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Recent Institute Publications

Zhang Q, Tamashunas A, Agrawal A, Torbati M, Katiyar A, Dickinson RB, Lammerding J, Lele TP. Local, transient tensile stress on the nuclear membrane causes membrane rupture. Mol Biol Cell. (2019)

Murphy SG, Alvarez L, Adams MC, Liu S, Chappie JS, Cava F, Dörr T. Endopeptidase regulation as a novel function of the Zur-dependent zinc starvation response. mBio. (2019)

Lan Y, Sullivan PM, Hu F. SMCR8 negatively regulates Akt and mTORC1 signaling to modulate lysosome biogenesis and tissue homeostasis. Autophagy (2019)

Thomas, L.L., van der Vegt, S.A., Fromme, J.C. A Steric Gating Mechanism Dictates the Substrate Specificity of a Rab-GEF. Developmental Cell. (2019)

Guiney EL, Zhu L, Sardana R, Emr SD, Baile MG. Methods for studying the regulation of membrane traffic by ubiquitin and the ESCRT pathway. Methods Enzymol. (2019)

Wierbowski SD, Fragoza R, Liang S, Yu H. Extracting complementary insights from molecular phenotypes for prioritization of disease-associated mutations. Current Opinion in Systems Biology. (2018)

Robinson, Dana Olivia, Coate, Jeremy E, Singh, Abhyudai, Hong, Lilan, Bush, Maxwell S., Doyle, Jeff J., Roeder, Adrienne H. K. Ploidy and Size at Multiple Scales in the Arabidopsis Sepal. Plant Cell. (2018)

Cammarata, Joseph and Roeder, Adrienne H.K. Development: Cell Polarity Is Coordinated over an Entire Plant Leaf. Current Biology. (2018)

Paushter D, Huan D, Feng T, Hu F. The lysosomal function of progranulin, a guardian against neurodegeneration. Acta Neuropathol. (2018) 

Zhou X, Paushter D, Sullivan PM, Hu F. The Interaction between progranulin with sortilin and the lysosome. Methods in Molecular Biology. (2018)

Weaver AI, Murphy SG, Umans U, Tallavajhala S, Onyekwere I, Wittels S, Shin JH, VanNieuwenhze M, Waldor MK, Dörr T. Genetic determinants of penicillin tolerance in Vibrio cholerae. Antimicrobial Agents and Chemotherapy. (2018)

Pelaseyed T, Bretscher A. Regulation of actin-based apical structures on epithelial cells. J Cell Sci. (2018)

Bumpus TW and Baskin JM. Greasing the wheels of lipid biology with chemical tools. Trends Biochem Sci. (2018)

Suzuki SW, Emr SD. Retrograde trafficking from the vacuole/lysosome membrane. Autophagy. (2018)

Poe AR, Wang B, Sapar ML, Ji H, Li K, Onabajo T, Fazliyeva R, Gibbs M, Qiu Y, Hu Y, Han C. Robust CRISPR/Cas9-mediated tissue specific mutagenesis reveals gene redundancy and perdurance in Drosophila. Genetics. (2018) 

Sapar ML, Ji H, Wang B, Poe AR, Dubey K, Ren X, Ni J, Han C. Phosphatidylserine externalization results from and causes neurite degeneration in Drosophila. Cell Reports. (2018) 

Hoyer N, Zielke P, Hu C, Petersen M, Sauter K, Scharrenberg R, Peng Y, Kim CC, Han C, Parrish JZ, Soba P. Ret and substrate-derived TGFβ maverick regulate space-filling dendrite growth in Drosophila sensory neurons. Cell Reports. (2018)

Sardana R, Zhu L, Emr SD. Rsp5 Ubiquitin ligase–mediated quality control system clears membrane proteins mistargeted to the vacuole membrane. J. Cell Biology. (2018)

