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<section id="publications">
<h1>Publications<a class="headerlink" href="#publications" title="Link to this heading">¶</a></h1>
<section id="dials-journal-articles">
<h2>DIALS Journal Articles<a class="headerlink" href="#dials-journal-articles" title="Link to this heading">¶</a></h2>
<ul>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1063/4.0000265" target="_blank">Laue-DIALS: Open-source software for polychromatic x-ray diffraction data</a></div>
<div class="line">Hewitt RA, Dalton KM, Mendez DA, Wang HK, Klureza MA, Brookner DE, Greisman JB, McDonagh D, Šrajer V, Sauter NK, Brewster AS, Hekstra DR.</div>
<div class="line"><em>Struct Dyn</em> <strong>11</strong>, 054701 (1 Sep 2024). [PMID:39386198] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC11462730/" target="_blank">PMC11462730</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798322004399" target="_blank">xia2.multiplex: a multi-crystal data-analysis pipeline</a></div>
<div class="line">Gildea RJ, Beilsten-Edmands J, Axford D, Horrell S, Aller P, Sandy J, Sanchez-Weatherby J, Owen CD, Lukacik P, Strain-Damerell C, Owen RL, Walsh MA, Winter G.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>78</strong>, 752-769 (01 Jun 2022). [PMID:35647922] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC9159281/" target="_blank">PMC9159281</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1002/pro.4224" target="_blank">DIALS as a toolkit</a></div>
<div class="line">Winter G, Beilsten-Edmands J, Devenish N, Gerstel M, Gildea RJ, McDonagh D, Pascal E, Waterman DG, Williams BH, Evans G.</div>
<div class="line"><em>Protein Sci</em> <strong>31</strong>, 232-250 (1 Jan 2022). [PMID:34747533] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC8740827/" target="_blank">PMC8740827</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798320003198" target="_blank">Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling</a></div>
<div class="line">Beilsten-Edmands J, Winter G, Gildea R, Parkhurst J, Waterman D, Evans G.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>76</strong>, 385-399 (01 Apr 2020). [PMID:32254063] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC7137103/" target="_blank">PMC7137103</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798319012877" target="_blank">SAD phasing of XFEL data depends critically on the error model</a></div>
<div class="line">Brewster AS, Bhowmick A, Bolotovsky R, Mendez D, Zwart PH, Sauter NK.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>75</strong>, 959-968 (01 Nov 2019). [PMID:31692470] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6834081/" target="_blank">PMC6834081</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798319003528" target="_blank">How best to use photons</a></div>
<div class="line">Winter G, Gildea RJ, Paterson NG, Beale J, Gerstel M, Axford D, Vollmar M, McAuley KE, Owen RL, Flaig R, Ashton AW, Hall DR.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>75</strong>, 242-261 (01 Mar 2019). [PMID:30950396] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6450062/" target="_blank">PMC6450062</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798318009191" target="_blank">Improving signal strength in serial crystallography with DIALS geometry refinement</a></div>
<div class="line">Brewster AS, Waterman DG, Parkhurst JM, Gildea RJ, Young ID, O’Riordan LJ, Yano J, Winter G, Evans G, Sauter NK.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>74</strong>, 877-894 (01 Sep 2018). [PMID:30198898] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6130462/" target="_blank">PMC6130462</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798318002978" target="_blank">Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguity</a></div>
<div class="line">Gildea RJ, Winter G.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>74</strong>, 405-410 (01 May 2018). [PMID:29717711] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5930348/" target="_blank">PMC5930348</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798317017235" target="_blank">DIALS: implementation and evaluation of a new integration package</a></div>
<div class="line">Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>74</strong>, 85-97 (01 Feb 2018). [PMID:29533234] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5947772/" target="_blank">PMC5947772</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2052252517010259" target="_blank">Background modelling of diffraction data in the presence of ice rings</a></div>
<div class="line">Parkhurst JM, Thorn A, Vollmar M, Winter G, Waterman DG, Fuentes-Montero L, Gildea RJ, Murshudov GN, Evans G.</div>
