Publications by BioXFEL Researchers Since Start of BioXFEL Grant
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Acknowledges BioXFEL NSF-STC
Citation: Díaz, R. E., Ecker, A. K., Correy, G. J., Asthana, P., Young, I. D., Faust, B., Thompson, M. C., Seiple, I. B., Van Dyken, S., Locksley, R. M., & Fraser, J. S. (2024). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. ELife, 12. CLOCKSS. https://doi.org/10.7554/elife.89918.3
Type: Journal-article
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Citation: Rao, J., Xin, R., Macdonald, C., Howard, M. K., Estevam, G. O., Yee, S. W., Wang, M., Fraser, J. S., Coyote-Maestas, W., & Pimentel, H. (2024). Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03279-7
Type: Journal-article
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Citation: Chang, C., Zhou, G., Lee Luo, C., Eleraky, S., Moradi, M., & Gao, Y. (2024). Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol η catalyzed DNA synthesis. Journal of Biological Chemistry, 300(6), 107361. https://doi.org/10.1016/j.jbc.2024.107361
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Yoniles, J., Summers, J. A., Zielinski, K. A., Antolini, C., Panjalingam, M., Lisova, S., Moss, F. R., Di Perna, M. A., Kupitz, C., Hunter, M. S., Pollack, L., Wakatsuki, S., & Dahlberg, P. D. (2024). Time-resolved cryogenic electron tomography for the study of transient cellular processes. Molecular Biology of the Cell, 35(7). https://doi.org/10.1091/mbc.e24-01-0042
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Rivera-Madera, A., Peña-Martínez, E., & Rodriguez-Martinez, J. (2024). Abstract 2307 Evaluating the thermal stability of congenital heart diseases-associated TBX5 missense mutants. Journal of Biological Chemistry, 300(3), 107071. https://doi.org/10.1016/j.jbc.2024.107071
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Peña-Martínez, E., Pomales-Matos, D., Rivera-Madera, A., Messon-Bird, J., Medina-Feliciano, J., Sanabria-Alberto, L., Barreiro-Rosario, A., Rivera-Del Valle, J., & Rodríguez-Martínez, J. (2024). Abstract 1473 Integrating Machine Learning and Functional Genomics to Prioritize CVD-associated Mutations Altering NKX2-5 and TBX5 DNA Binding. Journal of Biological Chemistry, 300(3), 106540. https://doi.org/10.1016/j.jbc.2024.106540
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Peña-Martínez, E. G., & Rodríguez-Martínez, J. A. (2024). Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases. Frontiers in Bioscience-Scholar, 16(1), 4. https://doi.org/10.31083/j.fbs1601004
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: 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 Lanen, S. G., She, Q.-B., Voss, S. R., Phillips, G. N., & Thorson, J. S. (2024). Biochemical and Structural Studies of the Carminomycin 4-O-Methyltransferase DnrK. Journal of Natural Products. https://doi.org/10.1021/acs.jnatprod.3c00947
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Kim, J., Moon, S., Romo, T. D., Yang, Y., Bae, E., & Phillips, G. N. (2024). Conformational dynamics of adenylate kinase in crystals. Structural Dynamics, 11(1). https://doi.org/10.1063/4.0000205
Type: Journal-article
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Citation: Ketawala, G., Reiter, C. M., Fromme, P., & Botha, S. (2024). The Pixel Anomaly Detection Tool: a user-friendly GUI for classifying detector frames using machine-learning approaches. Journal of Applied Crystallography, 57(2). https://doi.org/10.1107/s1600576724000116
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Wang, T., He, W., Pabit, S. A., Kirmizialtin, S., & Pollack, L. (2024). Sequence-dependent conformational preferences of disordered single-stranded RNA. Biophysical Journal, 123(3), 453a-454a. https://doi.org/10.1016/j.bpj.2023.11.2762
Type: Journal-article
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Citation: Greene, E. R., Muniz, R., Yamamura, H., Hoff, S., Arada, A., Bajaj, P., Chen, D., Lee, J. D., Bonomi, M., Kollman, J. M., & Fraser, J. (2024). Product-stabilized filamentation by human glutamine synthetase allosterically tunes activity. Biophysical Journal, 123(3), 352a. https://doi.org/10.1016/j.bpj.2023.11.2135
Type: Journal-article
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Citation: 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
Type: Journal-article
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Citation: Hoff, S., Bonomi, M., Fraser, J., & Greene, E. (2024). Extracting conformational heterogeneity from 2D and 3D cryo-EM data. Biophysical Journal, 123(3), 50a-51a. https://doi.org/10.1016/j.bpj.2023.11.376
Type: Journal-article
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Citation: Schmidt, M., & Stojković, E. A. (2024). Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography. Structural Dynamics, 11(1). https://doi.org/10.1063/4.0000233
Type: Journal-article
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Citation: Lapierre, L. A., Roland, J. T., Manning, E. H., Caldwell, C., Glenn, H. L., Vidalain, P.-O., Tangy, F., Hogue, B. G., de Haan, C. A. M., & Goldenring, J. R. (2024). Coronavirus M Protein Trafficking in Epithelial Cells Utilizes a Myosin Vb Splice Variant and Rab10. Cells, 13(2), 126. https://doi.org/10.3390/cells13020126
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Schmidt, M. (2023). Time-resolved Crystallography on Protein Photoreceptors and Enzymes. Integrated Structural Biology, 203-240. https://doi.org/10.1039/bk9781837670154-00203
Type: Book-chapter
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Citation: Peña-Martínez, E. G., Pomales-Matos, D. A., Rivera-Madera, A., Messon-Bird, J. L., Medina-Feliciano, J. G., Sanabria-Alberto, L., Barreiro-Rosario, A. C., Rivera-Del Valle, J., Rodríguez-Ríos, J. M., & Rodríguez-Martínez, J. A. (2023). Prioritizing cardiovascular disease-associated variants altering NKX2-5 and TBX5 binding through an integrative computational approach. Journal of Biological Chemistry, 299(12), 105423. https://doi.org/10.1016/j.jbc.2023.105423
Type: Journal-article
