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Publication Archive

2016 (January - June)

Diego Dibitetto, Matteo Ferrari, Chetan Rawal, Attila Balint, TaeHyung Kim, Zhaolei Zhang, Marcus Smolka, Grant W. Brown, Federica Marini, Achille Pellicioli. Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks. Nucleic Acids Res. (2016)

John David Wasilko, Yuxin Mao. Exploiting the ubiquitin and phosphoinositide pathways by the Legionella pneumophila effector, SidC. Current Genetics. (2016)

C. Stewart Gillmor, Adrienne Roeder, Patrick Sieber, Chris Somerville, Wolfgang Lukowitz. A genetic screen for mutations affecting cell division in the Arabidopsis thaliana embryo identifies seven loci required for cytokinesis. PLoS One. (2016)

Yi Liu and Marcus Smolka. TOPBP1 takes RADical command in recombinational DNA repair. J Cell Biol. (2016)

Michael Meyer, Ryan Lapcevic, Alfonso Romero, Mark Yoon, Jishnu Das, Juan Felipe Beltrán, Matthew Mort, Peter Stenson, David Cooper, Alberto Paccanaro, Haiyuan Yu. mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome. Hum Mutat. (2016)

Tommy Vo, Jishnu Das, Michael Meyer, Nicolas Cordero, Nurten Akturk, Xiaomu Wei, Benjamin Fair, Andrew Degatano, Robert Fragoza, Lisa Liu, Akihisa Matsuyama, Michelle Trickey, Sachi Horibata, Andrew Grimson, Hiroyuki Yamano, Minoru Yoshida, Frederick Roth, Jeffrey Pleiss, Yu Xia, Haiyuan Yu. A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human. Cell. (2016)

Gongshi Bai, Marcus Smolka, John Schimenti. Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation. PLOS Genetics. (2016)

Michael Meyer, Phillip Geske, Haiyuan Yu. BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers. Bioinformatics. (2016)

Brian Richardson, Steve Halaby, Margaret Gustafson, Chris Fromme. The Sec7 N-terminal regulatory domains facilitate membrane-proximal activation of the Arf1 GTPase. eLife. (2016)

Deike Omnusa, Andrew Manford, Jakob Badera, Scott D. Emr, Christopher Stefan. Phosphoinositide kinase signaling controls ER-PM cross-talk. Elife. (2016)

Celine Denais, Rachel Gilbert, Philipp Isermann, Alex McGregor, Mariska te Lindert, Bettina Weigelin, Patricia Davidson, Peter Friedl, Katarina Wolf, Jan Lammerding. Nuclear envelope rupture and repair during cancer cell migration. Science. (2016)

Peter M. Sullivan, Xiaolai Zhou, Adam Robins, Daniel H. Paushter, Dongsung Kim, Marcus Smolka, Fenghua Hu. The ALS/FTLD associated protein C9orf72 associates with SMCR8 and WDR41 to regulate the autophagy-lysosome pathway. Acta Neuropathologica Communications. (2016)

Steven Tang, Nicholas Buchkovich, Mike Henne, Sudeep Banjade, Yun Jung Kim, Scott D. Emr. 2016. ESCRT-III activation by parallel action of ESCRT-I/II and ESCRT-0/Bro1 during MVB biogenesis. Elife. (2016)

Nozomu Yachie, Evangelia Petsalaki, Joseph C Mellor, Jochen Weile, Yves Jacob,Marta Verby, Sedide B Ozturk, Siyang Li, Atina Cote, Roberto Mosca, Jennifer Knapp, Minjeong Ko, Analyn Yu, Marinella Gebbia, Nidhi Sahni, Song Yi, Tanya Tyagi, Dayag Sheykhkarimli, Jonathan Roth, Cassandra Wong, Louai Musa, Jamie Snider,Yi‐Chun Liu, Haiyuan Yu, Pascal Braun, Igor Stagljar, Tong Hao, Michael Calderwood, Laurence Pelletier, Patrick Aloy, David Hill, Marc Vidal, Frederick P Roth. Pooled‐matrix protein interaction screens using Barcode Fusion Genetics. Mol Syst Biol. (2016)

Amphun Chaiboonchoe, Lila Ghamsari, Bushra Dohai, Patrick Ng, Basel Khraiwesh, Ashish Jaiswal, Kenan Jijakli, Joseph Koussa, David R. Nelson, Hong Cai, Xinping Yang, Roger L. Chang, Jason Papin, Haiyuan Yu, Santhanam Balaji, Kourosh Salehi-Ashtiani. Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation. Mol BioSystems. (2016)

Greg Fedorchak, Jan Lammerding. Cellular and molecular remodelling of a host cell for vertical transmission of bacterial symbionts. Methods Mol Biol. (2016)

Jun-Bo Luan, Hong-Wei Shan, Philipp Isermann, Jia-Hsin Huang, Jan Lammerding, Shu-Sheng Liu, Angela E. Douglas. Cellular and molecular remodelling of a host cell for vertical transmission of bacterial symbionts. Proc Biol Sci. (2016)

2015

Shav-Tal Y, Lammerding J. Design (and) Principles of Nuclear Dynamics in Stockholm. Nucleus. (2015)