<div class="line"><em>IUCrJ</em> <strong>4</strong>, 626-638 (01 Sep 2017). [PMID:28989718] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5619854/" target="_blank">PMC5619854</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1600576716013595" target="_blank">Robust background modelling in <i>DIALS</i></a></div>
<div class="line">Parkhurst JM, Winter G, Waterman DG, Fuentes-Montero L, Gildea RJ, Murshudov GN, Evans G.</div>
<div class="line"><em>J Appl Crystallogr</em> <strong>49</strong>, 1912-1921 (01 Dec 2016). [PMID:27980508] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5139990/" target="_blank">PMC5139990</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798316002187" target="_blank">Diffraction-geometry refinement in the DIALS framework</a></div>
<div class="line">Waterman DG, Winter G, Gildea RJ, Parkhurst JM, Brewster AS, Sauter NK, Evans G.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>72</strong>, 558-75 (1 Apr 2016). [PMID:27050135] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4822564/" target="_blank">PMC4822564</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1399004714017039" target="_blank">New methods for indexing multi-lattice diffraction data</a></div>
<div class="line">Gildea RJ, Waterman DG, Parkhurst JM, Axford D, Sutton G, Stuart DI, Sauter NK, Evans G, Winter G.</div>
<div class="line"><em>Acta Crystallogr D Biol Crystallogr</em> <strong>70</strong>, 2652-66 (1 Oct 2014). [PMID:25286849] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4188007/" target="_blank">PMC4188007</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1600576714011996" target="_blank"><i>dxtbx</i>: the diffraction experiment toolbox</a></div>
<div class="line">Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton AW, Echols N, Evans G, Sauter NK, Winter G.</div>
<div class="line"><em>J Appl Crystallogr</em> <strong>47</strong>, 1459-1465 (01 Aug 2014). [PMID:25242914] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4119952/" target="_blank">PMC4119952</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1016/j.str.2014.01.002" target="_blank">Diffuse X-ray scattering to model protein motions</a></div>
<div class="line">Wall ME, Adams PD, Fraser JS, Sauter NK.</div>
<div class="line"><em>Structure</em> <strong>22</strong>, 182-4 (04 Feb 2014). [PMID:24507780] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4070675/" target="_blank">PMC4070675</a>] <a class="reference external" href="http://cci.lbl.gov/publications/download/diffuse.pdf" target="_blank">(Reprint)</a></div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S0907444913000863" target="_blank">New Python-based methods for data processing</a></div>
<div class="line">Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N.</div>
<div class="line"><em>Acta Crystallogr D Biol Crystallogr</em> <strong>69</strong>, 1274-82 (1 Jul 2013). [PMID:23793153] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC3689530/" target="_blank">PMC3689530</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1186/1751-0473-7-5" target="_blank">Automatic Fortran to C++ conversion with FABLE</a></div>
<div class="line">Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams PD.</div>
<div class="line"><em>Source Code Biol Med</em> <strong>7</strong>, 5 (28 May 2012). [PMID:22640868] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC3448510/" target="_blank">PMC3448510</a>]</div>
</div>
</li>
</ul>
</section>
<section id="dials-application-to-xfel-crystallography">
<h2>DIALS Application to XFEL Crystallography<a class="headerlink" href="#dials-application-to-xfel-crystallography" title="Link to this heading">¶</a></h2>
<ul>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1126/science.adh8160" target="_blank">Structure of a ribonucleotide reductase R2 protein radical</a></div>
<div class="line">Lebrette H, Srinivas V, John J, Aurelius O, Kumar R, Lundin D, Brewster AS, Bhowmick A, Sirohiwal A, Kim IS, Gul S, Pham C, Sutherlin KD, Simon P, Butryn A, Aller P, Orville AM, Fuller FD, Alonso-Mori R, Batyuk A, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Sjöberg BM, Kern J, Roos K, Högbom M.</div>
<div class="line"><em>Science</em> <strong>382</strong>, 109-113 (06 Oct 2023). [PMID:37797025] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC7615503/" target="_blank">PMC7615503</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/s41586-023-06038-z" target="_blank">Structural evidence for intermediates during O<sub>2</sub> formation in photosystem II</a></div>
<div class="line">Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK.</div>
<div class="line"><em>Nature</em> <strong>617</strong>, 629-636 (1 May 2023). [PMID:37138085] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC10191843/" target="_blank">PMC10191843</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/s41586-021-04218-3" target="_blank">Chemical crystallography by serial femtosecond X-ray diffraction</a></div>
