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Recent Institute Publications

Feathers, J.R., Spoth, K.A., Fromme, J.C. Experimental evaluation of super-resolution imaging and magnification choice in single-particle cryo-EM. J. Structural Biology:X. (2021)

Sanford, E.J., Comstock, W.J., Faça, V.M., Vega, S.C., Gnügge, R., Symington, L.S., Smolka, M.B. Phosphoproteomics reveals a distinctive Mec1/ATR signaling response upon DNA end hyper‐resection. EMBO. (2021)

Long, J.T., Lammerding, J. Nuclear Deformation Lets Cells Gauge Their Physical Confinement. Dev Cell. (2021)

Sulpizio, A.G., Minelli, M.E., Mao, Y. In vitro Glutamylation Inhibition of Ubiquitin Modification and Phosphoribosyl-Ubiquitin Ligation Mediated by Legionella pneumophila Effectors. Bio-Protocol. (2020)

Allen, S.E., Koreman, G.T., Sarkar, A., Wang, B., Wolfner, M.F., Han, C. Versatile CRISPR/Cas9-mediated mosaic analysis by gRNA-induced crossing-over for unmodified genomes. PLoS Bio. (2021)

Lanz, M.C., Yugandhar, K., Gupta, S., Sanford, E.J., Faça, V.M., Vega, S., Joiner, A.M.N., Fromme, J.C., Yu, H., Smolka, M.B. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep. (2021)

Shin, J.H., Choe, D., Ransegnola, B., Hong, H.R., Onyekwere, I., Cross, T., Shi, Q., Cho, B.K., Westblade, L.F., Brito, I.L., Dörr, T. A multifaceted cellular damage repair and prevention pathway promotes high-level tolerance to β-lactam antibiotics. EMBO Rep. (2021)  

Shah, P., Hobson, C.M., Svea, C., Colville, M.J., Paszek, M.J., Superfine, R., Lammerding, J. Nuclear Deformation Causes DNA Damage by Increasing Replication Stress. Curr Bio. (2020) 

Sardana, R., Emr, S.D., Membrane Protein Quality Control Mechanisms in the Endo-Lysosome System. Trends in Cell Bio. (2021)

Feng, T.C., Lecrampe, A., Hu, F.H. Physiological and pathological functions of TMEM106B: a gene associated with brain aging and multiple brain disorders. ACTA Neuropathologica. (2021)

Pang, W., Hu, F.H. Cellular and physiological functions of C9ORF72 and implications for ALS/FTD. J Neurochem. (2020) 

Dörr, Tobias. Understanding tolerance to cell wall–active antibiotics. Annals of NY Acad. of Sci. (2021)

Sulpizio, A.G., Shin, J.H., Minelli, M.E., Mao, Y. Radioactive Assay of in vitro Glutamylation Activity of the Legionella pneumophila Effector Protein SidJ. Bio-Protocol. (2020) 

Gingras, R.M., Lwin, K.M., Miller, A.M., Bretscher, A. Yeast Rgd3 is a phospho-regulated F-BAR-containing RhoGAP involved in the regulation of Rho3 distribution and cell morphology. Mol. Bio. of the Cell. (2020) 

Batrouni, A.G., Baskin, J.M. A MAP for PI3K activation on endosomes. Cell Signaling. (2020)

Westblade, L.F., Errington, J., Dörr, T. Antibiotic Tolerance. PLOS Pathogens. (2020)

Faca, V.M., Sanford, E.J., Tieu, J., Comstock, W., Gupta, S., Marshall, S., Yu, H., Smolka, M.B. Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. Scientific Reports. (2020)

Harline, K., Roeder, A.H.K. Plant Morphogenesis: Mechanical Feedback Position Is Crucial in Organ Flattening. Current Biology. (2020)

Shami Shah, A., Sun, H., Baskin, J.M. For Wnt signaling, fucosylation of LRP6 is a bitter pill. Cell Chem Bio. (2020)

Bruhn, C., Ajazi, A., Ferrari, E., Lanz, M.C., Batrin, R., Choudhary, R., Walvekar, A., Laxman, S., Longhese, M.P., Fabre, E., Smolka, M.B., Foiani, M. The Rad53(CHK1/CHK2)-Spt21(NPAT) and Tel1(ATM) axes couple glucose tolerance to histone dosage and subtelomeric silencing. Nature Comm. (2020)

Hong, L., Ko, C.S., Kang, S.E., Pruneda-Paz, J.L., and Roeder, A.H.K. A giant cell enhancer achieves cell-type specificity through activation via TCP and repression by Dof transcription factors. Preprint in BioRXIV. (2020)

Mai, S., Roscoe, J.M., Sheng, R.R., Ullah, M., Zhang, J., Katz, I.I., Yu, H., Xiong, W., Hu, F., Loss of TMEM106B and PGRN leads to severe lysosomal abnormalities and neurodegeneration in mice. EMBO Rep. (2020)

Flores, J., White, B.M., Brea, R.J., Baskin, J.M., Devaraj, N.K., Lipids: chemical tools for their synthesis, modification, and analysis. Chem Soc Rev. (2020)

Bandman, R.P., Moore, S.L., Killian, J.L., Feng, T.C., Cleland, T.A., Hu, F., Wang, M.D., Dextran-coated iron oxide nanoparticle-induced nanotoxicity in neuron cultures. Scientific Reports. (2020)