Jishnu Das, Michael Meyer, Haiyuan Yu. Studying Autism in Context. Cell Systems. (2015)

Shaogeng Tang, W. Mike Henne, Peter Borbat, Nicholas Buchkovich, Jack Freed, Yuxin Mao, Chris Fromme, Scott D. Emr. Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments. eLife. (2015)

Patricia Davidson, Josiah Sliz, Philipp Isermann, Celine Denais, Jan Lammerding. Design of a microfluidic device to quantify dynamic intra-nuclear deformation during cell migration through confining environments. Integr Biol (Camb). (2015)

Michael Mitchell, Celine Denais, Maxine Chan, Zhexiao Wang, Jan Lammerding, Michael King. Lamin A/C deficiency reduces circulating tumor cell resistance to fluid shear stress. Am J Physiol Cell Physiol. (2015)

Gerardo Tauriello, Heather Meyer, Richard S. Smith, Petros Koumoutsakos, Adrienne H.K. Roeder. Variability and constancy in cellular growth of Arabidopsis sepals. Plant Physiol. (2015)

Ming Li, Tatsuhiro Koshi, Scott D. Emr. Membrane-anchored ubiquitin ligase complex is required for the turnover of lysosomal membrane proteins. J Cell Biol. (2015)

Carolyn Jablonowski, Jose Cussiol, Susannah Oberly, Askar Yimit, Attila Balint, Taehyung Kim, Zhaolei Zhang, Grant W. Brown, Marcus B. Smolka. Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase. Genetics. (2015)

Cecile Sauvanet, Jessica Wayt, Thaher Pelaseyed, Anthony Bretscher. Structure, Regulation, and Functional Diversity of Microvilli on the Apical Domain of Epithelial Cells. Annu Rev Cell Dev Biol. (2015)

Cecile Sauvanet, Damien Garbett, Anthony Bretscher. The function and dynamics of the apical scaffolding protein E3KARP are regulated by cell-cycle phosphorylation. Mol Biol Cell. (2015)

Jose Silva, Davia Pompeu, Marcus Smolka, Fabio Gozzo, Moacyr Comar Jr, Marcos Eberlin, Paolo Granjeiro, Sergio Marangoni. Primary Structure of a Trypsin Inhibitor (Copaifera langsdorffii Trypsin Inhibitor-1) Obtained from C. langsdorffii Seeds. J Biomol Tech. (2015)

Brian Richardson, Chris Fromme. Biochemical methods for studying kinetic regulation of Arf1 activation by Sec7. Methods Cell Biol. (2015)

Xi Luo, Jon Wasilko, Yao Liu, Jiayi Sun, Xiaochun Wu, Zhao-Qing Luo, Mao Y. (2015) Structure of the Legionella Virulence Factor, SidC Reveals a Unique PI(4)P-Specific Binding Domain Essential for Its Targeting to the Bacterial Phagosome. PLoS Pathog. (2015)

1000 Genomes Project Consortium, Adam Auton, Lisa D. Brooks, Richard M. Durbin, Erik P. Garrison EP, Hyun Min Kang, Jan O. Korbel, Jonathan L. Marchini, Shane McCarthy, Gil A. McVean, Goncalo R. Abecasis. A global reference for human genetic variation. Nature. (2015)

Xiaolai Zhou, Lirong Sun, Francisco Bastos de Oliveira, Xiaoyang Qi, William J. Brown, Marcus B. Smolka, Ying Sun, Fenghua Hu. Prosaposin facilitates sortilin-independent lysosomal trafficking of progranulin. J Cell Biol. (2015)

Mike Henne, Lu Zhu, Zsolt Balogi, Chris Stefan, Jeffrey Pleiss. Mdm1/Snx13 is a novel ER-endolysosomal interorganelle tethering protein. J Cell Biol. (2015)

Monika Zwerger, Heidi Roschitzki-Voser, Reto Zbinden, Celine Denais, Harald Herrmann, Jan Lammerding, Markus Gruetter, Ohad Medalia. Altering lamina assembly identifies lamina-dependent and -independent functions for A-type lamins. J Cell Sci. (Epub 2015)

Dustin G. Thomas,  Aishwarya Yenepalli, Celine M. Denais, Andrew Rape, Jordan R. Beach, Yu-Li Wang, William P. Schiemann, Harihara Baskaran, Jan Lammerding, Thomas T. Egelhoff. Non-muscle myosin IIB is critical for nuclear translocation during 3-D invasion. J Cell Biol. 2015. 210(4): 583-594

Mike Henne, Jen Liou, Scott Emr. Molecular Mechanisms of inter-organelle ER-PM contact sites. Curr. Opin. in Cell Biology. (2015)

Attila Balint, TaeHyung Kim, David Gallo, Jose Renato Cussiol, Francisco Bastos de Oliveira, AskarYimit, Jiongwen Ou, Ryuichiro Nakato, Alexey Gurevich, Katsuhiko Shirahige, Marcus Smolka, ZhaoleiZhang, Grant Brown. Assembly of Slx4 signaling complexes behind DNA replication forks. EMBO J. (2015)

Kirk Donovan, Anthony Bretscher. Tracking individual secretory vesicles during exocytosis reveals an ordered and regulated process. J Cell Biol. (2015)