<div class="line">Schriber EA, Paley DW, Bolotovsky R, Rosenberg DJ, Sierra RG, Aquila A, Mendez D, Poitevin F, Blaschke JP, Bhowmick A, Kelly RP, Hunter M, Hayes B, Popple DC, Yeung M, Pareja-Rivera C, Lisova S, Tono K, Sugahara M, Owada S, Kuykendall T, Yao K, Schuck PJ, Solis-Ibarra D, Sauter NK, Brewster AS, Hohman JN.</div>
<div class="line"><em>Nature</em> <strong>601</strong>, 360-365 (1 Jan 2022). [PMID:35046599] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC8770144/" target="_blank">PMC8770144</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/s41586-018-0681-2" target="_blank">Structures of the intermediates of Kok's photosynthetic water oxidation clock</a></div>
<div class="line">Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK.</div>
<div class="line"><em>Nature</em> <strong>563</strong>, 421-425 (1 Nov 2018). [PMID:30405241] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6485242/" target="_blank">PMC6485242</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1073/pnas.1705624114" target="_blank">XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction</a></div>
<div class="line">Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF.</div>
<div class="line"><em>Proc Natl Acad Sci U S A</em> <strong>114</strong>, 13357-13362 (19 Dec 2017). [PMID:28835537] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5754760/" target="_blank">PMC5754760</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/nature20161" target="_blank">Structure of photosystem II and substrate binding at room temperature</a></div>
<div class="line">Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J.</div>
<div class="line"><em>Nature</em> <strong>540</strong>, 453-457 (15 Dec 2016). [PMID:27871088] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5201176/" target="_blank">PMC5201176</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/nature19825" target="_blank">De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure</a></div>
<div class="line">Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS.</div>
<div class="line"><em>Nature</em> <strong>539</strong>, 43-47 (03 Nov 2016). [PMID:27680699] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5161637/" target="_blank">PMC5161637</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.7554/eLife.07574" target="_blank">Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography</a></div>
<div class="line">Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS.</div>
<div class="line"><em>Elife</em> <strong>4</strong> (30 Sep 2015). [PMID:26422513] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4721965/" target="_blank">PMC4721965</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/nature15368" target="_blank">Structure of the toxic core of α-synuclein from invisible crystals</a></div>
<div class="line">Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS.</div>
<div class="line"><em>Nature</em> <strong>525</strong>, 486-90 (24 Sep 2015). [PMID:26352473] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4791177/" target="_blank">PMC4791177</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/nature14975" target="_blank">Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis</a></div>
<div class="line">Zhou Q, Lai Y, Bacaj T, Zhao M, Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Sauter NK, Cohen AE, Soltis SM, Alonso-Mori R, Chollet M, Lemke HT, Pfuetzner RA, Choi UB, Weis WI, Diao J, Südhof TC, Brunger AT.</div>
<div class="line"><em>Nature</em> <strong>525</strong>, 62-7 (03 Sep 2015). [PMID:26280336] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4607316/" target="_blank">PMC4607316</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1399004715006902" target="_blank">A revised partiality model and post-refinement algorithm for X-ray free-electron laser data</a></div>
<div class="line">Ginn HM, Brewster AS, Hattne J, Evans G, Wagner A, Grimes JM, Sauter NK, Sutton G, Stuart DI.</div>
<div class="line"><em>Acta Crystallogr D Biol Crystallogr</em> <strong>71</strong>, 1400-10 (1 Jun 2015). [PMID:26057680] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4461207/" target="_blank">PMC4461207</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.7554/eLife.05421" target="_blank">Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals</a></div>
<div class="line">Uervirojnangkoorn M, Zeldin OB, Lyubimov AY, Hattne J, Brewster AS, Sauter NK, Brunger AT, Weis WI.</div>
<div class="line"><em>Elife</em> <strong>4</strong> (17 Mar 2015). [PMID:25781634] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4397907/" target="_blank">PMC4397907</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/ncomms7435" target="_blank">Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data</a></div>