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Citation: Varkaris, A., Pazolli, E., Gunaydin, H., Wang, Q., Pierce, L., Boezio, A. A., Bulku, A., DiPietro, L., Fridrich, C., Frost, A., Giordanetto, F., Hamilton, E. P., Harris, K., Holliday, M., Hunter, T. L., Iskandar, A., Ji, Y., Larivée, A., LaRochelle, J. R., ... Kipp, D. R. (2023). Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia. Cancer Discovery, 14(2), 240-257. https://doi.org/10.1158/2159-8290.cd-23-0944
Type: Journal-article
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Citation: Maldonado‐Hernández, R., Quesada, O., González‐Feliciano, J. A., Baerga‐Ortiz, A., & Lasalde‐Dominicci, J. A. (2023). Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS. PROTEOMICS, 24(1-2). Portico. https://doi.org/10.1002/pmic.202300151
Type: Journal-article
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Citation: Gul, M., Yuksel, B., Bulut, H., & DeMirci, H. (2023). Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography. Acta Crystallographica Section D Structural Biology, 79(11), 1010-1017. https://doi.org/10.1107/s2059798323008070
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: He, W., San Emeterio, J., Woodside, M. T., Kirmizialtin, S., & Pollack, L. (2023). Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics. Nucleic Acids Research, 51(20), 11332-11344. https://doi.org/10.1093/nar/gkad809
Type: Journal-article
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Citation: Zielinski, K. A., Sui, S., Pabit, S. A., Rivera, D. A., Wang, T., Hu, Q., Kashipathy, M. M., Lisova, S., Schaffer, C. B., Mariani, V., Hunter, M. S., Kupitz, C., Moss, F. R., Poitevin, F. P., Grant, T. D., & Pollack, L. (2023). RNA structures and dynamics with ... resolution revealed by x-ray free-electron lasers. Science Advances, 9(39). https://doi.org/10.1126/sciadv.adj3509
Type: Journal-article
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Citation: Snell, E. H., Garman, E. F., Grime, G. W., Cohen, A. E., & Bowman, S. E. J. (2023). The mythical metal - insights on the accuracy of metal identification in structural biology. Acta Crystallographica Section A Foundations and Advances, 79(a1), a281-a281. https://doi.org/10.1107/s2053273323097188
Type: Journal-article
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Citation: Liu, Z., Gu, K. K., Shelby, M. L., Gilbile, D., Lyubimov, A. Y., Russi, S., Cohen, A. E., Narayanasamy, S. R., Botha, S., Kupitz, C., Sierra, R. G., Poitevin, F., Gilardi, A., Lisova, S., Coleman, M. A., Frank, M., & Kuhl, T. L. (2023). A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography. Acta Crystallographica Section D Structural Biology, 79(10), 944-952. https://doi.org/10.1107/s2059798323007027
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Wolff, A. M., Nango, E., Young, I. D., Brewster, A. S., Kubo, M., Nomura, T., Sugahara, M., Owada, S., Barad, B. A., Ito, K., Bhowmick, A., Carbajo, S., Hino, T., Holton, J. M., Im, D., O'Riordan, L. J., Tanaka, T., Tanaka, R., Sierra, R. G., ... Thompson, M. C. (2023). Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nature Chemistry. https://doi.org/10.1038/s41557-023-01329-4
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Alsina-Sánchez, Á. M., Montalvo-Vázquez, S., Grafals-Ruiz, N., Acosta, C., Ormé, E. M., Rodríguez, I., Delgado-Rivera, S. M., Tinoco, A. D., Dharmawardhane, S., & Montes-González, I. C. (2023). Synthesis of Novel Heterocyclic Ferrocenyl Chalcones and Their Biological Evaluation. ACS Omega. https://doi.org/10.1021/acsomega.3c01830
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Ishigami, I., Carbajo, S., Zatsepin, N., Hikita, M., Conrad, C. E., Nelson, G., Coe, J., Basu, S., Grant, T., Seaberg, M. H., Sierra, R. G., Hunter, M. S., Fromme, P., Fromme, R., Rousseau, D. L., & Yeh, S.-R. (2023). Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography. Journal of the American Chemical Society. https://doi.org/10.1021/jacs.3c07803
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Kim, D.-H., Wang, Y., Jung, H., Field, R. L., Zhang, X., Liu, T.-C., Ma, C., Fraser, J. S., Brestoff, J. R., & Van Dyken, S. J. (2023). A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin. Science, 381(6662), 1092-1098. https://doi.org/10.1126/science.add5649
Type: Journal-article
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Citation: Malla, T. N., Zielinski, K., Aldama, L., Bajt, S., Feliz, D., Hayes, B., Hunter, M., Kupitz, C., Lisova, S., Knoska, J., Martin-Garcia, J. M., Mariani, V., Pandey, S., Poudyal, I., Sierra, R. G., Tolstikova, A., Yefanov, O., Yoon, C. H., Ourmazd, A., ... Schmidt, M. (2023). Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-41246-1
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Taha, T. Y., Suryawanshi, R. K., Chen, I. P., Correy, G. J., McCavitt-Malvido, M., O'Leary, P. C., Jogalekar, M. P., Diolaiti, M. E., Kimmerly, G. R., Tsou, C.-L., Gascon, R., Montano, M., Martinez-Sobrido, L., Krogan, N. J., Ashworth, A., Fraser, J. S., & Ott, M. (2023). A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo. PLOS Pathogens, 19(8), e1011614. https://doi.org/10.1371/journal.ppat.1011614
Type: Journal-article
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Citation: Koh, D., Sonker, M., Arriaga, E. A., & Ros, A. (2023). Numerical modeling reveals improved organelle separation for dielectrophoretic ratchet migration. ELECTROPHORESIS. Portico. https://doi.org/10.1002/elps.202300091
Type: Journal-article
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Citation: Schmidt, M. (2023). Practical considerations for the analysis of time-resolved x-ray data. Structural Dynamics, 10(4). https://doi.org/10.1063/4.0000196
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Zhang, L., Li, Y. (Henry), Kibler, K., Kraberger, S., Varsani, A., Turk, J., Elmadbouly, N., Aliskevich, E., Spaccarelli, L., Estifanos, B., Enow, J., Zanetti, I. R., Saldevar, N., Lim, E., Schlievert, J., Browder, K., Wilson, A., Juan, F. A., Pinteric, A., ... Lucas, A. R. (2023). Viral anti‐inflammatory serpin reduces immuno‐coagulopathic pathology in
Type: Journal-article