 Hubbard TP, Billings G, Dörr T, Sit B, Warr AR, Kuehl CJ, Kim M, Delgado F, Mekalanos JJ, Lewnard JA, Waldor MK. A live vaccine rapidly protects against cholera in an infant rabbit model. Science Translational Medicine. (2018)

Elacqua, J.J., McGregor, A.L., Lammerding, J. Automated analysis of cell migration and nuclear envelope rupture in confined environments. PLoS ONE. (2018)

Singh, A., Brito, I., Lammerding, J. Beyond Tissue Stiffness and Bioadhesivity: Advanced Biomaterials to Model Tumor Microenvironments and Drug Resistance. Trends in Cancer. (2018)

Yadav SK, Feigelson SW, Roncato F, Antman-Passig M, Shefi O, Lammerding J, Alon R. Elevated nuclear lamin A is permissive for granulocyte transendothelial migration but not for motility through collagen I barriers. Journal of Leukocyte Biology. (2018)

Whitewoods, Chris D., Cammarata, Joseph, Nemec Venza, Zoe, Sang, Stephanie, Crook, Ashley D., Aoyama, Tsuyoshi, Wang, Xiao Y., Waller, Manuel, Kamisugi, Yasuo, Cuming, Andrew C., Szövényi, Péter, Nimchuk, Zachary L., Roeder, Adrienne H.K., Scanlon, Michael J. and Harrison, C. Jill. CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol. (2018)

Hong, Lilan, Dumond, Mathilde, Zhu, Mingyuan, Tsugawa, Satoru, Li, Chun-Biu, Boudaoud, Arezki, Hamant, Olivier, and Roeder, Adrienne H.K. Heterogeneity and robustness in plant morphogenesis: from cells to organs. Annual Review of Plant Biology. (2108)

Kim D, Liu Y, Oberly S, Freire R, Smolka MB. ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells. Nucleic Acids Res. (2018)

Lanz MC, Oberly S, Sanford EJ, Sharma S, Chabes A, Smolka MB. Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling. Genes Dev. (2018)

Chen S, Fragoza R, Klei L, Liu Y, Wang J, Roeder K, Devlin B, and Yu H. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Nature Genetics. (2018)

Zhou J, Wan J, Shu XE, Mao Y, Liu XM, Yuan X, Zhang X, Hess ME, Brüning JC, Qian SB. N6-Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response. Mol Cell. (2018)

Aleksandra Sapala, Adam Runions, Anne-Lise Routier-Kierzkowska, Mainak Das Gupta, Lilan Hong, Hugo Hofhuis, Stéphane Verger, Gabriella Mosca, Chun-Biu Li, Angela Hay, Olivier Hamant, Adrienne HK Roeder, Miltos Tsiantis, Przemyslaw Prusinkiewicz Why plants make puzzle cells, and how their shape emerges. eLife. (2018)  

Bastos de Oliveira FM, Kim D, Lanz M, Smolka MB. Quantitative Analysis of DNA Damage Signaling Responses to Chemical and Genetic Perturbations. Methods Mol Biol. (2018)

Wei X, Calvo-Vidal MN, Chen S, Wu G, Revuelta MV, Sun J, Zhang J, Walsh MF, Nichols KE, Joseph V, Snyder C, Vachon CM, McKay JD, Wang SP, Jayabalan DS, Jacobs LM, Becirovic D, Waller RG, Artomov M, Viale A, Patel J, Phillip JM, Chen-Kiang S, Curtin K, Salama M, Atanackovic D, Niesvizky R, Landgren O, Slager SL, Godley LA, Churpek J, Garber JE, Anderson KC, Daly MJ, Roeder RG, Dumontet C, Lynch HT, Mullighan CG, Camp NJ, Offit K, Klein RJ, Yu H, Cerchietti L, Lipkin SM. Germline mutations in lysine specific demethylase 1 (LSD1/KDM1A) confer susceptibility to multiple myeloma. Cancer Res. (2018) 

