Jose Alfonso Rodriguez*

Jose Alfonso Rodriguez

Associate Professor, Chemistry and Biochemistry, University of California Los Angeles

UC Profile
Rodriguez group

Education and Training

UCLAPhD2012Molecular Biology

Publications

  1. Richards LS, Flores MD, Zink S, Schibrowsky NA, Sawaya MR, Rodriguez JA. Cryo-EM structure of a human LECT2 amyloid fibril reveals a network of polar ladders at its core.. Structure (London, England : 1993), 2023.
  2. Saha A, Pattison A, Mecklenburg M, Brewster A, Ercius P, Rodriguez JA. Beyond MicroED: Ab Initio Structure Elucidation using 4D-STEM.. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada, 2023.
  3. Richards LS, Flores MD, Millán C, Glynn C, Zee CT, Sawaya MR, Gallagher-Jones M, Borges RJ, Usón I, Rodriguez JA. Fragment-Based Ab Initio Phasing of Peptidic Nanocrystals by MicroED.. ACS bio & med chem Au, 2023.
  4. Richards LS, Flores MD, Zink S, Schibrowsky NA, Sawaya MR, Rodriguez JA. Cryo-EM Structure of a Human LECT2 Amyloid Fibril Reveals a Network of Polar Ladders at its Core.. bioRxiv : the preprint server for biology, 2023.
  5. Gordon J, Chapus FL, Viverette EG, Williams JG, Deterding LJ, Krahn JM, Borgnia MJ, Rodriguez J, Warren AJ, Stanley RE. Cryo-EM reveals the architecture of the PELP1-WDR18 molecular scaffold.. Nature communications, 2022.
  6. Glynn C, Hernandez E, Gallagher-Jones M, Miao J, Sigurdson CJ, Rodriguez JA. Structural consequences of sequence variation in mammalian prion β2α2 loop segments.. Frontiers in neuroscience, 2022.
  7. Ferrero S, Flores MD, Short C, Vazquez CA, Clark LE, Ziegenbein J, Zink S, Fuentes D, Payes C, Batto MV, Collazo M, García CC, Abraham J, Cordo SM, Rodriguez JA, Helguera G. Correction for Ferrero et al., "Antibody-Based Inhibition of Pathogenic New World Hemorrhagic Fever Mammarenaviruses by Steric Occlusion of the Human Transferrin Receptor 1 Apical Domain".. Journal of virology, 2022.
  8. Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis.. Cell, 2021.
  9. Ferrero S, Flores MD, Short C, Vazquez CA, Clark LE, Ziegenbein J, Zink S, Fuentes D, Payes C, Batto MV, Collazo M, García CC, Abraham J, Cordo SM, Rodriguez JA, Helguera G. Antibody-Based Inhibition of Pathogenic New World Hemorrhagic Fever Mammarenaviruses by Steric Occlusion of the Human Transferrin Receptor 1 Apical Domain.. Journal of virology, 2021.
  10. Zee CT, Saha A, Sawaya MR, Rodriguez JA. Ab Initio Determination of Peptide Structures by MicroED.. Methods in molecular biology (Clifton, N.J.), 2021.
  11. Gallagher-Jones M, Rodriguez JA. Structures from the Mesophase: MicroED Targets Crystals Extracted from LCP.. Structure (London, England : 1993), 2020.
  12. Richards LS, Millán C, Miao J, Martynowycz MW, Sawaya MR, Gonen T, Borges RJ, Usón I, Rodriguez JA. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER.. Acta crystallographica. Section D, Structural biology, 2020.
  13. Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination.. F1000Research, 2020.
  14. Glynn C, Sawaya MR, Ge P, Gallagher-Jones M, Short CW, Bowman R, Apostol M, Zhou ZH, Eisenberg DS, Rodriguez JA. Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core.. Nature structural & molecular biology, 2020.
  15. Gallagher-Jones M, Bustillo KC, Ophus C, Richards LS, Ciston J, Lee S, Minor AM, Rodriguez JA. Atomic structures determined from digitally defined nanocrystalline regions.. IUCrJ, 2020.
  16. Griner SL, Seidler P, Bowler J, Murray KA, Yang TP, Sahay S, Sawaya MR, Cascio D, Rodriguez JA, Philipp S, Sosna J, Glabe CG, Gonen T, Eisenberg DS. Structure-based inhibitors of amyloid beta core suggest a common interface with tau.. eLife, 2019.
