METHODS IN CRYO-EM AND CRYO-ET
Rapid structural analysis of bacterial ribosomes in situ. Powell BM, Brant TS, Davis JH*, Mosalaganti S*. In revision 2024 [bioRxiv] [pdf].
Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. Powell BM, Davis JH. Nature Methods 2024 [pubmed] [bioRxiv] [pdf].
Application of Monolayer Graphene to Cryo-Electron Microscopy Grids for High-resolution Structure Determination. Grassetti AV, May BM, Davis JH. JoVE 2023 [pubmed] [bioRxiv] [pdf].
Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN. Kinman LF, Powell BM, Zhong ED, Berger B*, Davis JH*. Nature Protocols 2023 [pubmed] [bioRxiv] [pdf].
Cryo-EM at ACA 2022. Subramaniam S, Kotecha A, Davis JH. IUCRj 2022 [pubmed] [pdf].
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nature Methods 2021. Zhong ED, Bepler T, Berger B*, Davis JH* [pubmed] [bioRxiv] [pdf].
Exploring generative atomic models in cryo-EM reconstruction. Zhong ED, Lerer A, Davis JH*, Berger B*. NeurIPS Workshop: Machine Learning in Structural Biology 2020 [arXiv] [pdf].
CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images. Zhong ED, Lerer A, Davis JH*, Berger B*. International conference on computer vision 2021 [pdf].
Reconstructing continuous distributions of 3D protein structures from cryo-EM images. Zhong ED, Bepler T, Davis JH*, Berger B*. International conference on learning representations 2020 [arXiv] [pdf].
ribosome biogenesis
KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion. Sun J*, Kinman LF*, Jahagirdar D, Ortega J, Davis JH*. Nature Structural and Molecular Biology 2023 [pubmed] [bioRxiv] [pdf].
Imaging structurally dynamic ribosomes with cryogenic electron microscopy. Webster SM, May MB, Powell BM, Davis JH. Accepted Book Chapter in “Cryo-Electron Microscopy in Structural Biology”, in press [arXiv] [pdf].
The role of Era in assembly and homeostasis of the ribosomal small subunit. Razi A, Davis JH, Hao Y, Jahagirdar D, Thurlow B, Basu K, Jain N, Gomez-Blanco J, Britton RA, Vargas J, Guarne A, Woodson SA, Williamson JR, Ortega J. Nucleic Acids Research 2019 [pubmed] [pdf].
PROTEOLYSIS, autophagy, AND PROTEOSTASIS
An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins. Ghanbarpour A*, Telusma B, Powell BM, Zhang JJ, Bolstad I, Vargas C, Keller S, Baker TA, Sauer RT*, Davis JH*. In review 2024 [bioRxiv] [pdf].
Integrated proteasomal and lysosomal activity shape mTOR-regulated proteome remodeling. Cui DS, Davis JH. In review 2024 [bioRxiv] [pdf].
NCOA4 initiates ferritinophagy by avidly binding GATE16 using two short linear interactions motifs. Lee A, Davis JH. In revision 2024 [bioRxiv] [pdf].
A proteolytic AAA+ machine poised to unfold a protein substrate. under review. Ghanbarpour A, Sauer RT*, Davis JH*. In revision 2023 [bioRxiv] [pdf].
A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation. Ghanbarpour A, Cohen SE, Fei X, Kinman LF, Bell A, Zhang JJ, Baker TA, Davis JH*, Sauer RT*. Nature Communications 2023 [pubmed] [bioRxiv] [pdf].
The SspB adapter drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery. Ghanbarpour A, Fei X, Baker TA, Davis JH*, Sauer RT* PNAS 2023 [pubmed] [bioRxiv] [pdf].
OTHER WORK FROM THE DAVIS LAB
Conformational landscape of the yeast SAGA complex as revealed by cryo-EM. Vasyliuk D, Felt J, Zhong ED, Berger B, Davis JH, Yip CK Scientific Reports 2022 [pubmed] [pdf].
Structures of radial spokes and associated complexes important for ciliary motility. Gui M, Ma M, Erica S, Wang X, Koh F, Zhong ED, Berger B, Davis JH, Dutcher S, Zhang R, Brown A. Nature Structural and Molecular Biology 2021 [pubmed] [pdf].