Publications


Interpreting macromolecular diffraction through simulation

Young ID, Mendez D, Poon BK, Blaschke JP, Wittwer F, Wall ME, Sauter NK
Methods in Enzymology, 2023

Key Figure


Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography

Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O’Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC.
Nature Chemistry, 2023

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Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Díaz RE, Ecker AK, Correy GJ, Asthana P, Young ID, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS.
eLife, 2023

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Changes in an enzyme ensemble during catalysis observed by high resolution XFEL crystallography

Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kuputz C, Poitevin F, Moss FR 3rd, Brewster AS, Sauter NK, Young ID, Wolff AM, Tiwari VK, Kumar N, Berkowitz DB, Hadt RG, Thompson MC, Follmer AH, Wall ME, Wilson MA.
bioRxiv (and forthcoming in Science Advances), 2023

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Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.

Tsai K*, Stojković V*, Lee DJ*, Young ID, Szal T, Vazquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG.
Nature Structural and Molecular Biology, 2022


De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Tetreau G*, Sawaya MR*, De Zitter E*, Andreeva EA+, Banneville A-S+, Schibrowsky N+, Coquelle N, Brewster AS, Grünbein ML, Kovacs GN, Hunter MS, Kloos M, Sierra RG, Schiro G, Qiao P, Stricker M, Bideshi D, Young ID, Zala N, Engilberge S, Gorel A, Signor L, Teulon J-M, Hilpert M, Foucar L, Bielecki J, Bean R, de Wijn R, Sato T, Kirkwood H, Letrun R, Batyuk A, Snigireva I, Fenel D, Schubert R, Canfield EJ, Alba MM, Laporte F, Després L, Bacia M, Roux A, Chapelle C, Riobé F, Maury O, Ling WL, Boutet S, Mancuso A, Gutsche I, Girard E, Barends TRM, Pellequer J-L, Park H-W, Laganowsky AD, Rodriguez J, Burghammer M, Shoeman RL, Doak RB, Weik M, Sauter NK, Federici B, Cascio D, Schlichting I, Colletier J-P.
Nature Communications, 2022


Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.

Tsai K, Stojković V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG.
eLife, 2022

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Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition

Hussein R*, Ibrahim M*, Bhowmick A*, Simon PS*, Chatterjee R*, Lassalle L, Doyle M, Bogacz I, Kim I-S, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J.
Nature Communications, 2021


Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I

Keable SM*, Kölsch A*, Simon PS*, Dasgupta M, Chatterjee R, Subramanian SK, Hussein R, Ibrahim M, Kim I-S, Bogacz I, Makita H, Pham CC, Fuller FD, Gul S, Paley D, Lassalle L, Sutherlin KD, Bhowmick A, Moriarty NW, Young ID, Blaschke JP, de Lichtenberg C, Chernev P, Cheah MH, Park S, Park G, Kim J, Lee SJ, Park J, Tono K, Owada S, Hunter MS, Batyuk A, Oggenfuss R, Sander M, Zerdane S, Ozerov D, Nass K, Lemke H, Mankowsky R, Brewster AS, Messinger J, Sauter NK, Yachandra VK, Yano J, Zouni A, Kern J.
Scientific Reports, 2021


X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis

Rabe P, Kamps JJAG, Sutherlin KD, Linyard JDS, Aller P, Pham CC, Makita H, Clifton J, McDonough MA, Leissing TM, Shutin D, Lang PA, Butryn A, Brem J, Gul S, Fuller FD, Kim IS, Cheah MH, Fransson T, Bhowmick A, Young ID, O’Riordan L, Brewster AS, Pettinati I, Doyle M, Joti Y, Owada S, Tono K, Batyuk A, Hunter MS, Alonso-Mori R, Bergmann U, Owen RL, Sauter NK, Claridge TDW, Robinson CV, Yachandra VK, Yano J, Kern JF, Orville AM, Schofield CJ
Science Advances, 2021


CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Gupta M*, Azumaya CM*, Moritz M*, Pourmal S*, Diallo A*, Merz GE*, Jang G*, Bouhaddou M*, Fossati*, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M,, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss III FR, Paul MD, Pawar KI, Pelin A, Pospiech Jr. TH, Puchase C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, QCRG Structural Biology Consortium, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA.
Research Square (preprint under review), 2021

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Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein

Weinberg ZY, Hilburger CE, Kim M, Cao L, Khalid M, Elmes S, Diwanji D, Hernandez E, Lopez J, Schaefer K, Smith AM, Zhou F, QCRG Structural Biology Consortium, Kumar GR, Ott M, Baker D, El-Samad H.
bioRxiv, 2021

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Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.

Schuller M*, Correy GJ*, Gahbauer S*, Fearon D*, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DS, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Mortiz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett MJ, Brandao Neto J, Cohen EA, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla PM, Fuchs M, Gorrie-Stone JT, Holton MJ, Johnson GM, Krojer T, Meigs G, Powell JA, Rack J, Rangel LV, Russi S, Skyner ER, Smith AC, Soares SA, Wierman LJ, Zhu K, O’Brien P, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I.
Science Advances, 2021

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An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

Schoof M*, Faust B*, Saunders RA*, Sangwan S*, Rezelj V*, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A.
Science, 2020

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Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2.

Bracken CJ, Lim SA, Solomon P, Rettko NJ, Nguyen DP, Zha BS, Schaefer K, Byrnes JR, Zhou J, Lui I, Liu J, Pance K, QCRG Structural Biology Consortium, Zhou XX, Leung KK, Wells JA
Nature Chemical Biology, 2020

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Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

Gordon DE*, Hiatt J*, Bouhaddou M*, Rezelj VV*, Ulferts S*, Braberg H*, Jureka AS*, Obernier K*, Guo JZ*, Batra J*, Kaake RM*, Weckstein AR*, Owens TW*, Gupta M*, Pourmal S*, Titus EW*, Cakir M*, Soucheray M, McGregor M, Cakir Z, Jang G, O’Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR 3rd, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH Jr, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL; Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ.
Science, 2020


Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism

Ibrahim M*, Fransson T*, Chatterjee R*, Cheah MH*, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim I-S, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northern T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J.
Proceedings of the National Academy of Science, 2020


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

Stojković V, Myasnikov AG, Young ID, Frost A, Fraser JS, Fujimori DG.
Nucleic Acids Research, 2020

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Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade

Tetreau G*, Banneville A-S*, Andreeva EA*, Brewster AS*, Hunter MS, Sierra RG, Teulon J-M, Young ID, Burke N, Grünewald TA, Beaudouin J, Snigireva I, Fernandez-Luna MT, Burt A, Park H-W, Signor L, Bafna JA, Sadir R, Fenel D, Boeri-Erba E, Bacia M, Zala N, Laporte F, Després L, Weik M, Boutet S, Rosenthal M, Coquelle N, Burghammer M, Cascio D, Sawaka MR, Winterhalter M, Gratton E, Gutsche I, Federici B, Pellequer J-L, Sauter NK, Colletier J-P.
Nature Communications, 2020


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

Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson A, Tanaka R, Tanaka T, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC.
IUCrJ, 2020


Photoreversible interconversion of a phytochrome photosensory module in the crystalline state

Burgie ES*, Clinger JA*, Miller MD, Brewster AS, Aller P, Butryn A, Fuller FD, Gul S, Young ID, Pham CC, Kim I-S, Bhowmick A, O’Riordan LJ, Sutherlin KD, Heinemann JV, Batyuk A, Alonso-Mori R, Hunter MS, Koglin JE, Yano J, Yachandra VK, Sauter NK, Cohen AE, Kern J, Orville AM, Phillips Jr GN, Vierstra RD.
Proceedings of the National Academy of Science, 2020


Structural isomers of the S2 state in photosystem II: do they exist at room temperature and are they important for function?