<div class="line">Ginn HM, Messerschmidt M, Ji X, Zhang H, Axford D, Gildea RJ, Winter G, Brewster AS, Hattne J, Wagner A, Grimes JM, Evans G, Sauter NK, Sutton G, Stuart DI.</div>
<div class="line"><em>Nat Commun</em> <strong>6</strong>, 6435 (09 Mar 2015). [PMID:25751308] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4403592/" target="_blank">PMC4403592</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1600577514028203" target="_blank">XFEL diffraction: developing processing methods to optimize data quality</a></div>
<div class="line">Sauter NK.</div>
<div class="line"><em>J Synchrotron Radiat</em> <strong>22</strong>, 239-48 (1 Mar 2015). [PMID:25723925] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4344359/" target="_blank">PMC4344359</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1399004714026145" target="_blank">Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns</a></div>
<div class="line">Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK.</div>
<div class="line"><em>Acta Crystallogr D Biol Crystallogr</em> <strong>71</strong>, 357-66 (1 Feb 2015). [PMID:25664747] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4321489/" target="_blank">PMC4321489</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1399004714025875" target="_blank">Data Exploration Toolkit for serial diffraction experiments</a></div>
<div class="line">Zeldin OB, Brewster AS, Hattne J, Uervirojnangkoorn M, Lyubimov AY, Zhou Q, Zhao M, Weis WI, Sauter NK, Brunger AT.</div>
<div class="line"><em>Acta Crystallogr D Biol Crystallogr</em> <strong>71</strong>, 352-6 (1 Feb 2015). [PMID:25664746] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4321488/" target="_blank">PMC4321488</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1399004714024134" target="_blank">Improved crystal orientation and physical properties from single-shot XFEL stills</a></div>
<div class="line">Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD.</div>
<div class="line"><em>Acta Crystallogr D Biol Crystallogr</em> <strong>70</strong>, 3299-309 (01 Dec 2014). [PMID:25478847] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4257623/" target="_blank">PMC4257623</a>] <a class="reference external" href="http://cci.lbl.gov/publications/download/Mosaicity_wa5077.pdf" target="_blank">(Reprint)</a></div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1073/pnas.1418733111" target="_blank">Goniometer-based femtosecond crystallography with X-ray free electron lasers</a></div>
<div class="line">Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO.</div>
<div class="line"><em>Proc Natl Acad Sci U S A</em> <strong>111</strong>, 17122-7 (02 Dec 2014). [PMID:25362050] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4260607/" target="_blank">PMC4260607</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1073/pnas.1413456111" target="_blank">Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam</a></div>
<div class="line">Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier JP, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park HW, Federici BA, Sauter NK, Schlichting I, Eisenberg DS.</div>
<div class="line"><em>Proc Natl Acad Sci U S A</em> <strong>111</strong>, 12769-74 (02 Sep 2014). [PMID:25136092] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4156696/" target="_blank">PMC4156696</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1098/rstb.2013.0590" target="_blank">Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers</a></div>
<div class="line">Kern J, Hattne J, Tran R, Alonso-Mori R, Laksmono H, Gul S, Sierra RG, Rehanek J, Erko A, Mitzner R, Wernet P, Bergmann U, Sauter NK, Yachandra V, Yano J.</div>
<div class="line"><em>Philos Trans R Soc Lond B Biol Sci</em> <strong>369</strong>, 20130590 (17 Jul 2014). [PMID:24914169] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4052878/" target="_blank">PMC4052878</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1098/rstb.2013.0324" target="_blank">The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser</a></div>
<div class="line">Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J, Yachandra VK.</div>
<div class="line"><em>Philos Trans R Soc Lond B Biol Sci</em> <strong>369</strong>, 20130324 (17 Jul 2014). [PMID:24914152] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4052861/" target="_blank">PMC4052861</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/ncomms5371" target="_blank">Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy</a></div>
<div class="line">Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK.</div>
<div class="line"><em>Nat Commun</em> <strong>5</strong>, 4371 (09 Jul 2014). [PMID:25006873] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4151126/" target="_blank">PMC4151126</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1038/nmeth.2887" target="_blank">Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers</a></div>