Kirk Donovan, Anthony Bretscher. Head-to-tail regulation is critical for the in vivo function of myosin V. JCB. (2015)

Pierre Barbier de Reuille, Anne-Lise Routier-Kierzkowska, Daniel Kierzkowski, George W. Bassel, Thierry Schüpbach, Gerardo Tauriello, Namrata Bajpai, Sören Strauss, Alain Weber, Annamaria Kiss, Agata Burian, Hugo Hofhuis, Aleksandra Sapala, Marcin Lipowczan, Maria B. Heimlicher, Sarah Robinson, Emmanuelle M. Bayer, Konrad Basler, Petros Koumoutsakos, Adrienne HK Roeder, Tinri Aegerter-Wilmsen, Naomi Nakayama, Miltos Tsiantis, Angela Hay, Dorota Kwiatkowska, Ioannis Xenarios, Cris Kuhlemeier, Richard S. Smith. MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife. (2015)

George Dialynas, Om K. Shrestha, Jessica M. Ponce, Monika Zwerger, Dylan A. Thiemann, Grant H. Young, Steven A. Moore, Liping Yu, Jan Lammerding, Lori L. Wallrath. Myopathic lamin mutations cause reductive stress and activate the Nrf2/Keap-1 pathway. PLoS Genetics. 2015. 11(5): e1005231. (Epub 2015)

Yuanquan Song, David Sretavan, Ernesto A Salegio, Jim Berg, Xi Huang, Tong Cheng, Xin Xiong, Shan Meltzer, Chun Han, Trong-Tuong Nguyen, Jacqueline C Bresnahan, Michael S Beattie, Lily Yeh Jan, Yuh Nung Jan. Regulation of axon regeneration by the RNA repair and splicing pathway. Nat Neurosci. (2015)

Jose Cussiol, Carolyn Jablonowski, Askar Yimit, Grant Brown, Marcus Smolka. Dampening DNA damage checkpoint signalling via coordinated BRCT domain interactions. EMBO Journal. (2015)

Mintie Pu, Zhuoyu Ni, Minghui Wang, Xiujuan Wang, Haiyuan Yu, et al. Trimethylation of Lys36 on H3 restricts gene expression change during aging and impacts life span. Genes and Dev. (2015)

Jishnu Das, Kaitlyn Gayvert, Florentina Bunea, Marten Wegkamp, Haiyuan Yu. ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers. BMC Genomics (2015)

Dana Robinson, Adrienne Roeder. Themes and variations in cell type patterning in the plant epidermis. Curr. Opin. in Gen. and Dev. (2015)

Peter Soba P, Chun Han, Yi Zheng, Daniel Perea, Irene Miguel-Agliaga, Lily Yeh Jan, Yuh Nung Jan. The Ret receptor regulates sensory neuron dendrite growth and integrin mediated adhesion. Elife. (2015)

Francisco Bastos de Oliveira, Dongsung Kim, José Renato Cussiol, Jishnu Das, Min Cheol Jeong, Lillian Doerfler, Kristina Hildegard Schmidt, Haiyuan Yu, Marcus Smolka. Phosphoproteomics Reveals Distinct Modes of Mec1/ATR Signaling during DNA Replication. Mol. Cell. (2015)

Ming Li, Yueguang Rong, Ya-Shan Chuang, Dan Peng, Scott Emr. Ubiquitin-dependent lysosomal membrane protein sorting and degradation. Mol. Cell. (2015)

Chris Fromme. Membrane trafficking: licensing a cargo receptor for ER export. Curr. Biol. (2015)

2014

Li Xu, Anthony Bretscher. Rapid Glucose Depletion Immobilizes Active Myosin V on Stabilized Actin CablesCurr. Biol. (2014)

Xiaomu Wei, Jishnu Das, Robert Fragoza, Jin Liang, Francisco Bastos de Oliveira, Hao Ran Lee, Xiujuan Wang, Matthew Mort, Peter Stenson, David Cooper, Steven Lipkin, Marcus Smolka, Haiyuan Yu. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PLoS Genetics. (2014)

Jishnu Das, Kaitlyn Gayvert, Haiyuan Yu. Predicting cancer prognosis using functional genomics datasets. Cancer Informatics. (2014)

Xiaojian Gong, Xiaofang Chen, Dongmin Yu, Nannan Zhang, Zhongliang Zhu, Liwen Niu, Yuxin Mao, Hunghua Ge. Crystal structure of Legionella pneumophila dephospho-CoA kinase reveals a non-canonical conformation of P-loop. J Struct Biol. (2014)

Xian Qu, Prerana Chatty, Adrienne Roeder. Endomembrane trafficking protein SEC24A regulates cell size patterning in Arabidopsis thaliana. Plant Physiol. (2014)

Caitlin M. McDonold and Chris Fromme. Four GTPases differentially regulate the Sec7 Arf-GEF to direct traffic at the trans-Golgi network. Dev. Cell. (2014)

Damien Garbett and Anthony Bretscher. The surprising dynamics of scaffolding proteins. Mol Biol Cell. (2014)

