter 8. Crystallography with X-ray Free Electron Lasers. Chemical Biology, pp.181–224. Available at: http://dx.doi.org/10.1039/9781788010504-00181. N. A. Zatsepin

  68. Characterization and use of the spent beam for serial operation of LCLS

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    10 Apr 2015 | BioXFEL Publications | Contributor(s): Sébastien Boutet, Lutz Foucar, Thomas R. M. Barends, Sabine Botha, R. Bruce Doak, Jason E. Koglin, Marc Messerschmidt, Karol Nass, Ilme Schlichting, M. Marvin Seibert, Robert L. Shoeman, Garth J. Williams

    X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort …

  69. Characterization of a Spatially resolved multi-element laser ablation ion source

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    26 Nov 2021 | BioXFEL Publications | Contributor(s): K. Murray, C. Chambers, D. Chen, Z. Feng, J. Fraser, Y. Ito, Y. Lan, S. Mendez, M. Medina Peregrina, H. Rasiwala, L. Richez, N. Roy, R. Simpson, J. Dilling, W. Fairbank, A.A. Kwiatkowski, T. Brunner

    http://dx.doi.org/10.1016/j.ijms.2021.116763 journal-article Murray, K., Chambers, C., Chen, D., Feng, Z., Fraser, J., Ito, Y., Lan, Y., Mendez, S., Medina Peregrina, M., Rasiwala, H., Richez, L., Roy, N., Simpson, R., Dilling, J., Fairbank, W., Kwiatkowski, A. A., & Brunner, T. (2022). …

  70. Characterization of High Numerical Aperture Multilayer Laue Lenses

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    10 Aug 2018 | BioXFEL Publications | Contributor(s): Kevin T. Murray, Andrew J. Morgan, Mauro Prasciolu, Istvan Mohacsi, Henry Chapman, Saša Bajt

    http://dx.doi.org/10.1017/s1431927618013740 journal-article Murray, K.T. et al., 2018. Characterization of High Numerical Aperture Multilayer Laue Lenses. Microscopy and Microanalysis, 24(S2), pp.282–283. Available at: http://dx.doi.org/10.1017/s1431927618013740. Kevin T. Murray and Andrew J. …

  71. Characterization of protein nanocrystals based on the reversibility of crystallization

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    10 May 2016 | BioXFEL Publications | Contributor(s): Katerina Dörner, Jose M. Martin-Garcia, Christopher Kupitz, Zhen Gong, T. Conn Mallet, Liqing Chen, Rebekka M. Wachter, Petra Fromme

    http://dx.doi.org/10.1021/acs.cgd.6b00384 Katerina Dörner and Jose M. Martin-Garcia and Christopher Kupitz and Zhen Gong and T. Conn Mallet and Liqing Chen and Rebekka M. Wachter and Petra Fromme Dörner, K. et al., 2016. Characterization of Protein Nanocrystals Based on the Reversibility of …

  72. Characterizing and Tuning the Properties of Polydiacetylene Films for Sensing Applications

    0.0 out of 5 stars 

    26 Oct 2021 | BioXFEL Publications | Contributor(s): Tanner J. Finney, Sanjai J. Parikh, Amir Berman, Darryl Y. Sasaki, Tonya L. Kuhl

    http://dx.doi.org/10.1021/acs.langmuir.1c02004 journal-article Finney, T. J., Parikh, S. J., Berman, A., Sasaki, D. Y., & Kuhl, T. L. (2021). Characterizing and Tuning the Properties of Polydiacetylene Films for Sensing Applications. Langmuir, 37(44), 12940–12951. …

  73. Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers

    0.0 out of 5 stars 

    21 Sep 2020 | BioXFEL Publications | Contributor(s): George Douglas Calvey, Andrea Katz, Kara Zielinski, Boris Dzikovski, Lois Pollack

    http://dx.doi.org/10.1021/acs.analchem.0c02569 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Calvey, G.D. et al., 2020. Characterizing Enzyme Reactions in Microcrystals for Effective Mix-and-Inject Experiments using X-ray Free-Electron Lasers. Analytical Chemistry, 92(20), …

  74. Cheetah documentation

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    What is Cheetah and how do you use it?