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Citation: DeMirci, H., Johnson, J., Tolar, B., Tosun, B., Yoshikuni, Y., Francis, C., & Wakatsuki, S. (2023). Crystal Structure of 4-Hydroxybutyryl-CoA Synthetase (ADP-forming): A Key Enzyme in the Thaumarchaeal Hydroxypropionate/Hydroxybutyrate cycle. https://doi.org/10.21203/rs.3.rs-3173078/v1
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Du, S., Wankowicz, S. A., Yabukarski, F., Doukov, T., Herschlag, D., & Fraser, J. S. (2023). Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data. Methods in Enzymology. https://doi.org/10.1016/bs.mie.2023.06.009
Type: Book-chapter
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Citation: Pan, T., Jin, S., Miller, M. D., Kyrillidis, A., & Phillips, G. N. (2023). A deep learning solution for crystallographic structure determination. IUCrJ, 10(4), 487-496. https://doi.org/10.1107/s2052252523004293
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Gul, M., Ayan, E., Destan, E., Johnson, J. A., Shafiei, A., Kepceoğlu, A., Yilmaz, M., Ertem, F. B., Yapici, İ., Tosun, B., Baldir, N., Tokay, N., Nergiz, Z., Karakadioğlu, G., Paydos, S. S., Kulakman, C., Ferah, C. K., Güven, -., Atalay, N., ... DeMi̇rci̇, H. (2023). Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-33989-0
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Zielinski, K. A., Katz, A. M., Calvey, G. D., Pabit, S. A., Milano, S. K., Aplin, C., San Emeterio, J., Cerione, R. A., & Pollack, L. (2023). Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering. IUCrJ, 10(3), 363-375. https://doi.org/10.1107/s2052252523003482
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Orta-Rivera, A. M., Meléndez-Contés, Y., Rivera-Berríos, N., Gómez-Cardona, A. M., Ramos-Rodríguez, A., Cruz-Santiago, C., González-Dumeng, C., López, J., Escribano, J., Rivera-Otero, J. J., Díaz-Rivera, J., Díaz-Vélez, S. C., Feliciano-Delgado, Z., & Tinoco, A. D. (2023). Copper Based Antibacterial Compounds: Potential Targeting Pathways and Current Drug Design Trends. https://doi.org/10.20944/preprints202304.1124.v1
Type: Posted-content
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Chen, J. P. J., Pande, K., Donatelli, J. J., Martin, A. V., Ayyer, K., Chapman, H. N., Bean, R., Schmidt, K. E., & Kirian, R. A. (2023). Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder. Ultramicroscopy, 249, 113728. https://doi.org/10.1016/j.ultramic.2023.113728
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Casadei, C., Hosseinizadeh, A., Schertler, G., Ourmazd, A., & Santra, R. (2022). Randomness in time-resolved serial crystallography data: alternatives to the binning and averaging approach. Acta Crystallographica Section A Foundations and Advances, 78(a2), e111-e111. https://doi.org/10.1107/s2053273322095742
Type: Journal-article
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Citation: Saha, S., -zden, C., Samkutty, A., Russi, S., Cohen, A., Stratton, M. M., & Perry, S. L. (2023). Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature. Lab on a Chip, 23(8), 2075-2090. https://doi.org/10.1039/d2lc01194h
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Meisburger, S. P., Case, D. A., & Ando, N. (2023). Robust total X-ray scattering workflow to study correlated motion of proteins in crystals. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36734-3
Type: Journal-article
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Citation: Lynch, M. L., Snell, M. E., Potter, S. A., Snell, E. H., & Bowman, S. E. J. (2023). 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening. Acta Crystallographica Section D Structural Biology, 79(3), 198-205. https://doi.org/10.1107/s2059798323001274
Type: Journal-article
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Citation: Macdonald, C. B., Nedrud, D., Grimes, P. R., Trinidad, D., Fraser, J. S., & Coyote-Maestas, W. (2023). DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology. Genome Biology, 24(1). https://doi.org/10.1186/s13059-023-02880-6
Type: Journal-article
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Citation: Schmidt, M. (2023). Biological function investigated by time-resolved structure determination. Structural Dynamics, 10(1), 010901. https://doi.org/10.1063/4.0000177
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Freeman, D., Giannakis, D., Mintz, B., Ourmazd, A., & Slawinska, J. (2023). Data assimilation in operator algebras. Proceedings of the National Academy of Sciences, 120(8). https://doi.org/10.1073/pnas.2211115120
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Greene, E. R., Muniz, R., Arada, A., Lee, D. J., Chen, D., Thompson, E., Yamamura, H., Kollman, J. M., & Fraser, J. (2023). Reaction coordinate dependent fibrillar formation of human glutamine synthetase tunes activity. Biophysical Journal, 122(3), 474a. https://doi.org/10.1016/j.bpj.2022.11.2541
Type: Journal-article
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Citation: Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Perera, S. M. D. C., Kosheleva, I. V., Salas-Estrada, L., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2023). X-ray scattering exhibits time-resolved view of rhodopsin activation. Biophysical Journal, 122(3), 191a. https://doi.org/10.1016/j.bpj.2022.11.1170
Type: Journal-article
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Citation: Madani, A., Krause, B., Greene, E. R., Subramanian, S., Mohr, B. P., Holton, J. M., Olmos, J. L., Xiong, C., Sun, Z. Z., Socher, R., Fraser, J. S., & Naik, N. (2023). Large language models generate functional protein sequences across diverse families. Nature Biotechnology. https://doi.org/10.1038/s41587-022-01618-2
Type: Journal-article
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Citation: Dsouza, R., Mashayekhi, G., Etemadpour, R., Schwander, P., & Ourmazd, A. (2023). Energy landscapes from cryo-EM snapshots: a benchmarking study. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-28401-w
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Jernigan, R. J., Logeswaran, D., Doppler, D., Nagaratnam, N., Sonker, M., Yang, J.-H., Ketawala, G., Martin-Garcia, J. M., Shelby, M. L., Grant, T. D., Mariani, V., Tolstikova, A., Sheikh, M. Z., Yung, M. C., Coleman, M. A., Zaare, S., Kaschner, E. K., Rabbani, M. T., Nazari, R., ... Fromme, P. (2023). Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser. Structure, 31(2), 138-151.e5. https://doi.org/10.1016/j.str.2022.12.009