  17. Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP, Eisenberg DS. Author Correction: Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.. Nature structural & molecular biology, 2019.
  18. Glynn C, Rodriguez JA. Data-driven challenges and opportunities in crystallography.. Emerging topics in life sciences, 2019.
  19. Zee CT, Glynn C, Gallagher-Jones M, Miao J, Santiago CG, Cascio D, Gonen T, Sawaya MR, Rodriguez JA. Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ.. IUCrJ, 2019.
  20. Gallagher-Jones M, Ophus C, Bustillo KC, Boyer DR, Panova O, Glynn C, Zee CT, Ciston J, Mancia KC, Minor AM, Rodriguez JA. Nanoscale mosaicity revealed in peptide microcrystals by scanning electron nanodiffraction.. Communications biology, 2019.
  21. Jones CG, Martynowycz MW, Hattne J, Fulton TJ, Stoltz BM, Rodriguez JA, Nelson HM, Gonen T. The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination.. ACS central science, 2018.
  22. Pryor A, Rana A, Xu R, Rodriguez JA, Yang Y, Gallagher-Jones M, Jiang H, Kanhaiya K, Nathanson M, Park J, Kim S, Kim S, Nam D, Yue Y, Fan J, Sun Z, Zhang B, Gardner DF, Dias CSB, Joti Y, Hatsui T, Kameshima T, Inubushi Y, Tono K, Lee JY, Yabashi M, Song C, Ishikawa T, Kapteyn HC, Murnane MM, Heinz H, Miao J. Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity.. Scientific reports, 2018.
  23. Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP, Eisenberg DS. Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.. Nature structural & molecular biology, 2018.
  24. Hattne J, Shi D, Glynn C, Zee CT, Gallagher-Jones M, Martynowycz MW, Rodriguez JA, Gonen T. Analysis of Global and Site-Specific Radiation Damage in Cryo-EM.. Structure (London, England : 1993), 2018.
  25. Hughes MP, Sawaya MR, Boyer DR, Goldschmidt L, Rodriguez JA, Cascio D, Chong L, Gonen T, Eisenberg DS. Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks.. Science (New York, N.Y.), 2018.
  26. Gallagher-Jones M, Glynn C, Boyer DR, Martynowycz MW, Hernandez E, Miao J, Zee CT, Novikova IV, Goldschmidt L, McFarlane HT, Helguera GF, Evans JE, Sawaya MR, Cascio D, Eisenberg DS, Gonen T, Rodriguez JA. Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp.. Nature structural & molecular biology, 2018.
  27. Krotee P, Griner SL, Sawaya MR, Cascio D, Rodriguez JA, Shi D, Philipp S, Murray K, Saelices L, Lee J, Seidler P, Glabe CG, Jiang L, Gonen T, Eisenberg DS. Common fibrillar spines of amyloid-β and human islet amyloid polypeptide revealed by microelectron diffraction and structure-based inhibitors.. The Journal of biological chemistry, 2017.
  28. Mogul R, Vaishampayan P, Bashir M, McKay CP, Schubert K, Bornaccorsi R, Gomez E, Tharayil S, Payton G, Capra J, Andaya J, Bacon L, Bargoma E, Black D, Boos K, Brant M, Chabot M, Chau D, Cisneros J, Chu G, Curnutt J, DiMizio J, Engelbrecht C, Gott C, Harnoto R, Hovanesian R, Johnson S, Lavergne B, Martinez G, Mans P, Morales E, Oei A, Peplow G, Piaget R, Ponce N, Renteria E, Rodriguez V, Rodriguez J, Santander M, Sarmiento K, Scheppelmann A, Schroter G, Sexton D, Stephenson J, Symer K, Russo-Tait T, Weigel B, Wilhelm MB. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert.. Frontiers in microbiology, 2017.
  29. Pryor A, Yang Y, Rana A, Gallagher-Jones M, Zhou J, Lo YH, Melinte G, Chiu W, Rodriguez JA, Miao J. GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging.. Scientific reports, 2017.
  30. Rodriguez JA, Jiang L, Eisenberg DS. Toward the Atomic Structure of PrPSc.. Cold Spring Harbor perspectives in biology, 2017.
  31. Rodriguez JA, Eisenberg DS, Gonen T. Taking the measure of MicroED.. Current opinion in structural biology, 2017.
