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XFELs open a new era in structural chemical biology
17 Nov 2015 | BioXFEL Publications | Contributor(s): Petra Fromme
http://dx.doi.org/10.1038/nchembio.1968 Petra Fromme Fromme, P., 2015. XFELs open a new era in structural chemical biology. Nat Chem Biol, 11(12), pp.895–899. Available at: …
https://www.bioxfel.org/resources/875
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Polarizability of Six-Helix Bundle and Triangle DNA Origami and Their Escape Characteristics from a Dielectrophoretic Trap
16 Nov 2015 | BioXFEL Publications | Contributor(s): Lin Gan, Fernanda Camacho-Alanis, Alexandra Ros
http://dx.doi.org/10.1021/acs.analchem.5b02524 Lin Gan and Fernanda Camacho-Alanis and Alexandra Ros Gan, L., Camacho-Alanis, F. & Ros, A., 2015. Polarizability of Six-Helix Bundle and Triangle DNA …
https://www.bioxfel.org/resources/1086
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BioXFEL Graduate Student Cross-Training Scholarship
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, …
https://www.bioxfel.org/resources/CTS
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BioXFEL Scholar Application Form
10 Nov 2015 | Teaching Materials
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https://www.bioxfel.org/resources/658
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Serial femtosecond crystallography of soluble proteins in lipidic cubic phase
10 Nov 2015 | Teaching Materials
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal …
https://www.bioxfel.org/resources/681
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Indexing ambiguity in SFX resolved using expectation maximization algorithm
10 Nov 2015 | Teaching Materials
Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in …
https://www.bioxfel.org/resources/680
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Stable Chromosome Condensation Revealed by Chromosome Conformation Capture
05 Nov 2015 | BioXFEL Publications | Contributor(s): Kyle P. Eagen, Tom A. Hartl, Roger D. Kornberg
journal-article http://dx.doi.org/10.1016/j.cell.2015.10.026 Eagen, K.P., Hartl, T.A. & Kornberg, R.D., 2015. Stable Chromosome Condensation Revealed by Chromosome Conformation Capture. Cell, …
https://www.bioxfel.org/resources/1256
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Chromatin-remodeling and the initiation of transcription
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 …
https://www.bioxfel.org/resources/1449
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Introduction to XRayView Crystallographic Software
04 Nov 2015 | Teaching Materials
Dr. George Phillips introduces the basic concepts of crystallography focusing on the reciprocal lattice and Ewald sphere construction and using the XRayView software developed in his lab to help …
https://www.bioxfel.org/resources/679
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The Importance of Ligand-Receptor Conformational Pairs in Stabilization: Spotlight on the N/OFQ G Protein-Coupled Receptor
03 Nov 2015 | BioXFEL Publications | Contributor(s): Rebecca L. Miller, Aaron A. Thompson, Claudio Trapella, Remo Guerrini, Davide Malfacini, Nilkanth N Patel, Gye Won Han, Vadim Cherezov, Girolamo Caló, Vsevolod Katritch, Raymond C. Stevens
http://dx.doi.org/10.1016/j.str.2015.07.024 Rebecca L. Miller and Aaron A. Thompson and Claudio Trapella and Remo Guerrini and Davide Malfacini and Nilkanth Patel and Gye Won Han and Vadim Cherezov …
https://www.bioxfel.org/resources/1084
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High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction
02 Nov 2015 | BioXFEL Publications | Contributor(s): Jessica L. Thomaston, Mercedes Alfonso-Prieto, Rahel Woldeyes, James Fraser, Michael L. Klein, Giacomo Fiorin, William F. DeGrado
http://dx.doi.org/10.1073/pnas.1518493112 Jessica L. Thomaston and Mercedes Alfonso-Prieto and Rahel A. Woldeyes and James S. Fraser and Michael L. Klein and Giacomo Fiorin and William F. DeGrado …
https://www.bioxfel.org/resources/860
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Nucleation and Growth of Membrane Protein CrystalsIn Meso—A Fluorescence Microscopy Study
02 Nov 2015 | BioXFEL Publications | Contributor(s): Andrey Bogorodskiy, Fedor Frolov, Alexey Mishin, Ekaterina Round, Vitaly Polovinkin, Vadim Cherezov, Valentin Gordeliy, Georg Büldt, Thomas Gensch, Valentin Borshchevskiy
journal-article http://dx.doi.org/10.1021/acs.cgd.5b01061 Bogorodskiy, A. et al., 2015. Nucleation and Growth of Membrane Protein CrystalsIn Meso—A Fluorescence Microscopy Study. Crystal Growth & …