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Gahbauer, S., Correy, G. J., Schuller, M., Ferla, M. P., Doruk, Y. U., Rachman, M., Wu, T., Diolaiti, M., Wang, S., Neitz, R. J., Fearon, D., Radchenko, D. S., Moroz, Y. S., Irwin, J. J., Renslo, A. R., Taylor, J. C., Gestwicki, J. E., von Delft, F., Ashworth, A., ... Fraser, J. S. (2023). Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences, 120(2). https://doi.org/10.1073/pnas.2212931120
Type: Journal-article
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Citation: Cakilkaya, B., Kavakli, I. H., & DeMirci, H. (2023). The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region. Journal of Biological Chemistry, 299(1), 102794. https://doi.org/10.1016/j.jbc.2022.102794
Type: Journal-article
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Citation: Gates, C., Ananyev, G., Roy-Chowdhury, S., Fromme, P., & Dismukes, G. C. (2022). Regulation of light energy conversion between linear and cyclic electron flow within photosystem II controlled by the plastoquinone/quinol redox poise. Photosynthesis Research. https://doi.org/10.1007/s11120-022-00985-w
Type: Journal-article
Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Westenhoff, S., Meszaros, P., & Schmidt, M. (2022). Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins. Current Opinion in Structural Biology, 77, 102481. https://doi.org/10.1016/j.sbi.2022.102481
Type: Journal-article
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Citation: Ciftci, H., Sever, B., Ayan, E., Can, M., DeMirci, H., Otsuka, M., TuYuN, A. F., Tateishi, H., & Fujita, M. (2022). Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies. Pharmaceuticals, 15(10), 1255. https://doi.org/10.3390/ph15101255
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Citation: Sonker, M., Doppler, D., Egatz-Gomez, A., Zaare, S., Rabbani, M. T., Manna, A., Cruz Villarreal, J., Nelson, G., Ketawala, G. K., Karpos, K., Alvarez, R. C., Nazari, R., Thifault, D., Jernigan, R., Oberthür, D., Han, H., Sierra, R., Hunter, M. S., Batyuk, A., ... Ros, A. (2022). Electrically stimulated droplet injector for reduced sample consumption in serial crystallography. Biophysical Reports, 2(4), 100081. https://doi.org/10.1016/j.bpr.2022.100081
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Wu, K., Moore, J. A., Miller, M. D., Chen, Y., Lee, C., Xu, W., Peng, Z., Duan, Q., Phillips, G. N., Uribe, R. A., & Xiao, H. (2022). Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid. Protein Science, 31(10). Portico. https://doi.org/10.1002/pro.4443
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Citation: San Emeterio, J., Pabit, S. A., & Pollack, L. (2022). Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis. Methods in Enzymology, 41-83. https://doi.org/10.1016/bs.mie.2022.08.007
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Citation: Wang, T., Pabit, S., Henning-Knechtel, A., He, W., Kirmizaltin, S., & Pollack, L. (2022). Determining the structural ensembles of disordered RNA and proteins using an integrated approach. Acta Crystallographica Section A Foundations and Advances, 78(a1), a168-a168. https://doi.org/10.1107/s205327332209831x
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Citation: 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. Acta Crystallographica Section A Foundations and Advances, 78(a1), a28-a28. https://doi.org/10.1107/s2053273322099715
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Citation: Aplin, C., Milano, S. K., Zielinski, K. A., Pollack, L., & Cerione, R. A. (2022). Evolving Experimental Techniques for Structure-Based Drug Design. The Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.2c04344
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Citation: Shiriaeva, A., Park, D., Kim, G., Lee, Y., Hou, X., Jarhad, D. B., Kim, G., Yu, J., Hyun, Y. E., Kim, W., Gao, Z.-G., Jacobson, K. A., Han, G. W., Stevens, R. C., Jeong, L. S., Choi, S., & Cherezov, V. (2022). GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A2A Adenosine Receptor. Journal of Medicinal Chemistry. https://doi.org/10.1021/acs.jmedchem.2c00462
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Citation: Casadei, C. M., Hosseinizadeh, A., Schertler, G. F. X., Ourmazd, A., & Santra, R. (2022). Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis. Structural Dynamics, 9(4), 044101. https://doi.org/10.1063/4.0000156
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Citation: Holmes, S., Kirkwood, H. J., Bean, R., Giewekemeyer, K., Martin, A. V., Hadian-Jazi, M., Wiedorn, M. O., Oberthür, D., Marman, H., Adriano, L., Al-Qudami, N., Bajt, S., Barák, I., Bari, S., Bielecki, J., Brockhauser, S., Coleman, M. A., Cruz-Mazo, F., Danilevski, C., ... Darmanin, C. (2022). Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-32434-6
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Citation: Nagaratnam, N., Martin-Garcia, J. M., Yang, J.-H., Goode, M. R., Ketawala, G., Craciunescu, F. M., Zook, J. D., Sonowal, M., Williams, D., Grant, T. D., Fromme, R., Hansen, D. T., & Fromme, P. (2022). Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis. PLOS ONE, 17(8), e0267370. https://doi.org/10.1371/journal.pone.0267370
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Citation: Donatelli, J., & Spence, J. (2022). Structure Determination from Multiple-Scattering Electron Crystallography. Microscopy and Microanalysis, 28(S1), 2766-2767. https://doi.org/10.1017/s1431927622010418
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Citation: Koliyadu, J. C. P., Letrun, R., Kirkwood, H. J., Liu, J., Jiang, M., Emons, M., Bean, R., Bellucci, V., Bielecki, J., Birnsteinova, S., de Wijn, R., Dietze, T., E, J., Grunert, J., Kane, D., Kim, C., Kim, Y., Lederer, M., Manning, B., Mills, G., Morillo, L. L., Reimers, N., Rompotis, D., Round, A., Sikorski, M., Takem, C. M. S., Vagovic, P., Venkatesan, S., Wang, J., Wegner, U., Mancuso, A. P. & Sato, T. (2022). J. Synchrotron Rad. 29, 1273-1283.