Feng, T., Sheng, R.R., Solé-Domènech, S., Ulla, M., Zhou, X., Mendoza, C.S., Enriquez, L.C.M., Katz, I.I., Paushter, D.H., Sullivan, P.M., Wu, X., Maxfield, F., Hu, F. A Role of the Frontotemporal Lobar Degeneration Risk Factor TMEM106B in Myelination. Brain. (2020)

Beck, W.H.J., Kim, D., Das, J., Yu, H., Smolka, M.B., Mao, Y. Glucosylation by the Legionella Effector SetA Promotes the Nuclear Localization of the Transcription Factor TFEB. iScience. (2020)

Poe. A.R., Xu, Y., Zhang, C., Lei, J., Kailyn, L., Labib, D., Han, C. Low FoxO expression in Drosophila somatosensory neurons protects dendrite growth under nutrient restriction. ELife. (2020)

Bumpus, T.W., Liang, D., Baskin, J.M. IMPACT: Imaging phospholipase D activity with clickable alcohols via transphosphatidylation. Methods Enzymol. (2020) 

Shin, J.H., Sulpizio, A.G., Kelley, A., Alvarez, L., Murphy, S.G., Fan, L., Cava, F., Mao, Y., Saper, M.A., Dörr, T. Structural basis of peptidoglycan endopeptidase regulation. PNAS. (2020)

Moreno, S., Canales, J., Hong, L., Robinson, D., Roeder, A.H.K., Gutiérrez, R.A., Nitrate defines shoot size through compensatory roles for endoreplication and cell division in Arabidopsis thaliana. Current Bio. (2020)

Shin, J.H., Lanz, M., Smolka, M.B., Dorr, T. Characterization of an anti-FLAG antibody binding protein in V. Cholerae. Biochem and Bioph Research Comm. (2020)

Zhu, M., Chen, W., Mirabet, V., Hong, L., Bovio, S., Strauss, S., Schwarz, E.M., Tsugawa, S., Wang, Z., Smith, R.S., Li, C., Hamant, O., Boudaoud, A., Roeder, A.H.K. Robust organ size requires robust timing of initiation orchestrated by focused auxin and cytokinin signaling. Nature Plants. (2020)

Zhu, L., Sardana, R., Jin, D.K., Emr, S. Calcineurin-dependent regulation of endocytosis by a plasma membrane ubiquitin ligase adaptor, Rcr1. JCB. (2020)

Hernandez, S.B., Dorr, T., Waldor, M.K., Cava, F. Modulation of Peptidoglycan Synthesis by Recycled Cell Wall Tetrapeptides. Cell Reports. (2020)

Waterman, D.P., Haber, J.E., Smolka, M.B. Checkpoint responses to DNA Double-Strand Breaks. Annu Rev Biochem. (2020)

Vijaya Lakshmi Vadde, B., Roeder, A.H.K. Can the French Flag and Reaction Diffusion models explain flower patterning? Celebrating the 50th Anniversary of the French Flag Model. J. Exp Bot. (2020)

Zhu, M., Roeder, A.H.K. Plants are better engineers: the complexity of plant organ morphogenesis. Curr Opin Genet Dev. (2020)

Moreno, S., Canales, J., Hong, L., Robinson, D., Roeder, A.H.K., Gutiérrez, R.A. Nitrate Defines Shoot Size through Compensatory Roles for Endoreplication and Cell Division in Arabidopsis thaliana. Current Biology. (2020)

Dörr, T., Moynihan, P.J., Mayer, C. Editorial: Bacterial Cell Wall Structure and Dynamics. Frontiers in Microbiology. (2020)

Pourhaghighi, R., Ash, P.E.A., Phanse, S., Goebels, F., Hu, L.Z.M., Chen, S., Zhang, Y., Wierbowski, S.D., ... Yu, H., Bader, G.D., Wolozin, B., Emili, ABraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Systems. (2020)

Pahari, S., Li, G., Murthy, A.K., Liang, S., Fragoza, R., Yu, H., Alexov E. SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. Int'l J Mol Sci. (2020)

Kosciuk, T., Price, I.R., Zhang, X., Zhu, C., Johnson, K.N., Zhang, S., Halaby, S.L., Komaniecki, G.P., Yang, M., DeHart, C.J., Thomas, P.M., Kelleher, N.L., Fromme, J.C., Lin, H. NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle. Nat Commun. (2020)

Thomas, L.L., Fromme, J.C. Extensive GTPase crosstalk regulates Golgi trafficking and maturation. Curr Opinion in Cell Biology. (2020)

Jorgensen, J.R., Tei, R., Baskin, J.M., Kornmann, B., Emr, S.D. ESCRT-III and ER-PM contacts maintain lipid homeostasis. Molecular Biology of the Cell. (2020)

Ji, H., Han, C. LarvaSPA, A Method for Mounting Drosophila Larva for Long-Term Time-Lapse Imaging. Journal of Visual Experimentation. (2020)

Yugandhar, K., Wang, T.Y., Leung, A.K.Y., Lanz, M.C., Motorykin, I., Liang, J., Shayhidin, E.E., Smolka, M.B., Zhang, S., Yu, H. MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. Mol Cell Proteomics Papers in Press. (2019)

Daughtry, J.L., Cao, W., Ye, J., Baskin, J.M. Clickable Galactose Analogues for Imaging Glycans in Developing Zebrafish ACS Chemical Biology. (2020)

Tei, R., Baskin, J.M. Spatiotemporal control of phosphatidic acid signaling with optogenetic, engineered phospholipase Ds. Journal of Cell Bio. (2020)

Publications archive