https://www.bioxfel.org/resources/1265
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Crystal Structure of the Zorbamycin-Binding Protein ZbmA, the Primary Self-Resistance Element in Streptomyces flavoviridis ATCC21892
29 Oct 2015 | BioXFEL Publications | Contributor(s): Jeffrey D. Rudolf, Lance Bigelow, Changsoo Chang, Marianne E. Cuff, Jeremy R. Lohman, Chin-Yuan Chang, Ming Ma, Dong Yang, Shonda Clancy, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen
http://dx.doi.org/10.1021/acs.biochem.5b01008 Jeffrey D. Rudolf and Lance Bigelow and Changsoo Chang and Marianne E. Cuff and Jeremy R. Lohman and Chin-Yuan Chang and Ming Ma and Dong Yang and Shonda …
https://www.bioxfel.org/resources/1087
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Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit
27 Oct 2015 | BioXFEL Publications | Contributor(s): Daniel A. Keedy, James Fraser, Henry Van Den Bedem
http://dx.doi.org/10.1371/journal.pcbi.1004507 Daniel A. Keedy and James S. Fraser and Henry van den Bedem Keedy, D.A., Fraser, J.S. & van den Bedem, H., 2015. Exposing Hidden Alternative Backbone …
https://www.bioxfel.org/resources/975
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Accurate determination of segmented X-ray detector geometry
22 Oct 2015 | BioXFEL Publications | Contributor(s): Oleksandr Yefanov, Valerio Mariani, Cornelius Gati, Thomas A. White, Henry Chapman, Anton Barty
http://dx.doi.org/10.1364/oe.23.028459 Oleksandr Yefanov and Valerio Mariani and Cornelius Gati and Thomas A. White and Henry N. Chapman and Anton Barty Yefanov, O. et al., 2015. Accurate …
https://www.bioxfel.org/resources/861
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Structure of an RNA polymerase II preinitiation complex
20 Oct 2015 | BioXFEL Publications | Contributor(s): Kenji Murakami, Kuang-Lei Tsai, Nir Kalisman, David Bushnell, Francisco J. Asturias, Roger Kornberg
journal-article http://dx.doi.org/10.1073/pnas.1518255112 Murakami, K. et al., 2015. Structure of an RNA polymerase II preinitiation complex. Proceedings of the National Academy of Sciences, …
https://www.bioxfel.org/resources/1323
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Overview of Serial Femtosecond Crystallography
14 Oct 2015 | Teaching Materials | Contributor(s): Petra Fromme
Dr. Petra Fromme discusses an introductory overview to the field of serial crystallography and recent results showing the potential power of the technique.
https://www.bioxfel.org/resources/668
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Virus Crystallography
14 Oct 2015 | Teaching Materials | Contributor(s): Robert M Lawrence
Dr. Rob Lawrence describes the unique problems associated with crystallization of virus particles and different methods to overcome them.
https://www.bioxfel.org/resources/667
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When Your Crystals Bite
14 Oct 2015 | Teaching Materials | Contributor(s): George Phillips
Dr. George Phillips describes properties of crystals such as twinning and other defects and how they can adversely affect crystallographic analysis.
https://www.bioxfel.org/resources/666
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Optimizing crystallization hits - small to large and large to small
14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft
Joe Luft describes methods for optimizing initial results from crystallization screening trials for both macro and nanocrystals.
https://www.bioxfel.org/resources/665
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Practical Considerations for Crystallographic Data Analysis
14 Oct 2015 | Teaching Materials | Contributor(s): Tom Grant
Dr. Thomas Grant explains how crystal quality affects diffraction data and how you can detect and ameliorate problems in crystallographic data.
https://www.bioxfel.org/resources/664
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Applications of TEM for Evaluation and Optimization of Crystal Growth
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.
https://www.bioxfel.org/resources/663
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What is the outcome of your crystallization experiment
14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft
Joe Luft discusses the detection of hits in crystallization screening experiments for both macro and nanocrystals.
https://www.bioxfel.org/resources/662
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Strategies to sample crystallization space
14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft
Joe Luft discusses crystallization screening strategies to maximize the likelihood of success.