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Citation: Chen, Y.-L., He, W., Kirmizialtin, S., & Pollack, L. (2022). Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. Cell Reports Physical Science, 3(7), 100971. https://doi.org/10.1016/j.xcrp.2022.100971
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Citation: DeMirci, H., & Ayan, E. (2023). A Brief Atlas of Insulin. Current Diabetes Reviews, 19(6). https://doi.org/10.2174/1573399819666220610150342
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Citation: Correy, G. J., Kneller, D. W., Phillips, G., Pant, S., Russi, S., Cohen, A. E., Meigs, G., Holton, J. M., Gahbauer, S., Thompson, M. C., Ashworth, A., Coates, L., Kovalevsky, A., Meilleur, F., & Fraser, J. S. (2022). The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Science Advances, 8(21). https://doi.org/10.1126/sciadv.abo5083
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Citation: Kabayiza, F., Woodruff, S. B., & Bauer, W. J. (2022). The Gamification of XFEL Education Using XFEL Crystal Blaster. Crystals, 12(5), 671. https://doi.org/10.3390/cryst12050671
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Citation: Giannakis, D., Ourmazd, A., Pfeffer, P., Schumacher, J., & Slawinska, J. (2022). Embedding classical dynamics in a quantum computer. Physical Review A, 105(5). https://doi.org/10.1103/physreva.105.052404
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Citation: Ando, N., Meisburger, S. P., & Case, D. A. (2022). Correlated motions in enzymes. The FASEB Journal, 36(S1). Portico. https://doi.org/10.1096/fasebj.2022.36.s1.0i154
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Citation: Awel, S., Lavin-Varela, S., Roth, N., Horke, D. A., Rode, A. V., Kirian, R. A., Küpper, J., & Chapman, H. N. (2022). Optical Funnel to Guide and Focus Virus Particles for X-Ray Diffractive Imaging. Physical Review Applied, 17(4). https://doi.org/10.1103/physrevapplied.17.044044
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Citation: Cruz Villarreal, J., Kruithoff, R., Egatz-Gomez, A., Coleman, P. D., Ros, R., Sandrin, T. R., & Ros, A. (2022). MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. Analytical and Bioanalytical Chemistry, 414(13), 3945-3958. https://doi.org/10.1007/s00216-022-04038-y
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Citation: Mobley, B. R., Schmidt, K. E., Chen, J. P. J., & Kirian, R. A. (2022). A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities. Acta Crystallographica Section A Foundations and Advances, 78(3), 200-211. https://doi.org/10.1107/s2053273322001395
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Citation: Wells, D. J., Berntsen, P., Balaur, E., Kewish, C. M., Adams, P., Aquila, A., Binns, J., Boutet, S., Broomhall, H., Caleman, C., Christofferson, A., Conn, C. E., Dahlqvist, C., Flueckiger, L., Gian Roque, F., Greaves, T. L., Hejazian, M., Hunter, M., Hadian Jazi, M., ... Darmanin, C. (2022). Observations of phase changes in monoolein during high viscous injection. Journal of Synchrotron Radiation, 29(3), 602-614. https://doi.org/10.1107/s1600577522001862
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Citation: Wankowicz, S. A., de Oliveira, S. H., Hogan, D. W., van den Bedem, H., & Fraser, J. S. (2022). Ligand binding remodels protein side-chain conformational heterogeneity. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.74114
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Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD
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Citation: Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Alvarez, R. C., Perera, S. M. D. C., Kosheleva, I. V., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2022). Time-resolved functional expansion of visual rhodopsin detected by x-ray scattering. Biophysical Journal, 121(3), 285a-286a. https://doi.org/10.1016/j.bpj.2021.11.1313
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Citation: Greene, E. R., Thompson, E., Lee, D. J., Arada, A., Chen, D., & Fraser, J. (2022). Connecting glutamine synthetase biophysics to the cellular environment. Biophysical Journal, 121(3), 348a. https://doi.org/10.1016/j.bpj.2021.11.1035
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Citation: Pulavarti, S. V. S. R. K., Maguire, J. B., Yuen, S., Harrison, J. S., Griffin, J., Premkumar, L., Esposito, E. A., Makhatadze, G. I., Garcia, A. E., Weiss, T. M., Snell, E. H., Kuhlman, B., & Szyperski, T. (2022). From Protein Design to the Energy Landscape of a Cold Unfolding Protein. The Journal of Physical Chemistry B, 126(6), 1212-1231. https://doi.org/10.1021/acs.jpcb.1c10750
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Rodríguez, I., Fernández-Vega, L., Maser-Figueroa, A. N., Sang, B., González-Pagán, P., & Tinoco, A. D. (2022). Exploring Titanium(IV) Complexes as Potential Antimicrobial Compounds. Antibiotics, 11(2), 158. https://doi.org/10.3390/antibiotics11020158
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Citation: Assalauova, D., Kim, Y. Y., Bobkov, S., Khubbutdinov, R., Rose, M., Alvarez, R., Andreasson, J., Balaur, E., Contreras, A., DeMirci, H., Gelisio, L., Hajdu, J., Hunter, M. S., Kurta, R. P., Li, H., McFadden, M., Nazari, R., Schwander, P., Teslyuk, A., ... Vartanyants, I. A. (2022). An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum. IUCrJ, 9(2), 328-328. https://doi.org/10.1107/s2052252522000501
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Citation: Ertem, F. B., Guven, O., Buyukdag, C., Gocenler, O., Ayan, E., Yuksel, B., Gul, M., Usta, G., Cakılkaya, B., Johnson, J. A., Dao, E. H., Su, Z., Poitevin, F., Yoon, C. H., Kupitz, C., Hayes, B., Liang, M., Hunter, M. S., Batyuk, A., ... DeMirci, H. (2022). Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography. STAR Protocols, 3(1), 101158. https://doi.org/10.1016/j.xpro.2022.101158
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Ciftci, H., Sever, B., Ocak, F., Bayrak, N., Yıldız, M., Yıldırım, H., DeMirci, H., Tateishi, H., Otsuka, M., Fujita, M., & TuYuN, A. F. (2022). In Vitro and In Silico Study of Analogs of Plant Product Plastoquinone to Be Effective in Colorectal Cancer Treatment. Molecules, 27(3), 693. https://doi.org/10.3390/molecules27030693