  32. Krotee P, Rodriguez JA, Sawaya MR, Cascio D, Reyes FE, Shi D, Hattne J, Nannenga BL, Oskarsson ME, Philipp S, Griner S, Jiang L, Glabe CG, Westermark GT, Gonen T, Eisenberg DS. Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity.. eLife, 2017.
  33. 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. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure.. Nature, 2016.
  34. 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. Structure of the toxic core of α-synuclein from invisible crystals.. Nature, 2015.
  35. Rodriguez JA, Xu R, Chen CC, Huang Z, Jiang H, Chen AL, Raines KS, Pryor A, Nam D, Wiegart L, Song C, Madsen A, Chushkin Y, Zontone F, Bradley PJ, Miao J. Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells.. IUCrJ, 2015.
  36. Rodriguez JA. Accessible atomic structures from sub-micron protein crystals.. Acta crystallographica. Section A, Foundations and advances, 2015.
  37. Xu R, Jiang H, Song C, Rodriguez JA, Huang Z, Chen CC, Nam D, Park J, Gallagher-Jones M, Kim S, Kim S, Suzuki A, Takayama Y, Oroguchi T, Takahashi Y, Fan J, Zou Y, Hatsui T, Inubushi Y, Kameshima T, Yonekura K, Tono K, Togashi T, Sato T, Yamamoto M, Nakasako M, Yabashi M, Ishikawa T, Miao J. Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses.. Nature communications, 2014.
  38. Miao J, Rodriguez JA. Phasing tiny crystals.. IUCrJ, 2013.
  39. Rodriguez JA, Xu R, Chen CC, Zou Y, Miao J. Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities.. Journal of applied crystallography, 2013.
  40. Menet JS, Rodriguez J, Abruzzi KC, Rosbash M. Nascent-Seq reveals novel features of mouse circadian transcriptional regulation.. eLife, 2012.
  41. Vodala S, Pescatore S, Rodriguez J, Buescher M, Chen YW, Weng R, Cohen SM, Rosbash M. The oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs.. Cell metabolism, 2012.
  42. Rodriguez J, Menet JS, Rosbash M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila.. Molecular cell, 2012.
  43. Khodor YL, Rodriguez J, Abruzzi KC, Tang CH, Marr MT, Rosbash M. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila.. Genes & development, 2011.
  44. Abruzzi KC, Rodriguez J, Menet JS, Desrochers J, Zadina A, Luo W, Tkachev S, Rosbash M. Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression.. Genes & development, 2011.
  45. van der Linden AM, Beverly M, Kadener S, Rodriguez J, Wasserman S, Rosbash M, Sengupta P. Genome-wide analysis of light- and temperature-entrained circadian transcripts in Caenorhabditis elegans.. PLoS biology, 2010.
  46. Kula-Eversole E, Nagoshi E, Shang Y, Rodriguez J, Allada R, Rosbash M. Surprising gene expression patterns within and between PDF-containing circadian neurons in Drosophila.. Proceedings of the National Academy of Sciences of the United States of America, 2010.
  47. Menet JS, Abruzzi KC, Desrochers J, Rodriguez J, Rosbash M. Dynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNA.. Genes & development, 2010.
  48. Blitzblau HG, Bell GW, Rodriguez J, Bell SP, Hochwagen A. Mapping of meiotic single-stranded DNA reveals double-stranded-break hotspots near centromeres and telomeres.. Current biology : CB, 2007.
  49. Daniels TR, Delgado T, Rodriguez JA, Helguera G, Penichet ML. The transferrin receptor part I: Biology and targeting with cytotoxic antibodies for the treatment of cancer.. Clinical immunology (Orlando, Fla.), 2006.
  50. Ng PP, Helguera G, Daniels TR, Lomas SZ, Rodriguez JA, Schiller G, Bonavida B, Morrison SL, Penichet ML. Molecular events contributing to cell death in malignant human hematopoietic cells elicited by an IgG3-avidin fusion protein targeting the transferrin receptor.. Blood, 2006.