John E. Paczkowski and Chris Fromme.  Structural basis for membrane binding and remodeling by the exomer secretory vesicle cargo adaptor. Dev. Cell. (2014)

Heather M. Meyer, Adrienne HK RoederStochasticity in plant cellular growth and patterning. Front. Plant Sci. (2014)

Ashley Kaminski, Greg Fedorchak, Jan Lammerding.  The cellular mastermind(?)-mechanotransduction and the nucleus. Prog. Mol. Biol. Transl. Sci. (2014)

Amanda M. Weiskoff and Chris Fromme. Distinct N-terminal regions of the exomer secretory vesicle cargo Chs3 regulate its trafficking itinerary. Front. Cell Dev. Biol. (2014)

Patricia Davidson, Celine Denais, Maya Bakshi, Jan Lammerding. Nuclear Deformability Constitutes a Rate-Limiting Step During Cell Migration in 3-D EnvironmentsCell Mol. BioEng. J. (2014)

Jessica Wayt, Anthony Bretscher. Cordon Bleu serves as a platform at the basal region of microvilli where it regulates microvillar length through its WH2 domains. Mol Biol Cell. (2014)

Gregory R. Fedorchak, Ashley Kaminski, Jan Lammerding. Cellular mechanosensing: Getting to the nucleus of it all. Prog Biophys Mol Biol. (2014)

FoSheng Hsu, Xi Luo, Jiazhang Qiu, Yan-Bin Teng, Jianping Jin, Marcus B. Smolka, Zhao-Qing Luo, Yuxin Mao. The Legionella effector SidC defines a unique family of ubiquitin ligases important for bacterial phagosomal remodeling. Proc Natl Acad Sci USA. (2014)

Chris Fromme and Nava Segev. Regulation of vesicle trafficking: GTPases and friends. Mol. Biol. Cell. (2014)

Patricia M. Davidson, Jan Lammerding. Broken nuclei - lamins, nuclear mechanics, and disease. Trends Cell Biol. (2014)

Owen A. Brady, Xiaolai Zhou, Fenghua Hu. Regulated intramembrane proteolysis of the frontotemporal lobar degeneration (FTLD) risk factor,TMEM106B, by Signal Peptide Peptidase-like 2a (SPPL2a). J Biol Chem. (2014)

Chun Han, Yuanquan Song, Hui Xiao, Denan Wang, Nathalie C. Franc, Lily Yeh Jan, Yuh-Nung Jan. Epidermal Cells Are the Primary Phagocytes in the Fragmentation and Clearance of Degenerating Dendrites in Drosophila. Neuron (2014)

Veronica Guariglia-Oropeza, Renato H. Orsi, Haiyuan Yu, Kathryn J. Boor, Martin Wiedmann and Claudia Guldimann. Regulatory network features in Listeria monocytogenes—changing the way we talk. Front Cell Infect Microbiol. (2014)

Jishnu Das, Hao Ran Lee, Adithya Sagar, Robert Fragoza, Jin Liang, Xiaomu Wei, Xiujuan Wang, Matthew Mort, Peter D. Stenson, David N. Cooper and Haiyuan Yu. Elucidating Common Structural Features of Human Pathogenic Variations Using Large-Scale Atomic-Resolution Protein Networks. Hum Mutat. (2014)

Raghuvir Viswanatha, Anthony Bretscher and Damien Garbett. Dynamics of ezrin and EBP50 in regulating microvilli on the apical aspect of epithelial cells. Biochem Soc Trans. (2014)

2013

Raghuvir Viswanatha, Jessica Wayt, Patrice Y. Ohouo, Marcus B. Smolka and Anthony Bretscher. Interactome analysis reveals ezrin can adopt multiple conformational states. J Biol Chem. (2013)

Jishnu Das, Robert Fragoza, Hao Ran Lee, Nicolas A. Cordero, Yu Guo, Michael J. Meyer, Tommy V. Vo, Xiujuan Wangab, Haiyuan Yu. Exploring mechanisms of human disease through structurally resolved protein interactome networks. Mol Biosyst. (2013)

Anthony Bretscher. Deconstructing formin-dependent actin cable assembly. PNAS (2013)

Ira Mellman, Scott D. Emr. A Nobel Prize for membrane traffic: Vesicles find their journey’s end. Journal Cell Bio. (2013)

Nicholas J. Buchkovich, William Mike Henne, Shaogeng Tang, Scott D. Emr. Essential N-Terminal Insertion Motif Anchors the ESCRT-III Filament during MVB Vesicle Formation. Dev. Cell (2013)

William Mike Henne, Harald Stenmark, Scott D. Emr. Molecular mechanisms of the membrane sculpting ESCRT pathway. Cold Spring Harb Perspect Biol. (2013)

Irina Chernyakov, Felipe Santiago-Tirado, Anthony Bretscher. Active Segregation of Yeast Mitochondria by Myo2 Is Essential and Mediated by Mmr1 and Ypt11. Curr Biol. (2013)

Chenxi Tian, Herong Shi, Shan Xiong, Fenghua Hu, Wen-Cheng Xiong, Jun Liu. The neogenin/DCC homolog UNC-40 promotes BMP signaling via the RGM protein DRAG-1 in C. elegans. Development (2013)