Meyer MJ, Beltrán JF, Liang S, Fragoza R, Rumack A, Liang J, Wei X, Yu H. Interactome INSIDER: a structural interactome browser for genomic studies. Nat Methods. (2018)

Shin M, van Leeuwen J, Boone C, Bretscher A. Yeast Aim21/Tda2 both regulates free actin by reducing barbed end assembly and forms a complex with Cap1/Cap2 to balance actin assembly between patches and cables. Mol Biol Cell. (2018)

Halaby SL, Fromme JC. The HUS-box is required for allosteric regulation of the Sec7 Arf-GEF. J Biol Chem. (2018)

Duan H, de Navas LF, Hu F, Sun K, Mavromatakis YE, Viets K, Zhou C, Kavaler J, Johnston RJ Jr., Tomlinson A, Lai EC. The mir-279/996 cluster represses receptor tyrosine kinase signaling to determine cell fates in the Drosophila eye. Development. (2018)

Kirby TJ, Lammerding J. Emerging views of the nucleus as a cellular mechanosensor. Nat Cell Biol. (2018)

Bakhoum SF, Ngo B, Laughney AM, Cavallo JA, Murphy CJ, Ly P, Shah P, Sriram RK, Watkins TBK, Taunk NK, Duran M, Pauli C, Shaw C, Chadalavada K, Rajasekhar VK, Genovese G, Venkatesan S, Birkbak NJ, McGranahan N, Lundquist M, LaPlant Q, Healey JH, Elemento O, Chung CH, Lee NY, Imielenski M, Nanjangud G, Pe'er D, Cleveland DW, Powell SN, Lammerding J, Swanton C, Cantley LC. Chromosomal instability drives metastasis through a cytosolic DNA response. Nature. (2018)

Sho W. Suzuki, Scott D. Emr Membrane protein recycling from the vacuole/lysosome membrane. J. Cell Biology. (2018)

Robinson, Dana O. and Roeder, Adrienne H.K. Small RNAs Turn Over a New Leaf as Morphogens. Preview for Developmental Cell 43, 253-254. (2018)

Morelli FF, Verbeek DS, Bertacchini J, Vinet J, Mediani L, Marmiroli S, Cenacchi G, Nasi M, De Biasi S, Brunsting JF, Lammerding J, Pegoraro E, Angelini C, Tupler R, Alberti S, Carra S. Aberrant Compartment Formation by HSPB2 Mislocalizes Lamin A and Compromises Nuclear Integrity and Function. Cell Rep. (2017)

Lees JA, Zhang Y, Oh MS, Schauder CM, Yu X, Baskin JM, Dobbs K, Notarangelo LD, De Camilli P, Walz T, Reinisch KM. Architecture of the human PI4KIIIα lipid kinase complex. Proc Natl Acad Sci. (2017)

Malty R, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott N, Xiong X, Vlasblom J, Prasad B, Foster B, Alberio T, Garavaglia B, Yu H, Bader G, Nakamura K, Parkinson J, Babu M. A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-kB Signaling. Cell Systems 5, 1–14. (2017)

Zhou X, Paushter D, Feng T, Sun L, Reinheckel T, Hu F. Lysosomal processing of progranulin. Molecular Neurodegeneration 12:62. (2017)

Mekhdjian AH, Kai F, Rubashkin MG, Prahl LS, Przybyla LM, McGregor AL, Bell ES, Barnes JM, DuFort CC, Ou G, Chang AC, Cassereau L, Tan SJ, Pickup MW, Lakins JN, Ye X, Davidson MW, Lammerding J, Odde DJ, Dunn AR, Weaver VM. Integrin-mediated traction force enhances paxillin molecular associations and adhesion dynamics that increase the invasiveness of tumor cells into a three-dimensional extracellular matrix. Mol Biol Cell. (2017)