  75. Cheetah documentation - all keywords

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    21 Jul 2015 | Series | Contributor(s): Richard Kirian, Nadia Zatsepin

    List of all Cheetah's keywords

  76. Cheetah documentation page 2

    0.0 out of 5 stars 

    23 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Richard Kirian

    Cheetah documentation Page 2. Click here for Page 1. Click here for a list of all keywords.  The official Cheetah website is http://www.desy.de/~barty/cheetah/   These pages will not reproduce all the content from the Cheetah site, but are meant as an addendum.   Running Cheetah …

  77. Cheetah Tutorial

    0.0 out of 5 stars 

    03 Sep 2014 | Teaching Materials

    Anton Barty (CFEL)

  78. Chemically Stable Lipids for Membrane Protein Crystallization

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    12 May 2017 | BioXFEL Publications | Contributor(s): Andrii Ishchenko, Lingling Peng, Egor Zinovev, Alexey Vlasov, Sung Chang Lee, Alexander Kuklin, Alexey Mishin, Valentin Borshchevskiy, Qinghai Zhang, Vadim Cherezov

    http://dx.doi.org/10.1021/acs.cgd.7b00458 journal-article Ishchenko, A. et al., 2017. Chemically Stable Lipids for Membrane Protein Crystallization. Crystal Growth & Design. Available at: http://dx.doi.org/10.1021/acs.cgd.7b00458. Andrii Ishchenko and Lingling Peng and Egor Zinovev and Alexey …

  79. Chromatin potentiates transcription

    0.0 out of 5 stars 

    30 Jan 2017 | BioXFEL Publications | Contributor(s): Shigeki Nagai, Ralph E. Davis, Pierre Jean Mattei, Kyle Patrick Eagen, Roger Kornberg

    journal-article http://dx.doi.org/10.1073/pnas.1620312114 Nagai, S. et al., 2017. Chromatin potentiates transcription. Proceedings of the National Academy of Sciences, 114(7), pp.1536–1541. Available at: http://dx.doi.org/10.1073/pnas.1620312114. Shigeki Nagai and Ralph E. Davis and Pierre Jean …

  80. Chromatin-remodeling and the initiation of transcription

    0.0 out of 5 stars 

    05 Nov 2015 | BioXFEL Publications | Contributor(s): Yahli Lorch, Roger Kornberg

    http://dx.doi.org/10.1017/s0033583515000116 AbstractThe nucleosome serves as a general gene repressor by the occlusion of regulatory and promoter DNA sequences. Repression is relieved by the SWI/SNF-RSC family of chromatin-remodeling complexes. Research reviewed here has revealed the essential …

  81. Chromatin-remodeling for transcription

    0.0 out of 5 stars 

    17 Mar 2017 | BioXFEL Publications | Contributor(s): Yahli Lorch, Roger Kornberg

    Abstract The nucleosome serves as a general gene repressor, preventing all initiation of transcription except that which is brought about by specific positive regulatory mechanisms. The positive mechanisms begin with chromatin-remodeling by complexes that slide, disrupt, or otherwise …

  82. Classical molecular dynamics

    0.0 out of 5 stars 

    11 Mar 2021 | BioXFEL Publications | Contributor(s): Charles L. Brooks, David Case, Steve Plimpton, Benoît Roux, David Van Der Spoel, Emad Tajkhorshid

    http://dx.doi.org/10.1063/5.0045455 journal-article Brooks, C.L. et al., 2021. Classical molecular dynamics. The Journal of Chemical Physics, 154(10), p.100401. Available at: http://dx.doi.org/10.1063/5.0045455. Charles L. Brooks and David A. Case and Steve Plimpton and Benoît Roux and David …

  83. Clustering and main sources of variance of SFX data

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    Wolfgang Brehm (University of Konstanz) Clustering approaches and variance analysis are explained using the example of the indexing ambiguity in serial crystallography. Recently published algorithms for detwinning and advancements thereof will be shown. Variance analysis can lead to a more …

  84. Co-flow injection for serial crystallography at X-ray free-electron lasers

    0.0 out of 5 stars 

    16 Dec 2021 | BioXFEL Publications | Contributor(s): Diandra Doppler, Mohammad T. Rabbani, Romain Letrun, Jorvani Cruz Villarreal, Dai Hyun Kim, Sahir Ilyas Gandhi, Ana Egatz-Gomez, Mukul Sonker, Joe Chen, Faisal Hammad Mekky Koua, Jayhow Yang, Mohamed Youssef, Victoria Mazalova, Saša Bajt, Megan Shelby, Matt A. Coleman, Max Oliver Wiedorn, Juraj Knoska, Silvan Schön, Tokushi Sato, Mark S. Hunter, Ahmad Hosseinizadeh, Christopher Kuptiz, Reza Nazari, Roberto C. Alvarez, Konstantinos Karpos, Sahba Zaare, Zachary Dobson, Erin Discianno, Shangji Zhang, James D Zook, Johan Bielecki, Raphael De Wijn, Adam R. Round, Patrik Vagovic, Marco Kloos, Mohammad Vakili, Gihan Kaushylal Ketawala, Natasha Stander, Tien L. Olson, Katherine Morin, Jyotirmory Mondal, Jonathan Nguyen, José Domingo Meza-Aguilar, Gerdenis Kodis, Sara Vaiana, Jose M. Martin-Garcia, Valerio Mariani, Peter Schwander, Marius Schmidt, Marc Messerschmidt, Abbas Ourmazd, Nadia Zatsepin, Uwe Weierstall, Barry D. Bruce, Adrian P. Mancuso, Thomas Grant, Anton Barty, Henry Chapman, Matthias Frank, Raimund Fromme, John Spence, Sabine Botha, Petra Fromme, Richard Kirian, Alexandra Ros