https://www.bioxfel.org/resources/661
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Fundamentals of Crystal Growth
14 Oct 2015 | Teaching Materials | Contributor(s): Edward Snell, Eaton E Lattman
Dr. Ed Lattman discusses the foundations of crystallography and theoretical and practical considerations including X-ray radiation and production and crystallization nucleation, growth and …
https://www.bioxfel.org/resources/660
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2015 HWI Crystallization Workshop
13 Oct 2015 | Workshops | Contributor(s): Tom Grant, Bill Bauer, Edward Snell
Crystallization is the major bottleneck to 3D structure determination using X-ray crystallography. In this workshop we will discuss many tenets of successful crystallization for both conventional and …
https://www.bioxfel.org/resources/659
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Using XFELs to measure the solution structures of biomolecules
13 Oct 2015 | Teaching Materials
Dr. Lois Pollack presents an introduction to small and wide angle X-ray solution scattering techniques and describes the advances made possible by XFELs.
https://www.bioxfel.org/resources/657
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Single Particle Reconstruction
13 Oct 2015 | Teaching Materials
Dr. Dilano Saldin discusses recent advances in algorithms for single particle reconstruction from solution scattering data at XFELs.
https://www.bioxfel.org/resources/656
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Extraction of fast changes in the structure of a disordered ensemble of photoexcited biomolecules
13 Oct 2015 | Teaching Materials
Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized …
https://www.bioxfel.org/resources/655
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Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells
13 Oct 2015 | Teaching Materials
X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the `diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an …
https://www.bioxfel.org/resources/654
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Post-refinement method for snapshot serial crystallography
13 Oct 2015 | Teaching Materials
A post-refinement procedure has been devised for ‘snapshot’ diffraction data consisting entirely of partially recorded reflections, each diffraction pattern from a crystal in an orientation …
https://www.bioxfel.org/resources/653
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Mapping the continuous reciprocal space intensity of X-ray serial crystallography
13 Oct 2015 | Teaching Materials
Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 …
https://www.bioxfel.org/resources/652
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Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
13 Oct 2015 | Teaching Materials
We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton …
https://www.bioxfel.org/resources/651
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Double-focusing mixing jet for XFEL study of chemical kinetics
13 Oct 2015 | Teaching Materials
Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of …
https://www.bioxfel.org/resources/650
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High-resolution structure of viruses from random diffraction snapshots
13 Oct 2015 | Teaching Materials
The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. …
https://www.bioxfel.org/resources/649
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Deducing fast electron density changes in uncrystallized biomolecules
13 Oct 2015 | Teaching Materials
We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged …
https://www.bioxfel.org/resources/648
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Serial femtosecond crystallography of G-protein coupled receptors
13 Oct 2015 | Teaching Materials
G protein–coupled receptors (GPCRs) are eukaryotic membrane proteins that have a central role in cellular communication and have become key drug targets. To overcome the difficulties of growing …
https://www.bioxfel.org/resources/647
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Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel
09 Oct 2015 | Teaching Materials
Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This …
https://www.bioxfel.org/resources/646
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3D Single Particle Structure Recovery
07 Oct 2015 | Teaching Materials | Contributor(s): Ahmad Hosseinizadeh
Dr. Ahmad Hosseinizadeh discuss different pathways to recovering the structure of single particles from XFEL snapshots.
https://www.bioxfel.org/resources/645
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Energy Landscapes
07 Oct 2015 | Teaching Materials | Contributor(s): Ali Dashti
Energy landscapes and continuous conformational mapping of molecular machines.
https://www.bioxfel.org/resources/644
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Manifold Embedding
07 Oct 2015 | Teaching Materials | Contributor(s): Peter Schwander
From single particle snapshots to movies of molecular machines and energy landscapes.
https://www.bioxfel.org/resources/643
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Angular Momentum Decomposition
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.