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Tsai, K., Stojković, V., Noda-Garcia, L., Young, I. D., Myasnikov, A. G., Kleinman, J., Palla, A., Floor, S. N., Frost, A., Fraser, J. S., Tawfik, D. S., & Fujimori, D. G. (2022). Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.70017
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Citation: Ortiz, R., Koh, D., Kim, D. H., Rabbani, M. T., Anguaya Velasquez, C., Sonker, M., Arriaga, E. A., & Ros, A. (2022). Continuous organelle separation in an insulator‐based dielectrophoretic device. ELECTROPHORESIS, 43(12), 1283-1296. Portico. https://doi.org/10.1002/elps.202100326
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Citation: Doppler, D. et al., 2022. Co-flow injection for serial crystallography at X-ray free-electron lasers. Journal of Applied Crystallography, 55(1).
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Kosgei, A.J. et al., 2022. The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina. Acta Crystallographica Section F Structural Biology Communications, 78(1), pp.1-7.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Zhang, L., Yaron, J. R., Schutz, L., Aliskevich, E., Browder, K., Saldevar, N., Zanetti, I. R., Elmadbouly, N., Glenn, H., Li, Y., Kibler, K., Hogue, B., McFadden, G., & Lucas, A. R. (2021). Abstract 13747: Targeting Urokinase-Type Plasminogen Activator (uPA) and the uPA Receptor, Reduces Vascular Inflammation and Lung Hemorrhage in Systemic Lupus and SARS CoV2 Infection in Mouse Models of Respiratory Distress Syndromes. Circulation, 144(Suppl_2). https://doi.org/10.1161/circ.144.suppl_2.13747
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Subthreshold Erosion of an Organic Polymer Induced by Multiple Shots of an X-Ray Free-Electron Laser
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Citation: Durdagi, S. et al., 2020. Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing.
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Citation: Benjamín-Rivera, J.A. et al., 2020. Exploring Serum Transferrin Regulation of Nonferric Metal Therapeutic Function and Toxicity. Inorganics, 8(9), p.48.
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Citation: Kirian, R.A., Chen, J.P.J. & Spence, J.C.H., 2018. Phasing Serial Crystallography Data. X-ray Free Electron Lasers, pp.235-252.
Type: Book-chapter
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Citation: Stauch, B. et al., 2018. Advances in Structure Determination of G Protein-Coupled Receptors by SFX. X-ray Free Electron Lasers, pp.301-329.
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Citation: Morgan, A.J. et al., 2019. Ab initio phasing of the diffraction of crystals with translational disorder. Acta Crystallographica Section A Foundations and Advances, 75(1), pp.25-40.
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Citation: Jensen, S.C. et al., 2019. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. The Journal of Physical Chemistry Letters, pp.441-446.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Oyama, T., Hall, N.G. & Kobayashi, K., 2018. A generalized parametric divisor method for political apportionment. International Transactions in Operational Research, 28(1), pp.327-355.
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Citation: Li, C. et al., 2019. SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data. IUCrJ, 6(1), pp.72-84.
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Citation: Audet, M. et al., 2018. Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor. Nature Chemical Biology, 15(1), pp.11-17.
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Citation: Kim, D., Sonker, M. & Ros, A., 2018. Dielectrophoresis: From molecular to micrometer scale analytes. Analytical Chemistry.
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Citation: Carmona-Negrón, J.A. et al., 2019. Synthesis, structure, docking and cytotoxic studies of ferrocene-hormone conjugates for hormone-dependent breast cancer application. Dalton Transactions.
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Conformations of an RNA Helix-Junction-Helix Construct revealed by SAXS Refinement of MD Simulations
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Citation: Thompson, M.C. et al., 2018. Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme:
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Citation: Van Zundert, G. et al., 2018. qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps. Journal of Medicinal Chemistry.
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Citation: Casadei, C.M. et al., 2019. Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCrJ, 6(1).
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Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril
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Citation: Pande, K. et al., 2018. Free-electron laser data for multiple-particle fluctuation scattering analysis. Scientific Data, 5, p.180201.
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Citation: Welty, R. et al., 2018. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA, 24(12), pp.1828-1838.
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Citation: Rose, M. et al., 2018. Single-particle imaging without symmetry constraints at an X-ray free-electron laser.
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Citation: Hantke, M.F. et al., 2018. Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams. IUCrJ, 5(6).
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Citation: Annaval, T. et al., 2018. Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway. ACS Chemical Biology, 13(9), pp.2728-2738.
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Citation: Woitowich, N.C. et al., 2018. Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome. IUCrJ, 5(5), pp.619-634.
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Citation: Dao, E.H. et al., 2018. Structure of the 30S ribosomal decoding complex at ambient temperature. RNA, 24(12), pp.1667-1676.
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Citation: Murray, K.T. et al., 2018. Characterization of High Numerical Aperture Multilayer Laue Lenses. Microscopy and Microanalysis, 24(S2), pp.282-283.
