Publications

Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline.

Barad BA†, Medina M†, Fuentes D, Wiseman, RL, Grotjahn DA. Journal of Cell Biology 2023 †Equal contribution

Mapping Protein Dynamics at High-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. (2022) bioRxiv.

Nanoscale details of mitochondrial fission revealed by cryo-electron tomography.

Mageswaran, SK†, Grotjahn DA†§, Zeng X, Barad BA, Medina M, Hoang MH, Dobro MJ, Chang YW, Xu M, Yang WY, Jensen, GJ§. bioRxiv 2021 †Equal contribution §Corresponding authors

CellPAINT: Turnkey illustration of molecular cell biology

Gardner A, Ludovic A, Fuentes D, Maritan M, Barad BA, Medina, M, Olson AJ, Grotjahn DA, Goodsell DS. Front. Bioinform. 2021.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Jr. MAH, Hoh SW, Hou J, Hung L, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Nature Methods. 2021.

Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates

Barad BA, Liu L, Diaz RE, Basillo R, Van Dyken SJ, Locksley RM, Fraser JS. Protein Science. 2020.

Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme

Thompson MC, Barad BA, Wolff AM, Cho HS, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. Nature Chemistry. 2019.

Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers

Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG. Cell Reports. 2019.

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF. Proceedings of the National Academy of Sciences. 2017.

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

Wang RYR, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. eLife. 2016.

Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

Mavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo E, See S, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. eLife. 2016.

EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

Barad BA, Echols N, Wang RYR, Cheng Y, DiMaio F, Adams PD, Fraser JS. Nature Methods. 2015.