https://www.bioxfel.org/resources/642
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Imaging of Objects by Coherent Diffraction of X-Ray FEL Pulses
03 Oct 2015 | BioXFEL Publications | Contributor(s): Richard Kirian, Henry Chapman
http://dx.doi.org/10.1007/978-3-319-04507-8_27-1 Richard A. Kirian and Henry N. Chapman Kirian, R.A. & Chapman, H.N., 2015. Imaging of Objects by Coherent Diffraction of X-Ray FEL Pulses. Synchrotron …
https://www.bioxfel.org/resources/1069
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Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography
30 Sep 2015 | BioXFEL Publications | Contributor(s): Daniel A Keedy, Lillian R Kenner, Matthew Warkentin, Rahel Woldeyes, Jesse B Hopkins, Michael Thompson, Aaron S Brewster, Andrew H Van Benschoten, Elizabeth L Baxter, Monarin Uervirojnangkoorn, Scott E McPhillips, Jinhu Song, Roberto Alonso-Mori, James Holton, William I Weis, Axel T Brunger, S Michael Soltis, Henrik Lemke, Ana Gonzalez, Nicholas K Sauter, Aina E Cohen, Henry Van Den Bedem, Robert E Thorne, James Fraser
Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme …
https://www.bioxfel.org/resources/878
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Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases
29 Sep 2015 | BioXFEL Publications | Contributor(s): Jeremy R. Lohman, Ming Ma, Jerzy Osipiuk, Boguslaw Nocek, Youngchang Kim, Changsoo Chang, Marianne Cuff, Jamey Mack, Lance Bigelow, Hui Li, Michael Endres, Gyorgy Babnigg, Andrzej Joachimiak, George Phillips, Ben Shen
http://dx.doi.org/10.1073/pnas.1515460112 Jeremy R. Lohman and Ming Ma and Jerzy Osipiuk and Boguslaw Nocek and Youngchang Kim and Changsoo Chang and Marianne Cuff and Jamey Mack and Lance Bigelow …
https://www.bioxfel.org/resources/931
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Structural Basis for Ligand Recognition and Functional Selectivity at Angiotensin Receptor
29 Sep 2015 | BioXFEL Publications | Contributor(s): Haitao Zhang, Hamiyet Unal, Russell Desnoyer, Gye Won Han, Nilkanth N Patel, Vsevolod Katritch, Sadashiva S. Karnik, Vadim Cherezov, Raymond C. Stevens
http://dx.doi.org/10.1074/jbc.m115.689000 Haitao Zhang and Hamiyet Unal and Russell Desnoyer and Gye Won Han and Nilkanth Patel and Vsevolod Katritch and Sadashiva S. Karnik and Vadim Cherezov and …
https://www.bioxfel.org/resources/934
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Towards phasing using high X-ray intensity
29 Sep 2015 | BioXFEL Publications | Contributor(s): Lorenzo Galli, Sang-Kil Son, Thomas R. M. Barends, Thomas A. White, Anton Barty, Sabine Botha, Sébastien Boutet, Carl Caleman, R. Bruce Doak, Max H. Nanao, Karol Nass, Robert L. Shoeman, Nicusor Timneanu, Robin Santra, Ilme Schlichting, Henry Chapman
X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. …
https://www.bioxfel.org/resources/958
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Molecular architecture of the yeast Mediator complex
24 Sep 2015 | BioXFEL Publications | Contributor(s): Philip J Robinson, Michael J Trnka, Riccardo Pellarin, Charles H Greenberg, David Bushnell, Ralph Davis, Alma L Burlingame, Andrej Sali, Roger Kornberg
http://dx.doi.org/10.7554/elife.08719 Philip J Robinson and Michael J Trnka and Riccardo Pellarin and Charles H Greenberg and David A Bushnell and Ralph Davis and Alma L Burlingame and Andrej Sali …
https://www.bioxfel.org/resources/885
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Hollow cone illumination for fast TEM, and outrunning damage with electrons
23 Sep 2015 | BioXFEL Publications | Contributor(s): J C H Spence, G Subramanian, P Musumeci
http://dx.doi.org/10.1088/0953-4075/48/21/214003 J C H Spence and G Subramanian and P Musumeci Spence, J.C.H., Subramanian, G. & Musumeci, P., 2015. Hollow cone illumination for fast TEM, and …
https://www.bioxfel.org/resources/862
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Image reconstruction in serial femtosecond nanocrystallography using x-ray free-electron lasers
