Now showing items 1-20 of 30

    • All for One, and One for All: The Clonality of the Intestinal Stem Cell Niche 

      Karpowicz, Phillip Adam; Perrimon, Norbert (Faculty of 1000 Ltd, 2010)
      Intestinal epithelia are maintained by intestinal stem cells (ISCs) that divide to replace dying absorptive and secretory cells that make up this tissue. Lineage labeling studies, both in vertebrates and Drosophila, have ...
    • A Case Study of the Reproducibility of Transcriptional Reporter Cell-Based RNAi Screens in Drosophila 

      DasGupta, Ramanuj; Nybakken, Kent E.; Booker, Matthew; Mathey-Prevot, Bernard; Gonsalves, Foster; Changkakoty, Binita; Perrimon, Norbert (BioMed Central, 2007)
      Off-target effects have been demonstrated to be a major source of false-positives in RNA interference (RNAi) high-throughput screens. In this study, we re-assess the previously published transcriptional reporter-based ...
    • Comparative Analysis of Cas9 Activators Across Multiple Species 

      Chavez, Alejandro; Tuttle, Marcelle; Pruitt, Benjamin W; Ewen-Campen, Ben; Chari, Raj; Ter-Ovanesyan, Dmitry; Haque, Sabina J; Cecchi, Ryan J; Kowal, Emma J K; Buchthal, Joanna; Housden, Benjamin E; Perrimon, Norbert; Collins, James J; Church, George (2016)
      Several groups have generated programmable transcription factors based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare ...
    • Comparative RNAi Screening Identifies a Conserved Core Metazoan Actinome by Phenotype 

      Rohn, Jennifer L.; Sims, David; Liu, Tao; Fedorova, Marina; Schöck, Frieder; Dopie, Joseph; Vartiainen, Maria K.; Kiger, Amy A.; Perrimon, Norbert; Baum, Buzz (The Rockefeller University Press, 2011)
      Although a large number of actin-binding proteins and their regulators have been identified through classical approaches, gaps in our knowledge remain. Here, we used genome-wide RNA interference as a systematic method to ...
    • A computational framework for boosting confidence in high-throughput protein-protein interaction datasets 

      Hosur, Raghavendra; Peng, Jian; Vinayagam, Arunachalam; Stelzl, Ulrich; Xu, Jinbo; Perrimon, Norbert; Bienkowska, Jadwiga; Berger, Bonnie (BioMed Central, 2012)
      Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a ...
    • Control of the Mitotic Cleavage Plane by Local Epithelial Topology 

      Gibson, William Tyler; Veldhuis, James H.; Rubinstein, Boris; Cartwright, Heather N.; Perrimon, Norbert; Brodland, G. Wayne; Nagpal, Radhika; Gibson, Matthew C. (Elsevier (Cell Press), 2011)
      For nearly 150 years, it has been recognized that cell shape strongly influences the orientation of the mitotic cleavage plane (e.g. Hofmeister, 1863). However, we still understand little about the complex interplay between ...
    • COPI Activity Coupled with Fatty Acid Biosynthesis is Required for Viral Replication 

      Cherry, Sara; Kunte, Amit; Wang, Hui; Coyne, Carolyn; Rawson, Robert B; Perrimon, Norbert (Public Library of Science, 2006)
      During infection by diverse viral families, RNA replication occurs on the surface of virally induced cytoplasmic membranes of cellular origin. How this process is regulated, and which cellular factors are required, has ...
    • A Cross-Species Study of PI3K Protein-Protein Interactions Reveals the Direct Interaction of P85 and SHP2 

      Breitkopf, Susanne B.; Yang, Xuemei; Begley, Michael J.; Kulkarni, Meghana; Chiu, Yu-Hsin; Turke, Alexa B.; Lauriol, Jessica; Yuan, Min; Qi, Jie; Engelman, Jeffrey A.; Hong, Pengyu; Kontaridis, Maria I.; Cantley, Lewis C.; Perrimon, Norbert; Asara, John M. (Nature Publishing Group, 2016)
      Using a series of immunoprecipitation (IP) – tandem mass spectrometry (LC-MS/MS) experiments and reciprocal BLAST, we conducted a fly-human cross-species comparison of the phosphoinositide-3-kinase (PI3K) interactome in a ...
    • Diversity and dynamics of the Drosophila transcriptome 

      Brown, James B.; Boley, Nathan; Eisman, Robert; May, Gemma E.; Stoiber, Marcus H.; Duff, Michael O.; Booth, Ben W.; Wen, Jiayu; Park, Soo; Suzuki, Ana Maria; Wan, Kenneth H.; Yu, Charles; Zhang, Dayu; Carlson, Joseph W.; Cherbas, Lucy; Eads, Brian D.; Miller, David; Mockaitis, Keithanne; Roberts, Johnny; Davis, Carrie A.; Frise, Erwin; Hammonds, Ann S.; Olson, Sara; Shenker, Sol; Sturgill, David; Samsonova, Anastasia A.; Weiszmann, Richard; Robinson, Garret; Hernandez, Juan; Andrews, Justen; Bickel, Peter J.; Carninci, Piero; Cherbas, Peter; Gingeras, Thomas R.; Hoskins, Roger A.; Kaufman, Thomas C.; Lai, Eric C.; Oliver, Brian; Perrimon, Norbert; Graveley, Brenton R.; Celniker, Susan E. (2014)
      Animal transcriptomes are dynamic, each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. We identified new genes, transcripts, and proteins using ...
    • Dynamic Switch of Negative Feedback Regulation in Drosophila Akt–TOR Signaling 