<div class="line">Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK.</div>
<div class="line"><em>Nat Methods</em> <strong>11</strong>, 545-8 (1 May 2014). [PMID:24633409] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4008696/" target="_blank">PMC4008696</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1126/science.1234273" target="_blank">Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature</a></div>
<div class="line">Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J.</div>
<div class="line"><em>Science</em> <strong>340</strong>, 491-5 (26 Apr 2013). [PMID:23413188] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC3732582/" target="_blank">PMC3732582</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1073/pnas.1204598109" target="_blank">Room temperature femtosecond X-ray diffraction of photosystem II microcrystals</a></div>
<div class="line">Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H, Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B, Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA, DiFiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM, Sokaras D, Weng TC, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U, Yano J, Yachandra VK.</div>
<div class="line"><em>Proc Natl Acad Sci U S A</em> <strong>109</strong>, 9721-6 (19 Jun 2012). [PMID:22665786] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC3382516/" target="_blank">PMC3382516</a>]</div>
</div>
</li>
</ul>
</section>
<section id="dials-synchrotron-applications">
<h2>DIALS Synchrotron Applications<a class="headerlink" href="#dials-synchrotron-applications" title="Link to this heading">¶</a></h2>
<ul>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1073/pnas.1416744111" target="_blank">Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering</a></div>
<div class="line">Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC.</div>
<div class="line"><em>Proc Natl Acad Sci U S A</em> <strong>111</strong>, 17887-92 (16 Dec 2014). [PMID:25453071] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4273327/" target="_blank">PMC4273327</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S1600576714022730" target="_blank">Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in <i>JBluIce</i> beamline control system</a></div>
<div class="line">Pothineni SB, Venugopalan N, Ogata CM, Hilgart MC, Stepanov S, Sanishvili R, Becker M, Winter G, Sauter NK, Smith JL, Fischetti RF.</div>
<div class="line"><em>J Appl Crystallogr</em> <strong>47</strong>, 1992-1999 (01 Dec 2014). [PMID:25484844] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4248568/" target="_blank">PMC4248568</a>] <a class="reference external" href="http://cci.lbl.gov/publications/download/GMCA_dataprocessing_JAC.pdf" target="_blank">(Reprint)</a></div>
</div>
</li>
</ul>
</section>
<section id="dials-for-3ded-microed">
<h2>DIALS for 3DED/MicroED<a class="headerlink" href="#dials-for-3ded-microed" title="Link to this heading">¶</a></h2>
<ul>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2053229624011148" target="_blank">How to use DIALS to process chemical crystallography 3D ED rotation data from pixel array detectors</a></div>
<div class="line">Vypritskaia A, Zou X, Yang T, Waterman DG.</div>
<div class="line"><em>Acta Crystallogr C Struct Chem</em> <strong>81</strong>, 1-13 (01 Jan 2025). [PMID:39641675] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC11700371/" target="_blank">PMC11700371</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1021/acscentsci.4c00162" target="_blank">Cryo-tomography and 3D Electron Diffraction Reveal the Polar Habit and Chiral Structure of the Malaria Pigment Crystal Hemozoin</a></div>
<div class="line">Klar PB, Waterman DG, Gruene T, Mullick D, Song Y, Gilchrist JB, Owen CD, Wen W, Biran I, Houben L, Regev-Rudzki N, Dzikowski R, Marom N, Palatinus L, Zhang P, Leiserowitz L, Elbaum M.</div>
<div class="line"><em>ACS Cent Sci</em> <strong>10</strong>, 1504-1514 (28 Aug 2024). [PMID:39220700] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC11363319/" target="_blank">PMC11363319</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1016/j.str.2023.07.004" target="_blank">A standard data format for 3DED/MicroED</a></div>
<div class="line">Waterman DG, Frisina N, Owen CD, Winter G, Nunes P.</div>
<div class="line"><em>Structure</em> <strong>31</strong>, 1510-1517.e1 (07 Dec 2023). [PMID:37536337]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2052252523001902" target="_blank">Investigation of the milling characteristics of different focused-ion-beam sources assessed by three-dimensional electron diffraction from crystal lamellae</a></div>
<div class="line">Parkhurst JM, Crawshaw AD, Siebert CA, Dumoux M, Owen CD, Nunes P, Waterman D, Glen T, Stuart DI, Naismith JH, Evans G.</div>