Chatterjee R, Lassalle L, Gul S, Fuller FD, Young ID, Ibrahim M, de Lichtenberg C, Cheah MH, Zouni A, Messinger J, Yachandra VK, Kern J, Yano J.
Physiologia Plantarum, 2019


Processing serial crystallographic data from XFELs or synchrotrons using the cctbx.xfel GUI

Brewster AS, Young ID, Lyubimov AY, Bhowmick A, Sauter NK.
Computational Crystallographic Newsletter, 2019


Structures of the intermediates of Kok’s photosynthetic water oxidation clock

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.
Nature, 2018


Improving signal strength in serial crystallography with DIALS geometry refinement

Brewster AS, Waterman DG, Parkhurst JM, Gildea RJ, Young ID, O’Riordan LJ, Yano J, Winter G, Evans G, Sauter NK.
Acta Crystallographica D: Structural Biology, 2018

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DIALS: implementation and evaluation of a new integration package

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.
Acta Crystallographica D: Structural Biology, 2018

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High-speed fixed-target serial virus crystallography

Roedig P*, Ginn HM*, Pakendorf T, Sutton G, Harlos K, Walter TS, Meyer J, Fischer P, Duman R, Vartiainen I, Reime B, Warmer M, Brewster AS, Young ID, Michels-Clark T, Sauter NK, Kotecha A, Kelly J, Rowlands DJ, Sikorsky M, Nelson S, Damiani DS, Alonso-Mori R, Ren J, Fry EE, David C, Stuart DI, Wagner A, Meents A.
Nature Methods, 2017

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High-speed fixed-target serial virus crystallography

Meents A, Young ID, Wagner AH, Stuart DI, David C, Fry EE, Ren J, Alonso-Mori R, Damiani DS, Nelson S, Sikorsky M, Sauter NK, Michels Clark T, Roedig P, Brewster AS, Warmer M, Reime B, Vartiainen I, Duman R, Fischer P, Meyer J, Walter TS, Harlos K, Sutton G, Pakendorf T, Ginn HM.
Protocol Exchange, 2017

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Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

Fuller FD*, Gul S*, Chatterjee R, Bergie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Mengning L, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger Jr JM, Krebs C, Högbom M, Phillips Jr GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J.
Nature Methods, 2017


Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs

Alonso-Mori R, Asa K, Bergmann U, Brewster AS, Chatterjee R, Cooper JK, Frei HM, Fuller FD, Goggins E, Gul S, Fukuzawa H, Iablonskyi D, Ibrahim M, Katayama T, Kroll T, Kumagai Y, McClure BA, Messinger J, Motomura K, Nagaya K, Nishiyama T, Saracini C, Sato Y, Sauter NK, Sokaras D, Takanashi T, Togashi T, Ueda K, Weare WW, Weng T-C, Yabashi M, Yachandra VK, Young ID, Zouni A, Kern JF, Yano J.
Faraday Discussions, 2016


Structure of photosystem II and substrate binding at room temperature

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, Vo PL, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng T-C, 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.
Nature, 2016


Structural changes correlated with magnetic spin state isomorphism in the S2 state of the Mn4CaO5 cluster in the oxygen-evolving complex of photosystem II

Chatterjee R*, Han G*, Kern J, Gul S, Fuller FD, Garatchenko A, Young ID, Weng T-C, Norlund D, Alonso-Mori R, Bergmann U, Sokaras D, Hatakeyama M, Yachandra VK, Yano J.
Chemical Science, 2016


Processing XFEL data with cctbx.xfel and DIALS

Brewster AS, Waterman DG, Parkhurst JM, Gildea RJ, Michels-Clark TM, Young ID, Bernstein HJ, Winter G, Evans G, Sauter NK.
Computational Crystallographic Newsletter, 2016

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

Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H.
Nature Methods, 2015