Leila Toulabi, Xiaochun Wu, Yanshu Cheng and Yuxin Mao. Identification and structural characterization of a Legionella phosphoinositide phosphatase. JBC (2013)

Xiujuan Wang, Bram Thijssen and Haiyuan Yu. Target Essentiality and Centrality Characterize Drug Side Effects. PLOS (2013)

Yu Guo, Xiaomu Wei, Jishnu Das, Andrew Grimson, Steven M. Lipkin, Andrew G. Clark and Haiyuan Yu. Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Association” Principle. Am Jour Hum Genetics (2013)

Ekta Khurana, Yao Fu, Vincenza Colonna, Xinmeng Jasmine Mu, Hyun Min Kang, Tuuli Lappalainen, Andrea Sboner, Lucas Lochovsky, Jieming Chen, Arif Harmanci, Jishnu Das, Alexej Abyzov, Suganthi Balasubramanian, Kathryn Beal, Dimple Chakravarty, Daniel Challis, Yuan Chen, Declan Clarke, Laura Clarke, Fiona Cunningham, Uday S. Evani, Paul Flicek, Robert Fragoza, Erik Garrison, Richard Gibbs, Zeynep H. Gumus, Javier Herrero, Naoki Kitabayashi, Yong Kong, Kasper Lage, Vaja Liluashvili, Steven M. Lipkin, Daniel G. MacArthur, Gabor Marth, Donna Muzny, Tune H. Pers, Graham R. S. Ritchie, Jeffrey A. Rosenfeld, Cristina Sisu, Xiaomu Wei, Michael Wilson, Yali Xue, Fuli Yu, 1000 Genomes Project Consortium, Emmanouil T. Dermitzakis, Haiyuan Yu, Mark A. Rubin, Chris Tyler-Smith and Mark Gerstein. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science (2013)

Wenhan Zhu, Loubna A. Hammad, FoSheng Hsu, Yuxin Mao, Zhao-Qing Luo. Induction of caspase 3 activation by multiple Legionella pneumophila Dot/Icm substrates. Cellular Microbiology (2013)

Brian C. Richardson, J. Christopher Fromme. The Exomer Cargo Adaptor Features a Flexible Hinge Domain. Structure (2013)

Bong-Kwan Han, Scott D. Emr. The PI(3,5)P2-dependent Tup1 conversion regulates metabolic reprogramming from glycolysis to gluconeogenesis. JBC (2013)

Jishnu Das, Tommy V. Vo, Xiaomu Wei, Joseph C. Mellor, Virginia Tong, Andrew G. Degatano, Xiujuan Wang, Lihua Wang, Nicolas A. Cordero, Nathan Kruer-Zerhusen, Akihisa Matsuyama, Jeffrey A. Pleiss, Steven M. Lipkin, Minoru Yoshida, Frederick P. Roth, and Haiyuan Yu. Cross-Species Protein Interactome Mapping Reveals Species-Specific Wiring of Stress Response Pathways. Sci. Signal (2013)

Claudio Scafoglio, Marcus Smolka, Huilin Zhou, Valentina Perissi, Michael G. Rosenfeld. The Co-Repressor SMRT Delays DNA Damage-Induced Caspase Activation by Repressing Pro-Apoptotic Genes and Modulating the Dynamics of Checkpoint Kinase 2 Activation. PLos One (2013)

Chin Yee Ho, Diana E. Jaalouk, Maria K. Vartiainen & Jan Lammerding.Lamin A/C and emerin regulate MKL1-SRF activity by modulating actin dynamics. Nature (2013)

Michael J. Meyer, Jishnu Das, Xiujuan Wang, Haiyuan Yu. INstruct: a database of high quality three-dimensional structurally resolved protein interactome networks. Bioinformatics (2013)

R.H.J. Fick, Dmitry Fedorov, Adrienne Roeder, B.S. Manjunath. Simultaneous cell tracking and image alignment in 3D CLSM imagery of growing Arabidopsis thaliana sepals. ISBI (2013)

Yingying Zhao, Jason A. MacGurn, Max Liu, Scott D. Emr. The ART-Rsp5 ubiquitin ligase network comprises a plasma membrane quality control system that protects yeast cells from proteotoxic stress. eLife (2013)

Anthony Bretscher. Magazine or journal - what is the difference? The role of the monitoring editor. Molecular Biology of the Cell (2013)

Christopher J. Stefan, Andrew G. Manford, Scott D. Emr. ER-PM connections: sites of information transfer and inter-organelle communication. Current Opinion in Cell Biol. (2013)

Monika Zwerger, Diana E. Jaalouk, Maria L. Lombardi, Philipp Isermann, Monika Mauermann, George Dialynas, Harald Herrmann, Lori L. Wallrath, and Jan Lammerding. Myopathic lamin mutations impair nuclear stability in cells and tissue and disrupt nucleo-cytoskeletal coupling. Human Mol Genetics (2013)

Amy C. Rowat, Diana E. Jaalouk, Monika Zwerger,W. Lloyd Ung, Irwin A. Eydelnant, Don E. Olins, Ada L. Olins,Harald Herrmann, David A. Weitz and Jan Lammerding. Nuclear Envelope Composition Determines the Ability of Neutrophil-type Cells to Passage through Micron-scale Constrictions. JBC (2013)