    http://dx.doi.org/10.1107/s1600576721011079 Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel …

  85. Co-occurring Alterations in the RAS–MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer

    0.0 out of 5 stars 

    23 Sep 2019 | BioXFEL Publications | Contributor(s): Julia K. Rotow, Philippe Gui, Wei Wu, Victoria M. Raymond, Richard B. Lanman, Frederic J. Kaye, Nir Peled, Ferran Fece De La Cruz, Brandon Nadres, Ryan B. Corcoran, Iwei Yeh, Boris C. Bastian, Petr Starostik, Kimberly Newsom, Victor R. Olivas, Alexander M. Wolff, James Fraser, Eric A. Collisson, Caroline E. McCoach, D. Ross Camidge, Jose Pacheco, Lyudmila Bazhenova, Tianhong Li, Trever G. Bivona, Collin M. Blakely

    http://dx.doi.org/10.1158/1078-0432.ccr-19-1667 Abstract Purpose: Although patients with advanced-stage non–small cell lung cancers (NSCLC) harboring MET exon 14 skipping mutations (METex14) often benefit from MET tyrosine kinase inhibitor (TKI) …

  86. Coherent convergent-beam time-resolved X-ray diffraction

    0.0 out of 5 stars 

    09 Jun 2014 | BioXFEL Publications | Contributor(s): J. C. H. Spence, N. A. Zatsepin, C. Li

    http://dx.doi.org/10.1098/rstb.2013.0325 J. C. H. Spence and N. A. Zatsepin and C. Li Spence, J.C.H., Zatsepin, N.A. & Li, C., 2014. Coherent convergent-beam time-resolved X-ray diffraction. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130325–20130325. …

  87. Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

    0.0 out of 5 stars 

    29 Jul 2016 | BioXFEL Publications | Contributor(s): Anna Munke, Jakob Andreasson, Andrew Aquila, Salah Awel, Kartik Ayyer, Anton Barty, Richard J. Bean, Peter Berntsen, Johan Bielecki, Sébastien Boutet, Maximilian Bucher, Henry Chapman, Benedikt J. Daurer, Hasan Demirci, Veit Elser, Petra Fromme, Janos Hajdu, Max F. Hantke, Akifumi Higashiura, Brenda Hogue, Ahmad Hosseinizadeh, Yoonhee Kim, Richard Kirian, Hemanth K.N. Reddy, Ti-Yen Lan, Daniel S.D. Larsson, Haiguang Liu, N. Duane Loh, Filipe R.N.C. Maia, Adrian P. Mancuso, Kerstin Mühlig, Atsushi Nakagawa, Daewoong Nam, Garrett Charles Nelson, Carl Nettelblad, Kenta Okamoto, Abbas Ourmazd, Max Rose, Gijs Van Der Schot, Peter Schwander, M. Marvin Seibert, Jonas A. Sellberg, Raymond G. Sierra, Changyong Song, Martin Svenda, Nicusor Timneanu, Ivan A. Vartanyants, Daniel Westphal, Max Oliver Wiedorn, Garth J. Williams, Paulraj Lourdu Xavier, Chun Hong Yoon, James D Zook

    http://dx.doi.org/10.1038/sdata.2016.64 Anna Munke and Jakob Andreasson and Andrew Aquila and Salah Awel and Kartik Ayyer and Anton Barty and Richard J. Bean and Peter Berntsen and Johan Bielecki and Sébastien Boutet and Maximilian Bucher and Henry N. Chapman and Benedikt J. Daurer and Hasan …