21 Sep 2015 | BioXFEL Publications | Contributor(s): Joe Chen, Richard Kirian, Kenneth R. Beyerlein, Richard J. Bean, Andrew J. Morgan, Oleksandr M. Yefanov, Romain D. Arnal, David H. Wojtas, Phil J. Bones, Henry Chapman, John Spence, Rick P. Millane
http://dx.doi.org/10.1117/12.2187610 Joe P. J. Chen and Richard A. Kirian and Kenneth R. Beyerlein and Richard J. Bean and Andrew J. Morgan and Oleksandr M. Yefanov and Romain D. Arnal and David H. …
https://www.bioxfel.org/resources/965
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Strongly aligned gas-phase molecules at free-electron lasers
17 Sep 2015 | BioXFEL Publications | Contributor(s): Thomas Kierspel, Joss Wiese, Terry Mullins, Joseph Robinson, Andy Aquila, Anton Barty, Richard Bean, Rebecca Boll, Sébastien Boutet, Philip Bucksbaum, Henry Chapman, Lauge Christensen, Alan Fry, Mark S. Hunter, Jason E Koglin, Mengning Liang, Valerio Mariani, Andrew Morgan, Adi Natan, Vladimir Petrovic, Daniel Rolles, Artem Rudenko, Kirsten Schnorr, Henrik Stapelfeldt, Stephan Stern, Jan Thøgersen, Chun Hong Yoon, Fenglin Wang, Sebastian Trippel, Jochen Küpper
http://dx.doi.org/10.1088/0953-4075/48/20/204002 Thomas Kierspel and Joss Wiese and Terry Mullins and Joseph Robinson and Andy Aquila and Anton Barty and Richard Bean and Rebecca Boll and Sébastien …
https://www.bioxfel.org/resources/936
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Synchrotron topographic evaluation of strain around craters generated by irradiation with X-ray pulses from free electron laser with different intensities
11 Sep 2015 | BioXFEL Publications | Contributor(s): W. Wierzchowski, K. Wieteska, R. Sobierajski, D. Klinger, J. Pełka, D. Żymierska, C. Paulmann, S.P. Hau-Riege, R.A. London, A. Graf, T. Burian, J. Chalupský, J. Gaudin, J. Krzywinski, S. Moeller, M. Messerschmidt, J. Bozek, Ch. Bostedt
http://dx.doi.org/10.1016/j.nimb.2015.07.115 W. Wierzchowski and K. Wieteska and R. Sobierajski and D. Klinger and J. Pełka and D. Żymierska and C. Paulmann and S.P. Hau-Riege and R.A. London and …
https://www.bioxfel.org/resources/1082
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Structure of the toxic core of α-synuclein from invisible crystals
08 Sep 2015 | BioXFEL Publications | Contributor(s): Jose A. Rodriguez, Magdalena I. Ivanova, Michael R. Sawaya, Duilio Cascio, Francis E. Reyes, Dan Shi, Smriti Sangwan, Elizabeth L. Guenther, Lisa M. Johnson, Meng Zhang, Lin Jiang, Mark A. Arbing, Brent L. Nannenga, Johan Hattne, Julian Whitelegge, Aaron S. Brewster, Marc Messerschmidt, Sébastien Boutet, Nicholas K. Sauter, Tamir Gonen, David S. Eisenberg
http://dx.doi.org/10.1038/nature15368 Jose A. Rodriguez and Magdalena I. Ivanova and Michael R. Sawaya and Duilio Cascio and Francis E. Reyes and Dan Shi and Smriti Sangwan and Elizabeth L. Guenther …
https://www.bioxfel.org/resources/1091
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3rd BioXFEL International Conference
08 Sep 2015 | Downloads
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https://www.bioxfel.org/resources/639
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X-ray two-photon absorption with high fluence XFEL pulses
07 Sep 2015 | BioXFEL Publications | Contributor(s): J Hoszowska, J Szlachetko, J-Cl Dousse, W Błachucki, Y Kayser, Ch Milne, M Pajek, S Boutet, M Messerschmidt, G Williams, C T Chantler
http://dx.doi.org/10.1088/1742-6596/635/10/102009 J Hoszowska and J Szlachetko and J-Cl Dousse and W Błachucki and Y Kayser and Ch Milne and M Pajek and S Boutet and M Messerschmidt and G Williams …
https://www.bioxfel.org/resources/938
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Real-time observation of the initiation of RNA polymerase II transcription
02 Sep 2015 | BioXFEL Publications | Contributor(s): Furqan M. Fazal, Cong A. Meng, Kenji Murakami, Roger Kornberg, Steven M. Block
journal-article http://dx.doi.org/10.1038/nature14882 Fazal, F.M. et al., 2015. Real-time observation of the initiation of RNA polymerase II transcription. Nature, 525(7568), pp.274–277. Available …
https://www.bioxfel.org/resources/1270