Hong Lilan, Brown Joel, Segerson Nicholas A., Rose Jocelyn K.C., & Roeder Adrienne H.K. CUTIN SYNTHASE 2 Maintains Progressively Developing Cuticular Ridges in Arabidopsis Sepals. Molecular Plant (2017) 

Tsugawa, Satoru, Hervieux, Nathan, Kierzkowski, Daniel, Routier-Kierzkowska, Anne-Lise, Sapala, Aleksandra, Hamant, Olivier, Smith, Richard S., Roeder, Adrienne H.K., Boudaoud, A., and Li, Clones of cells switch from reduction to enhancement of size variability in Arabidopsis sepals. Development 144, 4398-4405. (2017)

Roeder, Adrienne .H.K.  Use it or average it: stochasticity in plant development. Current Opinion in Plant Biology 41, 8-15(2017)

Bumpus TW, Liang FJ, and Baskin JM. Ex Uno Plura: Differential labeling of phospholipid biosynthetic pathways with a single bioorthogonal alcohol. Biochemistry. (2017)

*Thomas, L.L., *Joiner, A.M.N., and Fromme, J.C. The TRAPPIII complex activates the GTPase Ypt1 (Rab1) in the secretory pathway. J. Cell Biol. 2017 Nov. 6 (2017)  *Denotes co-first authors

Bastos de Oliveira FM, Kim D, Lanz M, Smolka MB. Quantitative Analysis of DNA Damage Signaling Responses to Chemical and Genetic Perturbations. Methods Mol Biol. (2018)

Zhou X, Paushter DH, Feng T, Pardon CM, Mendoza CS, Hu F. Regulation of cathepsin D activity by the FTLD protein progranulin. Acta Neuropathologica Communications. (2017)

Zhou X, Sun L, Brady OA, Murphy KA, Hu F. Elevated TMEM106B levels exaggerate lipofuscin accumulation and lysosomal dysfunction in aged mice with progranulin deficiency. Acta Neuropathologica Communications. (2017)

Poe AR, Tang L, Wang B, Li Y, Sapar ML, Han C. Dendritic space-filling requires a neuronal type-specific extracellular permissive signal in Drosophila. Proc Natl Acad Sci U S A. (2017) 

Dahanukar A, Han C. A Bitter Taste of the Sun Makes Egg-Laying Flies Run. Genetics. (2017)

Gustafson MA, Fromme JC. Regulation of Arf activation occurs via distinct mechanisms at early and late Golgi compartments. Mol Biol Cell. (2017)

Zhao H, Patel V, Helmann JD, Dörr T. Don’t let sleeping dogmas lie: New views of peptidoglycan synthesis and its regulation. Molecular Microbiology. (2017)

Beckwith J, Bergman K, Carson MJ, Dörr T, Geller L, Pierce R, Krimsky S, Martin C, Santiago M, Vashlishan Murray A, Warren C, Zichterman C. Using Dialogues to Explore Genetics, Ancestry and Race. American Biology Teacher. (2017)

Yamaichi Y, Dörr T. Transposon Insertion Site Sequencing for Synthetic Lethal Screening. Methods Mol Biol. (2017)

Pelaseyed T, Viswanatha R, Sauvanet C, Filter JJ, Goldberg ML, Bretscher A. Ezrin activation by LOK phosphorylation involves a PIP2-dependent wedge mechanism. Elife. (2017)

Bumpus TW and Baskin JM. Clickable Substrate Mimics Enable Imaging of Phospholipase D Activity. ACS Cent Sci. (2017) 

Knopf KM, Murphy BL, MacMillan SN, Baskin JM, Barr MP, Boros E, and Wilson JJ. In Vitro Anticancer Activity and in Vivo Biodistribution of Rhenium(I) Tricarbonyl Aqua Complexes. J Am Chem Soc. (2017)

Zhou X, Sullivan PM, Sun L, Hu F. The interaction between progranulin and prosaposin is mediated by granulins and the linker region between saposin B and C. Journal of Neurochemistry. (2017)