      Kockel, Lutz; Kerr, Kimberly Sayer; Melnick, Michael; Brückner, Katja; Hebrok, Matthias; Perrimon, Norbert (Public Library of Science, 2010)
      Akt represents a nodal point between the Insulin receptor and TOR signaling, and its activation by phosphorylation controls cell proliferation, cell size, and metabolism. The activity of Akt must be carefully balanced, as ...
    • E2F and p53 Induce Apoptosis Independently during Drosophila Development but Intersect in the Context of DNA Damage 

      Moon, Nam-Sung; Morris, Erick J.; Patel, Reena; Di Stefano, Luisa; White, Kristin; Dyson, Nicholas John; Perrimon, Norbert (Public Library of Science, 2008)
      In mammalian cells, RB/E2F and p53 are intimately connected, and crosstalk between these pathways is critical for the induction of cell cycle arrest or cell death in response to cellular stresses. Here we have investigated ...
    • The Effect of Development and Ecology on the Evolution of Ovary Size in Drosophila 

      Sarikaya, Didem Pelin (2015-05-20)
      How the size of an organ is established and altered during evolution is poorly understood. The ovary of fruit flies of the genus Drosophila serves as an interesting model for understanding organ size evolution, as the ...
    • FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update 

      Hu, Yanhui; Comjean, Aram; Roesel, Charles; Vinayagam, Arunachalam; Flockhart, Ian; Zirin, Jonathan; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E. (Oxford University Press, 2017)
      The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) ...
    • FlyRNAi.org—The Database of the Drosophila RNAi Screening Center: 2012 Update 

      Flockhart, Ian; Booker, Matthew; Hu, Yanhui; McElvany, Benjamin D; Gilly, Quentin Carl; Mathey-Prevot, Bernard; Perrimon, Norbert; Mohr, Stephanie (Oxford University Press, 2011)
      FlyRNAi (http://www.flyrnai.org), the database and website of the Drosophila RNAi Screening Center (DRSC) at Harvard Medical School, serves a dual role, tracking both production of reagents for RNA interference (RNAi) ...
    • A Functional Genomic Analysis of Cell Morphology Using RNA Interference 

      Kiger, AA; Baum, B; Jones, MR; Coulson, A; Echeverri, C; Perrimon, Norbert; Jones, S (BioMed Central, 2003)
      Background: The diversity of metazoan cell shapes is influenced by the dynamic cytoskeletal network. With the advent of RNA-interference (RNAi) technology, it is now possible to screen systematically for genes controlling ...
    • Genetic Determinants of Phosphate Response in Drosophila 

      Bergwitz, Clemens; Wee, Mark J.; Sinha, Sumi; Huang, Joanne Hyunjung; DeRobertis, Charles; Mensah, Lawrence; Cohen, Jonathan Brewer; Friedman, Adam Amiel Laufer; Kulkarni, Meghana; Hu, Yanhui; Vinayagam, Arunachalam; Schnall-Levin, Michael; Berger, Bonnie; Perkins, Lizabeth A.; Mohr, Stephanie; Perrimon, Norbert (Public Library of Science, 2013)
      Phosphate is required for many important cellular processes and having too little phosphate or too much can cause disease and reduce life span in humans. However, the mechanisms underlying homeostatic control of extracellular ...
    • Integrating protein-protein interaction networks with phenotypes reveals signs of interactions 

      Vinayagam, Arunachalam; Zirin, Jonathan; Roesel, Charles; Hu, Yanhui; Yilmazel, Bahar; Samsonova, Anastasia A.; Neumüller, Ralph A.; Mohr, Stephanie E.; Perrimon, Norbert (2013)
      A major objective of systems biology is to organize molecular interactions as networks and to characterize information-flow within networks. We describe a computational framework to integrate protein-protein interaction ...
    • miR-190 Enhances HIF-Dependent Responses to Hypoxia in Drosophila by Inhibiting the Prolyl-4-hydroxylase Fatiga 

      De Lella Ezcurra, Ana Laura; Bertolin, Agustina Paola; Kim, Kevin; Katz, Maximiliano Javier; Gándara, Lautaro; Misra, Tvisha; Luschnig, Stefan; Perrimon, Norbert; Melani, Mariana; Wappner, Pablo (Public Library of Science, 2016)
      Cellular and systemic responses to low oxygen levels are principally mediated by Hypoxia Inducible Factors (HIFs), a family of evolutionary conserved heterodimeric transcription factors, whose alpha- and beta-subunits ...
    • Of flies and men: insights on organismal metabolism from fruit flies 

      Rajan, Akhila; Perrimon, Norbert (BioMed Central, 2013)
      The fruit fly Drosophila has contributed significantly to our general understanding of the basic principles of signaling, cell and developmental biology, and neurobiology. However, answers to questions pertaining to energy ...
    • Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis 

      Yilmazel, Bahar; Hu, Yanhui; Sigoillot, Frederic; Smith, Jennifer A; Shamu, Caroline E; Perrimon, Norbert; Mohr, Stephanie E (BioMed Central, 2014)
      Background: RNA interference (RNAi) is an effective and important tool used to study gene function. For large-scale screens, RNAi is used to systematically down-regulate genes of interest and analyze their roles in a ...