2012

Andrew G. Manford, Christopher J. Stefan, Helen L. Yuan, Jason A. MacGurn, Scott D. Emr. ER-to-plasma membrane tethering proteins regulate cell signaling and ER morphology. Developmental Cell (2012)

Owen A. Brady, Yanqiu Zheng, Kira Murphy, Marshall Huang, Fenghua Hu.The frontotemporal lobar degeneration risk factor, TMEM106B, regulates lysosomal morphology and function. Human Mol Genetics (2012)

Jishnu Das, Jaaved Mohammed and Haiyuan Yu. Genome-scale analysis of interaction dynamics reveals organization of biological networks.Bioinformatics (2012)

Jishnu Das and Haiyuan Yu. HINT: High-quality protein interactomes and their applications in understanding human disease. BMC Systems Biology (2012)

Jon E Paczkowski, Brian C Richardson, Amanda M Strassner and J Christopher Fromme. The exomer cargo adaptor structure reveals a novel GTPase-binding domain. EMBO (2012)

Wallace F Marshall, Kevin D Young, Matthew Swaffer, Elizabeth Wood, Paul Nurse, Akatsuki Kimura, Joseph Franke, John Wallingford, Virginia Walbot, Xian Qu and Adrienne H Roeder. What determines cell size? BMC Biology (2012)

Patrice Y. Ohouo and Marcus B. Smolka. The many roads to checkpoint activation. Cell Cycle (2012)

Raghuvir Viswanatha, Patrice Y. Ohouo, Marcus B. Smolka, and Anthony Bretscher. Local phosphocycling mediated by LOK/SLK restricts ezrin function to the apical aspect of epithelial cells. J. Cell Biol. (2012)

Patrice Ohouo, Yi Liu, Francisco M Bastos de Oliveira and Chu Jian "Frank" Ma and Marcus Smolka. DNA Repair Scaffolds Dampen Checkpoint Signaling by Counteracting the Rad9 Adaptor. Nature (2012)

Roeder AH, Cunha A, Ohno CK, Meyerowitz EM. Cell cycle regulates cell type in the Arabidopsis sepal. Development (2012)

Sungkwon Kang, Chae Un Kim, Xiaoling Gu, Roisin M. Owens, Sarah J. van Rijn, Vanissra Boonyaleepun, Yuxin Mao, Timothy A. Springer, Moonsoo M. Jin. Complex Structure of Engineered Modular Domains Defining Molecular Interaction between ICAM-1 and Integrin LFA-1. PLoS One (2012)

Marcus Smolka, Francisco M Bastos de Oliveira, Michael R Harris, and Robertus A M de Bruin. The checkpoint transcriptional response: Make sure to turn it off once you are satisfied. Cell Cycle (2012)

Roeder AH. When and where plant cells divide: a perspective from computational modeling. Current Opinion in Plant Biology (2012)

Roeder AH, Cunha A, Burl MC, Meyerowitz EM. A computational image analysis glossary for biologists. Development (2012)

Cunha A, Tarr PT, Roeder AH, Altinok A, Mjolsness E, Meyerowitz EM.Computational analysis of live cell images of the Arabidopsis thaliana plant. Methods in Cell Biology (2012)

Henne WM, Buchkovich N, Zhao Y, Emr S. The Endosomal Sorting Complex ESCRT-II Mediates the Assembly and Architecture of ESCRT-III Helice.Cell (2012)

Donovan K, Bretscher A. Myosin-V Is Activated by Binding Secretory Cargo and Released in Coordination with Rab/Exocyst Function. Dev. Cell (2012)

FoSheng Hsu, Wenhan Zhu, Lucy Brennan, Lili Tao, Zhao-Qing Luo, Yuxin Mao. Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase. PNAS (2012)

Garbett D, Bretscher A. PDZ interactions regulate rapid turnover of the scaffolding protein EBP50 in microvilli. J. Cell Biol. (2012)

Mi-Mi L, Votra SB, Kemphues K, Bretscher A, Pruyne D. Z-line formins promote contractile lattice growth and maintenance in striated muscles of C. elegans. J. Cell Biol. (2012)

Ling Y, Stefan CJ, Macgurn JA, Audhya A, Emr SD. The dual PH domain protein Opy1 functions as a sensor and modulator of PtdIns(4,5)P(2) synthesis. EMBO J. (2012)

Wood CS, Hung CS, Huoh YS, Mousley CJ, Stefan CJ, Bankaitis V, Ferguson KM, Burd CG. Local control of PtdIns4P signaling in the Golgi apparatus by Vps74 and Sac1 phosphoinositide phosphatase. Mol. Biol. Cell. (2012)

Richardson BC, McDonold CM, Fromme JC. The Sec7 Arf-GEF Is Recruited to the trans-Golgi Network by Positive Feedback. Dev. Cell. (2012)

Sher I, Hanemann O, Karplus AP, Bretscher AP. The Tumor Suppressor Merlin Controls Growth in Its Open State, and Phosphorylation Converts It to a Less-Active More-Closed State. Dev. Cell. (2012)