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Citation: Mancuso, A.P. et al., 2018. Developments Towards Imaging Nanoscale Biology with XFELs: Some Recent Examples and a Glance to the Future. Microscopy and Microanalysis, 24(S2), pp.76-77.
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Citation: Erk, B. et al., 2018. CAMP@FLASH: an end-station for imaging, electron- and ion-spectroscopy, and pump-probe experiments at the FLASH free-electron laser. Journal of Synchrotron Radiation, 25(5).
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Citation: Lan, T.-Y. et al., 2018. Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source. IUCrJ, 5(5).
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Citation: O'Sullivan, M.E. et al., 2018. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature. Nucleic Acids Research, 46(18), pp.9793-9804.
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Citation: O'Sullivan, M.E. et al., 2018. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature.
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Citation: Wojtas, D.H. et al., 2017. Orientation and analysis of XFEL serial diffraction patterns from fibrous molecular assemblies. 2017 International Conference on Image and Vision Computing New Zealand (IVCNZ).
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Citation: Abola, E.E. et al., Chapter 2. Delivery of GPCR Crystals for Serial Femtosecond Crystallography. Chemical Biology, pp.28-53.
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Citation: Zatsepin, N.A., Chapter 8. Crystallography with X-ray Free Electron Lasers. Chemical Biology, pp.181-224.
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Citation: Nogly, P. et al., 2018. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science, p.eaat0094.
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Citation: Keedy, D.A. et al., 2018. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife, 7.
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Citation: Olmos, J.L. et al., 2018. Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography. BMC Biology, 16(1).
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Citation: Nepal, P. & Saldin, D.K., 2018. Difference structures from time-resolved small-angle and wide-angle x-ray scattering. Physical Review B, 97(19).
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Citation: Beyerlein, K.R. et al., 2018. Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser. Proceedings of the National Academy of Sciences, p.201711220.
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Citation: Seuring, C. et al., 2018. Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene. Nature Communications, 9(1).
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Citation: Díaz Casas, A. et al., 2018. Molecular biophysical characterization of the third FF domain of Homo sapiens Prp40 homolog A. Journal of Molecular Structure, 1167, pp.174-179.
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Citation: Dashti, A. et al., 2018. Trajectories of the ribosome as a Brownian nanomachine. Single-Particle Cryo-Electron Microscopy, pp.463-475.
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Citation: Dashti, A. et al., 2018. Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots.
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Citation: Bajt, S. et al., 2017. X-ray focusing with efficient high-NA multilayer Laue lenses. Light: Science & Applications, 7(3), p.17162.
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Citation: Ishchenko, A., Gati, C. & Cherezov, V., 2018. Structural biology of G protein-coupled receptors: new opportunities from XFELs and cryoEM. Current Opinion in Structural Biology, 51, pp.44-52.
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Citation: Stauch, B. & Cherezov, V., 2018. Serial Femtosecond Crystallography of G Protein-Coupled Receptors. Annual Review of Biophysics, 47(1).
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Citation: Hoffmann, M.C. et al., 2018. Femtosecond profiling of shaped x-ray pulses. New Journal of Physics, 20(3), p.033008.
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Citation: Subramanian, G. et al., 2018. Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy. The Journal of Physical Chemistry Letters, pp.1542-1546.
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Citation: Kim, D. et al., 2018. Deterministic Ratchet for Sub-micrometer (Bio)particle Separation. Analytical Chemistry.
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Citation: Jönsson, H.O. et al., 2018. FreeDam - A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography. High Energy Density Physics.
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Citation: Dao, E.H. et al., 2018. Structure of the 30S ribosomal decoding complex at ambient temperature.
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Citation: Choi, J. et al., 2018. How 2'- O -Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation. Biophysical Journal, 114(3), p.592a.
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Citation: Awel, S. et al., 2018. Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals. Journal of Applied Crystallography, 51(1), pp.133-139.
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Citation: Van Zundert, G.C. et al., 2018. qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.
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Citation: Dicke, B. et al., 2018. Transferring the entatic-state principle to copper photochemistry. Nature Chemistry.
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Citation: Che, T. et al., 2018. Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor. Cell, 172(1-2), pp.55-67.e15.
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Citation: Casadei, C.M. et al., 2018. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals. IUCrJ, 5(1), pp.103-117.
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Citation: Casadei, C.M. et al., 2018. Resolution extension by image summing in serial femtosecond crystallography of two-dimensional membrane-protein crystals.
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Citation: Cleveland, T.E. et al., 2017. Small-angle X-ray and neutron scattering demonstrates that cell-free expression produces properly formed disc-shaped nanolipoprotein particles. Protein Science.
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Citation: Subramanian, G. et al., 2017. Picosecond to microsecond TR-XAS: intermediates in the photolysis of methylcobalamin. Acta Crystallographica Section A Foundations and Advances, 73(a2), pp.C1129-C1129.
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Citation: Taberman, H. et al., 2017. Mechanism and X-ray damage: beware of artefacts in xylose isomerase. Acta Crystallographica Section A Foundations and Advances, 73(a2), pp.C232-C232.
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Citation: Meents, A. et al., 2017. Low-background pink-beam serial crystallography. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a405-a405.
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Citation: 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.
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Citation: Thomaston, J.L. et al., 2017. XFEL structures of the influenza M2 proton channel at 1.4......: room-temperature water networks and insights into proton conduction. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a40-a40.
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Citation: Snell, E.H. et al., 2017. The influence of promiscuous metals on metalloprotein structure: complementary techniques to separate the good, the bad and the ugly. Acta Crystallographica Section A Foundations and Advances, 73(a1), pp.a237-a237.
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Citation: Keedy, D.A. et al., 2017. New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering.
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Citation: Rabbani, M.T., Schmidt, C.F. & Ros, A., 2017. Single-Walled Carbon Nanotubes Probed with Insulator-Based Dielectrophoresis. Analytical Chemistry, 89(24), pp.13235-13244.
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Citation: Li, D.-Z. et al., 2017. FBXW8-dependent degradation of MRFAP1 in anaphase controls mitotic cell death. Oncotarget, 8(57).