  88. Coherent diffractive imaging of microtubules using an X-ray laser

    0.0 out of 5 stars 

    13 Jun 2019 | BioXFEL Publications | Contributor(s): Gisela Brändén, Greger Hammarin, Rajiv Harimoorthy, Alexander Johansson, David Arnlund, Erik Malmerberg, Anton Barty, Stefan Tångefjord, Peter Berntsen, Daniel P. DePonte, Carolin Seuring, Thomas A. White, Francesco Stellato, Richard Bean, Kenneth R. Beyerlein, Leonard M. G. Chavas, Holger Fleckenstein, Cornelius Gati, Umesh Ghoshdastider, Lars Gumprecht, Dominik Oberthür, David Popp, Marvin Seibert, Thomas Tilp, Marc Messerschmidt, Garth J. Williams, N. Duane Loh, Henry Chapman, Peter Zwart, Mengning Liang, Sébastien Boutet, Robert C. Robinson, Richard Neutze

    http://dx.doi.org/10.1038/s41467-019-10448-x journal-article Brändén, G. et al., 2019. Coherent diffractive imaging of microtubules using an X-ray laser. Nature Communications, 10(1). Available at: http://dx.doi.org/10.1038/s41467-019-10448-x. Gisela Brändén and Greger Hammarin and Rajiv …

  89. Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

    0.0 out of 5 stars 

    27 Jun 2017 | BioXFEL Publications | Contributor(s): Hemanth K.N. Reddy, Chun Hong Yoon, Andrew Aquila, Salah Awel, Kartik Ayyer, Anton Barty, Peter Berntsen, Johan Bielecki, Sergey Bobkov, Maximilian Bucher, Gabriella A. Carini, Sebastian Carron, Henry Chapman, Benedikt Daurer, Hasan Demirci, Tomas Ekeberg, Petra Fromme, Janos Hajdu, Max Felix Hanke, Philip Hart, Brenda Hogue, Ahmad Hosseinizadeh, Yoonhee Kim, Richard Kirian, Ruslan P. Kurta, Daniel S.D. Larsson, N. Duane Loh, Filipe R.N.C. Maia, Adrian P. Mancuso, Kerstin Mühlig, Anna Munke, Daewoong Nam, Carl Nettelblad, Abbas Ourmazd, Max Rose, Peter Schwander, Marvin Seibert, Jonas A. Sellberg, Changyong Song, John Spence, Martin Svenda, Gijs Van Der Schot, Ivan A. Vartanyants, Garth J. Williams, P. Lourdu Xavier

    http://dx.doi.org/10.1038/sdata.2017.79 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Reddy, H.K.N. et al., 2017. Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source. Scientific Data, 4, p.170079. Available at: …

  90. Combined single cell AFM manipulation and TIRFM for probing the molecular stability of multilayer fibrinogen matrices

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    18 Oct 2013 | BioXFEL Publications | Contributor(s): W. Christenson, I. Yermolenko, B. Plochberger, F. Camacho-Alanis, A. Ros, T.P. Ugarova, R. Ros

    http://dx.doi.org/10.1016/j.ultramic.2013.10.009 journal-article Christenson, W. et al., 2014. Combined single cell AFM manipulation and TIRFM for probing the molecular stability of multilayer fibrinogen matrices. Ultramicroscopy, 136, pp.211–215. Available at: …

  91. Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse

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    17 Mar 2014 | BioXFEL Publications | Contributor(s): J. Szlachetko, C. J. Milne, J. Hoszowska, J.-Cl. Dousse, W. Błachucki, J. Sà, Y. Kayser, M. Messerschmidt, R. Abela, S. Boutet, C. David, G. Williams, M. Pajek, B. D. Patterson, G. Smolentsev, J. A. Van Bokhoven, M. Nachtegaal

    http://dx.doi.org/10.1063/1.4868260 journal-article Szlachetko, J. et al., 2014. Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse. Structural Dynamics, 1(2), p.021101. Available at: http://dx.doi.org/10.1063/1.4868260. J. Szlachetko …

  92. Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular Crystallography

    0.0 out of 5 stars 

    27 Jun 2014 | BioXFEL Publications | Contributor(s): Andrew E. Bruno, Amanda M. Ruby, Joseph Luft, Thomas D. Grant, Jayaraman Seetharaman, Gaetano T. Montelione, John F. Hunt, Edward Snell

    journal-article http://dx.doi.org/10.1371/journal.pone.0100782 NSF-STC Biology with X-ray Lasers (NSF-1231306) Bruno, A.E. et al., 2014. Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular …

  93. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

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    25 Feb 2020 | BioXFEL Publications | Contributor(s): Alexander M. Wolff, Iris Diane Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T. Biel, Sergio Carbajo, Aina E. Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D. Koralek, Minoru Kubo, Tomas Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry Van Den Bedem, Rahel Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sebastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James Fraser, Michael Thompson

    http://dx.doi.org/10.1107/s205225252000072x Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods …

  94. Comprehensive Research on Past and Future Therapeutic Strategies Devoted to Treatment of Amyotrophic Lateral Sclerosis

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    22 Feb 2022 | BioXFEL Publications | Contributor(s): Belgin Sever, Halilibrahim Ciftci, Hasan Demirci, Hilal Sever, Firdevs Ocak, Burak Yulug, Hiroshi Tateishi, Takahisa Tateishi, Masami Otsuka, Mikako Fujita, Ayşe Nazlı Başak

    http://dx.doi.org/10.3390/ijms23052400 Amyotrophic lateral sclerosis (ALS) is a rapidly debilitating fatal neurodegenerative disorder, causing muscle atrophy and weakness, which leads to paralysis and eventual death. ALS has a multifaceted nature affected by many pathological mechanisms, including …

  95. Computational crystallization

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    11 Jan 2016 | BioXFEL Publications | Contributor(s): Irem Altan, Patrick Charbonneau, Edward Snell

    http://dx.doi.org/10.1016/j.abb.2016.01.004 Irem Altan and Patrick Charbonneau and Edward H. Snell Altan, I., Charbonneau, P. & Snell, E.H., 2016. Computational crystallization. Archives of Biochemistry and Biophysics. Available at: http://dx.doi.org/10.1016/j.abb.2016.01.004. journal-article

  96. Computational design of a modular protein sense-response system

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    25 Nov 2019 | BioXFEL Publications | Contributor(s): Anum A. Glasgow, Yao-Ming Huang, Daniel J. Mandell, Michael Thompson, Ryan Ritterson, Amanda L. Loshbaugh, Jenna Pellegrino, Cody Krivacic, Roland A. Pache, Kyle A. Barlow, Noah Ollikainen, Deborah Jeon, Mark J. S. Kelly, James Fraser, Tanja Kortemme

    http://dx.doi.org/10.1126/science.aax8780 Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we …

  97. Computational design of thermostabilizing point mutations for G protein-coupled receptors

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    21 Jun 2018 | BioXFEL Publications | Contributor(s): Petr Popov, Yao Peng, Ling Shen, Raymond C Stevens, Vadim Cherezov, Zhi-Jie Liu, Vsevolod Katritch

    http://dx.doi.org/10.7554/elife.34729 Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational approach to …

  98. Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern

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    08 Feb 2024 | BioXFEL Publications | Contributor(s): Matthew P. Hancock, James Fraser, Andrej Sali

    http://dx.doi.org/10.1016/j.bpj.2023.11.1276 journal-article Hancock, M. P., Fraser, J. S., & Sali, A. (2024). Computing a Bayesian multi-state model of a protein structure from an X-ray diffraction pattern. Biophysical Journal, 123(3), 200a–201a. https://doi.org/10.1016/j.bpj.2023.11.1276 …

  99. Concentration of Sindbis virus with optimized gradient insulator-based dielectrophoresis

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    08 Feb 2016 | BioXFEL Publications | Contributor(s): Jie Ding, Robert M Lawrence, Paul V. Jones, Brenda Hogue, Mark A. Hayes

    http://dx.doi.org/10.1039/c5an02430g Jie Ding and Robert M. Lawrence and Paul V. Jones and Brenda G. Hogue and Mark A. Hayes Ding, J. et al., 2016. Concentration of Sindbis virus with optimized gradient insulator-based dielectrophoresis. Analyst. Available at: http://dx.doi.org/10.1039/c5an02430g. …

  100. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

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    30 Nov 2015 | BioXFEL Publications | Contributor(s): Raymond G Sierra, Cornelius Gati, Hartawan Laksmono, E Han Dao, Sheraz Gul, Franklin Fuller, Jan Kern, Ruchira Chatterjee, Mohamed Ibrahim, Aaron S Brewster, Iris Diane Young, Tara Michels-Clark, Andrew Aquila, Mengning Liang, Mark S. Hunter, Jason E Koglin, Sébastien Boutet, Elia A Junco, Brandon Hayes, Michael J Bogan, Christina Y Hampton, Elisabetta V Puglisi, Nicholas K Sauter, Claudiu A Stan, Athina Zouni, Junko Yano, Vittal K Yachandra, S Michael Soltis, Joseph D Puglisi, Hasan Demirci

    http://dx.doi.org/10.1038/nmeth.3667 Raymond G Sierra and Cornelius Gati and Hartawan Laksmono and E Han Dao and Sheraz Gul and Franklin Fuller and Jan Kern and Ruchira Chatterjee and Mohamed Ibrahim and Aaron S Brewster and Iris D Young and Tara Michels-Clark and Andrew Aquila and Mengning Liang …