Blake-Hodek KA, Williams BC, Zhao Y, Castilho PV, Chen W, Mao Y, Yamamoto TM, Goldberg ML. Determinants for Activation of the Atypical AGC Kinase Greatwall during M Phase Entry. Mol Cell Biol. (2012)

Zhong S, Hsu F, Stefan CJ, Wu X, Patel A, Cosgrove MS, Mao Y. Allosteric activation of the phosphoinositide phosphatase Sac1 by anionic phospholipids. Biochemistry. (2012)

Nepusz T, Yu H, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods. (2012)

MacGurn JA, Hsu PC, Emr SD. Ubiquitin and Membrane Protein Turnover: From Cradle to Grave. Annu Rev Biochem. (2012)

Macdonald C, Buchkovich NJ, Stringer DK, Emr SD, Piper RC. Cargo ubiquitination is essential for multivesicular body intralumenal vesicle formation. EMBO Rep. (2012)

Bastos de Oliveira FM, Harris MR, Brazauskas P, de Bruin RA, Smolka MB.Linking DNA replication checkpoint to MBF cell-cycle transcription reveals a distinct class of G1/S genes. Embo J. (2012)

Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR 3rd, Ideker T, Wittenberg C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO J. (2012)

Fromme JC, Kim J. A rapid and quantitative coat protein complex II vesicle formation assay using luciferase reporters. Anal Biochem. (2012)

Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nature Biotechnol. (2012)

Hokanson, DE, Bretscher, A. EPI64 interacts with Slp1/JFC1 to coordinate Rab8a and Arf6 membrane trafficking. Mol. Biol. of Cell. (2012)

Liu W, Santiago-Tirado FH, Bretscher A. Yeast formin Bni1p has multiple localization regions that function in polarized growth and spindle orientation. Mol. Biol. of Cell. (2012)

2011

Karotki, L. JT Huiskonen, CJ Stefan, NE Ziolkowska, R Roth, MA Surma, NJ Krogan, SD Emr, J Heuser, K Grunewald & TC Walther. Eisosome proteins assemble into a membrane scaffold. J. Cell Biol. (2011)

)MacGurn, JA, PC Hsu, MB Smolka & SD Emr. TORC1 Regulates Endocytosis via Npr1-Mediated Phosphoinhibition of a Ubiquitin Ligase Adaptor. Cell. (2011)

Ripoll JJ, Roeder AH, Ditta GS, Yanofsky MF. A novel role for the floral homeotic gene APETALA2 during Arabidopsis fruit development. Development. (2011)

Lombardi ML, Lammerding J. Keeping the LINC: the importance of nucleocytoskeletal coupling in intracellular force transmission and cellular function. Biochem Soc Trans. (2011)

Shi, Y, CJ Stefan, SM Rue, D Teis & SD Emr. Two novel WD40 domain-containing proteins, Ere1 and Ere2, function in the retromer-mediated endosomal recycling pathway. Mol. Biol. Cell. (2011)

Wang X, Gulbahce N, Yu H. Network-based methods for human disease gene prediction. Brief Funct Genomics. (2011)

Xue Z, He Y, Ye K, Gu Z, Mao Y, Qi L. A conserved structural determinant located at the interdomain region of mammalian inositol-requiring enzyme 1alpha. J Biol Chem. (2011)

Santiago-Tirado FH, Bretscher A. Membrane-trafficking sorting hubs: cooperation between PI4P and small GTPases at the trans-Golgi network. Trends Cell Biol. (2011)

Lombardi ML, Zwerger M, Lammerding J. Biophysical assays to probe the mechanical properties of the interphase cell nucleus: substrate strain application and microneedle manipulation. J Vis Exp. (2011)

Booth JG, Eilertson KE, Olinares PD, Yu H. A bayesian mixture model for comparative spectral count data in shotgun proteomics. Mol Cell Proteomics. (2011)

McMurray, MA, CJ Stefan, M Wemmer, G Odorizzi, SD Emr & J Thorner. Genetic interactions with mutations affecting septin assembly reveal ESCRT functions in budding yeast cytokinesis. Biol. Chem. (2011)

Henne, WM, NJ Buchkovich & SD Emr. The ESCRT Pathway. Dev. Cell. (2011)

Zheng Y, Brady OA, Meng PS, Mao Y, Hu F. C-terminus of progranulin interacts with the beta-propeller region of sortilin to regulate progranulin trafficking. PLoS One. (2011)

Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. BMC Genomics. (2011)

Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P & Vidal M. Next-generation sequencing to generate interactome datasets. Nature Methods. (2011)

Han BK & SD Emr. Phosphoinositide [PI(3,5)P2] lipid-dependent regulation of the general transcriptional regulator Tup1. Genes Dev. (2011)

Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev. (2011)

Ohouo, PY & Smolka, MB. A touching moment for Smc5/6: from ssDNA binding to repair. Cell Cycle. (2011)

Stefan, CJ, A Manford, D Baird, J Yamada-Hanff & SD Emr. Osh proteins regulate phosphoinositide metabolism at ER-plasma membrane contact sites. Cell. (2011)

Lalonde, D & Bretscher, A. The UBX Protein SAKS1 negatively regulates Endoplasmic Reticulum-Associated Degradation and p97-dependent degragation. J. Biol. Chem. (2011)