Etienne-Manneville S, Lammerding J. Connecting the plasma membrane to the nucleus by intermediate filaments. Molecular Biology of the Cell. (2017)

Zhou X, Sun L, Bracko O, Choi JW, Jia Y, Nana AL, Brady OA, Hernandez JCC, Nishimura N, Seeley WW, Hu F. Impaired prosaposin lysosomal trafficking in frontotemporal lobar degeneration due to progranulin mutations. Nature Communications. (2017)

Zhu L, Jorgensen JR, Li M, Chuang YS, Emr SD. ESCRTs function directly on the lysosome membrane to downregulate ubiquitinated lysosomal membrane proteins. Elife. (2017)

Heather Meyer, José Teles, Pau Formosa-Jordan, Yassin Refahi, Rita San-Bento, Gwyneth Ingram, Henrik Jönsson, James C. W. Locke, & Adrienne H.K. Roeder. Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. eLife. (2017) 

Ho HC, MacGurn JA, Emr SD. Deubiquitinating enzymes Ubp2 and Ubp15 regulate endocytosis by limiting ubiquitination and degradation of ARTs. Molecular Biology of the Cell. (2017)

Chen S, Beltrán JF, Esteban-Jurado C, Franch-Expósito S, Castellví-Bel S, Lipkin S, Wei X, Yu H. GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. Nucleic Acids Research. (2017)

Isermann P, Lammerding J. Consequences of a tight squeeze: Nuclear envelope rupture and repair. Nucleus. (2017)

Mekhdjian AH, Kai F, Rubashkin MG, Prahl LS, Przybyla LM, McGregor AL, Bell ES, Barnes JM, DuFort CC, Ou G, Chang AC, Cassereau L, Tan SJ, Pickup MW, Lakins JN, Ye X, Davidson MW, Lammerding J, Odde DJ, Dunn AR, Weaver VM. Integrin-mediated traction force enhances paxillin molecular associations and adhesion dynamics that increase the invasiveness of tumor cells into a three-dimensional extracellular matrix. Molecular Biology of the Cell. (2017)

Baskin JM, Aye Y. Meeting Proceedings, 2017 Cornell University Baker Symposium-Quo Vadis: The Boundless Trajectories of Chemical Biology. Biochemistry. (2017)

Siqi Liang, Nathaniel Tippens, Yaoda Zhou, Matthew Mort, Peter Stenson, David Cooper, Haiyuan Yu. iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations. Genome Biol. (2017)

Lilan Hong, Joel Brown, Nicholas Segerson, Jocelyn Rose, Adrienne H.K. Roeder. CUTIN SYNTHASE 2 Maintains Progressively Developing Cuticular Ridges in Arabidopsis Sepals. Molecular Plant. (2017) 

Elisa Cabrera, Santiago Hernández-Pérez, Stephane Koundrioukoff, Michelle Debatisse, Dongsung Kim, Marcus Smolka, Raimundo Freire, David Gillespie. PERK inhibits DNA replication during the Unfolded Protein Response via Claspin and Chk1. Oncogene. (2017)

Yi Liu, José Renato Cussiol, Diego Dibitetto, Jennie Rae Sims, Shyam Twayana, Robert Samuel Weiss, Raimundo Freire, Federica Marini, Achille Pellicioli, Marcus Smolka. TOPBP1/Dpb11 plays a conserved role in homologous recombination DNA repair through the coordinated recruitment of 53BP1/Rad9. J Cell Biol. (2017)

Lilan Hong, Adrienne Roeder. Plant Development: Differential Growth Rates in Distinct Zones Shape an Ancient Plant Form. Curr Biol. (2017)

Lwin K, Li D, Bretscher A. Kinesin-related Smy1 enhances the Rab-dependent association of myosin-V with secretory cargo. Mol Biol Cell. (2016)

Publications archive