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Citation: Olmos, J. et al., 2017. Enzyme Intermediates Captured "on-the-fly" by Mix-and-Inject Serial Crystallography.
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Citation: Kurta, R.P. et al., 2017. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses. Physical Review Letters, 119(15).
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Optimal Pulse Processing, Pile-Up Decomposition, and Applications of Silicon Drift Detectors at LCLS
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Citation: Li, X. et al., 2017. Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination. IUCrJ, 4(6), pp.741-750.
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Citation: Otten, R. et al., 2017. Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution.
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Citation: Thomaston, J.L. et al., 2017. XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proceedings of the National Academy of Sciences, 114(51), pp.13357-13362.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Campbell, K. et al., 2017. Peripheral Blood Biomarkers Associated With Toxicity and Treatment Characteristics After 131 I- Metaiodobenzylguanidine Therapy in Patients With Neuroblastoma. International Journal of Radiation Oncology*Biology*Physics, 99(2), pp.468-475.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Zhang, H. et al., 2017. Structural basis for selectivity and diversity in angiotensin II receptors. Nature, 544(7650), pp.327-332.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Fuller, F.D. et al., 2017. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nature Methods, 14(4), pp.443-449.
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Citation: Spence, J.C.H., 2017. Ondrej Krivanek's early scientific research. Ultramicroscopy, 180, pp.8-13.
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Citation: Kim, S.K. et al., 2017. An Engineered TGF-β Monomer that Functions as a Dominant Negative to Block TGF-β Signaling. Journal of Biological Chemistry, p.jbc.M116.768754.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Kupitz, C. et al., 2017. Structural enzymology using X-ray free electron lasers. Structural Dynamics, 4(4), p.044003.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Kirian, R.A. et al., 2016. Development of a photophoretic optical guide for femtosecond x-ray diffractive imaging of aerosolized nanoparticles (Conference Presentation) K. Dholakia & G. C. Spalding, eds. Optical Trapping and Optical Micromanipulation XIII.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Rawashdeh, O. et al., 2017. Learned motivation drives circadian physiology in the absence of the master circadian clock. The FASEB Journal, 31(1), pp.388-399.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Batyuk, A. et al., 2016. Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. Science Advances, 2(9), pp.e1600292-e1600292.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Herascu, N. et al., 2016. Spectral Hole Burning in Cyanobacterial Photosystem I with P700 in Oxidized and Neutral States. The Journal of Physical Chemistry B, 120(40), pp.10483-10495.
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Citation: Ishchenko, A., Cherezov, V. & Liu, W., 2016. Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography. Journal of Visualized Experiments, (115).
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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Citation: Abbey, B. et al., 2016. X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene. Science Advances, 2(9), pp.e1601186-e1601186.
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Citation: Robinson, P.J. et al., 2016. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell, 166(6), pp.1411-1422.e16.
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Citation: Saldin, D., 2016. Ghost imaging with x rays. Physics, 9.
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Citation: Falcone, R. et al., 2016. Frontiers of free-electron laser science II. Journal of Physics B: Atomic, Molecular and Optical Physics, 49(18), p.180201.
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Citation: Calvey, G.D. et al., 2016. Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers. Structural Dynamics, 3(5), p.054301.
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Funding: NSF-STC Biology with X-ray Lasers (NSF-1231306)
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The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction
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Citation: Chang, C.-Y. et al., 2016. Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 inStreptomyces globisporus. Biochemistry, 55(36), pp.5142-5154.
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Citation: Zhu, L. et al., 2016. Serial Femtosecond Crystallography of Membrane Proteins. The Next Generation in Membrane Protein Structure Determination, pp.151-160.
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Citation: Nogly, P. et al., 2016. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nature Communications, 7, p.12314.
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Citation: Rudolf, J.D. et al., 2016. Structure of the ent -Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene Synthase . Journal of the American Chemical Society, 138(34), pp.10905-10915.
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Citation: Munke, A. et al., 2016. Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Scientific Data, 3, p.160064.
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Citation: Hantke, M.F. et al., 2016. A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3, p.160061.
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Citation: White, T.A. et al., 2016. Serial femtosecond crystallography datasets from G protein-coupled receptors. Scientific Data, 3, p.160057.
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Citation: Lawrence, R.M., Zook, J.D. & Hogue, B.G., 2016. Full inactivation of alphaviruses in single particle and crystallized forms. Journal of Virological Methods, 236, pp.237-244.
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Citation: Liu, H. & Spence, J.C.H., 2016. XFEL data analysis for structural biology. Quantitative Biology, 4(3), pp.159-176.
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Citation: He, H. et al., 2016. Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm. Acta Crystallographica Section A Foundations and Advances, 72(5), pp.539-547.
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Citation: Huang, T. et al., 2016. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. The Journal of Antibiotics, 69(10), pp.731-740.
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Citation: Van Benschoten, A. et al., 2015. Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles.
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Citation: Nogly, P. et al., 2015. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. IUCrJ, 2(2), pp.168-176.
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Citation: Bhabha, G., Biel, J.T. & Fraser, J.S., 2015. Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes. Acc. Chem. Res., 48(2), pp.423-430.
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Citation: Helml, W. et al., 2014. Measuring the temporal structure of few-femtosecond free-electron laser X-ray pulses directly in the time domain. Nature Photonics, 8(12), pp.950-957.
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Citation: Weerth, R.S. et al., 2014. Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 ... resolution. Proteins: Structure, Function, and Bioinformatics, 83(2), pp.383-388.
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Citation: Subramanian, G. et al., 2015. Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts. Ultramicroscopy, 148, pp.87-93.
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Citation: Wang, D. et al., 2014. Double-focusing mixing jet for XFEL study of chemical kinetics. J Synchrotron Rad, 21(6), pp.1364-1366.
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Citation: Tarakeshwar, P. et al., 2014. Probing the Nature of Charge Transfer at Nano-Bio Interfaces: Peptides on Metal Oxide Nanoparticles. The Journal of Physical Chemistry Letters, 5(20), pp.3555-3559.
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