Santiago-Tirado, F, Legesse-Miller, A, Schott, D & Bretscher, A. PI4P and Rab inputs collaborate in myosin-V-dependent transport of secretory compartments in yeast. Developmental Cell. (2011)

Brady OA, Meng PS, Zheng Y, Mao Y & Hu F. Regulation of TDP-43aggregation by phosphorylation and p62/SQSTM1. Journal of Neurochemistry. (2011)

2010

Basso LR Jr, Bartiss A, Mao Y, Gast CE, Coelho PS, Snyder M, Wong B. Transformation of Candida albicans with a synthetic hygromycin B resistance gene. Yeast. (2010)

Hu F, Padukkavidana T, Vægter CB, Brady OA, Zheng Y, Mackenzie IR, Feldman HH, Nykjaer A & Strittmatter SM. Sortilin1-Mediated Endocytosis Determines Levels of the Fronto-Temporal Dementia Protein. Progranulin Neuron. (2010)

Mao Y, Wei G. A Feedback-Based Secure Path Approach for Wireless Sensor Network Data Collection. Sensors (Basel). (2010)

Garbett, D, Lalonde, D & Bretscher, A. The Scaffolding protein EBP50 regulates microvillar assembly in a phosphorylation-dependent manner. J. Cell Biol. (2010)

Ohouo, P, Oliveira, FM, Almeida, BS & Smolka, MB. DNA Damage Signaling Recruits the Rtt107-Slx4 Scaffolds via Dpb11 to Mediate Replication Stress Response. Mol. Cell. (2010)

Basso LR Jr, Gast CE, Mao Y, Wong B. Fluconazole transport into Candida albicans secretory vesicles by the membrane proteins Cdr1p, Cdr2p, and Mdr1p. Eukaryot Cell. (2010)

Garrenton, L, CJ Stefan, MA McMurray, SD Emr & J Thorner. Pheremone-induced anisotropy in yeast plasma membrane phosphatidylinositol-4,5-bisphosphate distribution is required for MAPK signaling.Proc. Natl. Acad. Sci. U.S.A. (2010)

Manford, A, T Xia, AK Saxena, CJ Stefan, F Hu, SD Emr & Y Mao. Crystal structure of the yeast Sac1: implication for its phosphoinositide phosphatase function. EMBO J. (2010)

Lalonde, D, Garbett, D & Bretscher, A. A regulated complex of the scaffolding proteins PDZK1 and EBP50 with ezrin contribute to microvillar organization. Mol. Cell Biol. (2010)

Gao, L, Liu, W & Bretscher, A. The yeast formin Bnr1p has two localization regions that show spatially and temporally distinct association with septin structures. Mol. Biol. Cell. (2010)

Fehon, RG, McClatchey, AI & Bretscher, A. Organizing the Cell Cortex: The role of ERM proteins. Nature Reviews Molecular Cell Biol. (2010)

Teis, D, S Saksena, BL Judson & SD Emr. ESCRT-II coordinates the assembly of ESCRT-III filaments for cargo sorting and multivesicular body vesicle formation. EMBO J. (2010)

Smolka, MB. Fine-tuning the DNA damage response: protein phosphatase 2A checks on CHK2. Cell Cycle. (2010)

2009

Emr S, Glick BS, Linstedt AD, Lippincott-Schwartz J, Luini A, Malhotra V, Marsh BJ, Nakano A, Pfeffer SR, Rabouille C, Rothman JE, Warren G, Wieland FT. Journeys through the Golgi--taking stock in a new era. J Cell Biol. (2009)

Tran JH, Chen CJ, Emr S, Schekman R. Cargo sorting into multivesicular bodies in vitro. PNAS. (2009)

Mao Y, Balkin DM, Zoncu R, Erdmann KS, Tomasini L, Hu F, Jin MM, Hodsdon ME, De Camilli P. A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism. EMBO J. (2009)

Gao L, Bretscher A. Polarized growth in budding yeast in the absence of a localized formin. Mol Biol. Cell. (2009)

Ilani T, Vasiliver-Shamis G, Vardhana S, Bretscher A, Dustin ML. T cell antigen receptor signaling and immunological synapse stability require myosin IIA. Nat Immonol. (2009)

Bretscher A. Epithelial polarity: dual Lkb1 pathways regulate apical microvilli. Dev. Cell. (2009)

Teis D, Saksena S, Emr SD. SnapShot: the ESCRT machinery. Cell. (2009)

LaLonde DP, Bretscher A. The scaffold protein PDZK1 undergoes a head-to-tail intramolecular association that negatively regulates its interaction with EBP50. Biochemistry. (2009)

Saksena S, Emr SD. ESCRTs and human disease. Biochem. Soc. Trans. (2009)

Saksena S, Wahlman J, Teis D, Johnson AE, Emr SD. Functional reconstitution of ESCRT-III assembly and disassembly. Cell. (2009)

Wagner MV, Smolka MB, de Bruin RA, Zhou H, Wittenberg C, Dowdy SF. Whi5 regulation by site specific CDK-phosphorylation in Saccharomyces cerevisiae. PLoS One. (2009)