<div class="line"><em>IUCrJ</em> <strong>10</strong>, 270-287 (01 May 2023). [PMID:36952226] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC10161776/" target="_blank">PMC10161776</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1002/pro.3967" target="_blank">Leginon: New features and applications</a></div>
<div class="line">Cheng A, Negro C, Bruhn JF, Rice WJ, Dallakyan S, Eng ET, Waterman DG, Potter CS, Carragher B.</div>
<div class="line"><em>Protein Sci</em> <strong>30</strong>, 136-150 (1 Jan 2021). [PMID:33030237] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC7737759/" target="_blank">PMC7737759</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.3389/fmolb.2021.648603" target="_blank">Small Molecule Microcrystal Electron Diffraction for the Pharmaceutical Industry-Lessons Learned From Examining Over Fifty Samples</a></div>
<div class="line">Bruhn JF, Scapin G, Cheng A, Mercado BQ, Waterman DG, Ganesh T, Dallakyan S, Read BN, Nieusma T, Lucier KW, Mayer ML, Chiang NJ, Poweleit N, McGilvray PT, Wilson TS, Mashore M, Hennessy C, Thomson S, Wang B, Potter CS, Carragher B.</div>
<div class="line"><em>Front Mol Biosci</em> <strong>8</strong>, 648603 (2021) [PMID:34327213] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC8313502/" target="_blank">PMC8313502</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.3389/fmolb.2020.00179" target="_blank">A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction</a></div>
<div class="line">Beale EV, Waterman DG, Hecksel C, van Rooyen J, Gilchrist JB, Parkhurst JM, de Haas F, Buijsse B, Evans G, Zhang P.</div>
<div class="line"><em>Front Mol Biosci</em> <strong>7</strong>, 179 (2020) [PMID:32850967] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC7417479/" target="_blank">PMC7417479</a>]</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798318007726" target="_blank">Electron diffraction data processing with DIALS</a></div>
<div class="line">Clabbers MTB, Gruene T, Parkhurst JM, Abrahams JP, Waterman DG.</div>
<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>74</strong>, 506-518 (01 Jun 2018). [PMID:29872002] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6096487/" target="_blank">PMC6096487</a>]</div>
</div>
</li>
</ul>
</section>
<section id="dials-newsletter-articles">
<h2>DIALS Newsletter Articles<a class="headerlink" href="#dials-newsletter-articles" title="Link to this heading">¶</a></h2>
<ul>
<li><div class="line-block">
<div class="line"><a class="reference external" href="http://cci.lbl.gov/publications/download/CCN_2014_p19.pdf">XFEL Detectors and ImageCIF</a></div>
<div class="line">Brewster AS, Hattne J, Parkhurst JM, Waterman DG, Bernstein HJ, Winter G, Sauter NK.</div>
<div class="line"><a class="reference external" href="http://www.phenix-online.org/newsletter"><em>Computational Crystallography Newsletter</em></a> <strong>5</strong>, 19-24 (2014).</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="http://www.ccp4.ac.uk/newsletters/newsletter49/content.html">The DIALS framework for integration software</a></div>
<div class="line">Waterman DG, Winter G, Parkhurst JM, Fuentes-Montero L, Hattne J, Brewster A,
Sauter NK, Evans G.</div>
<div class="line"><em>CCP4 Newsletter on Protein Crystallography</em> <strong>49</strong>, 16-19 (2013).</div>
<div class="line"><a class="reference external" href="http://cci.lbl.gov/publications/download/DIALS.pdf">(Reprint)</a></div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="http://cci.lbl.gov/publications/download/CCN_2012_p14.pdf">Viewing diffraction images in CCTBX</a></div>
<div class="line">Echols N, Hattne J, Gildea RJ, Adams PD, Sauter NK.</div>
<div class="line"><a class="reference external" href="http://www.phenix-online.org/newsletter"><em>Computational Crystallography Newsletter</em></a> <strong>3</strong>, 14-17 (2012).</div>
</div>
</li>
<li><div class="line-block">
<div class="line"><a class="reference external" href="http://cci.lbl.gov/publications/download/CCN_2011_p93.pdf">An extremely fast spotfinder for real-time beamline applications</a></div>
<div class="line">Sauter NK.</div>
<div class="line"><a class="reference external" href="http://www.phenix-online.org/newsletter"><em>Computational Crystallography Newsletter</em></a> <strong>2</strong>, 93 (2011).</div>
</div>
</li>
</ul>
</section>
<section id="dials-reports">
<h2>DIALS Reports<a class="headerlink" href="#dials-reports" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><dl class="simple">
<dt><a class="reference external" href="../documents/DIALS_Framework_Report.pdf">DIALS Framework Report</a></dt><dd><ul>
<li><p>The requirements for and the design of the DIALS framework is described in this report, submitted as the first project deliverable for the BioStruct-X 18 month report.</p></li>
</ul>
</dd>
</dl>
</li>
</ul>
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