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  • Publications | Department of Embryology
    Mullins MC Hendrickson HS Hendrickson EK Halpern ME Science 2001 May 18 292 5520 1385 8 Otx5 regulates genes that show circadian expression in the zebrafish pineal complex Gamse JT Shen YC Thisse C Thisse B Raymond PA Halpern ME Liang JO Nat Genet 2002 Jan 30 1 117 21 Epub 2001 Dec 20 Characterization of myelination in the developing zebrafish Brösamle C Halpern ME Glia 2002 Jul 39 1 47 57 The parapineal mediates left right asymmetry in the zebrafish diencephalon Gamse JT Thisse C Thisse B Halpern ME Development 2003 Mar 130 6 1059 68 Radiographic analysis of zebrafish skeletal defects Fisher S Jagadeeswaran P Halpern ME Dev Biol 2003 Dec 1 264 1 64 76 Leaning to the left laterality in the zebrafish forebrain Halpern ME Liang JO Gamse JT Trends Neurosci 2003 Jun 26 6 308 13 Review Directional asymmetry of the zebrafish epithalamus guides dorsoventral innervation of the midbrain target Gamse JT Kuan YS Macurak M Brösamle C Thisse B Thisse C Halpern ME Development 2005 Nov 132 21 4869 81 Epub 2005 Oct 5 Neuropilin asymmetry mediates a left right difference in habenular connectivity Kuan YS Yu HH Moens CB Halpern ME Development 2007 Mar 134 5 857 65 Epub 2007 Jan 24 Evolving into science advocates Halpern ME Hobin JA Dev Dyn 2008 May 237 5 1215 7 No abstract available Gal4 UAS transgenic tools and their application to zebrafish Halpern ME Rhee J Goll MG Akitake CM Parsons M Leach SD Zebrafish 2008 Summer 5 2 97 110 Review Nogo Nogo receptor signalling in PNS axon outgrowth and pathfinding Brösamle C Halpern ME Mol Cell Neurosci 2009 Apr 40 4 401 9 Epub 2008 Nov 8 Determining the function of zebrafish epithalamic asymmetry Facchin L Burgess HA Siddiqi M Granato M Halpern

    Original URL path: http://emb.carnegiescience.edu/labs/marnie-halpern/publications (2013-06-13)
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  • Ingolia Lab | Department of Embryology
    plays a key role in diverse processes including cellular stress responses developmental patterning and synaptic plasticity In my postdoctoral work I developed a ribosome profiling technique that allows precise and quantitative measurements of genome wide translation It can be used to study translational control as well as to annotate the actual protein coding sequences in complicated genomes and transcriptomes Ribosome profiling also revealed extensive translation upstream of many genes This unexpected translation points to the regulated use of alternate sites of initiation including substantial initiation at non AUG codons We believe that start codon selection is an underappreciated point of control in gene expression The use of alternate sites of initiation can produce functionally distinct protein isoforms as well as affect the amount of protein synthesized This poses several questions that we want to address What genes show regulated changes in translation during normal physiological processes or during stress How does the translation initiation apparatus change its start site preferences in different circumstances How does the sequence of the transcript contribute to initiation site selection and in particular how do different start sites affect each other People Nicholas Ingolia Principal Investigator Staff member Carnegie Institution Adjunct Assistant Professor Johns Hopkins University Biology Adjunct Assistant Professor Johns Hopkins Medical Institute Molecular Biology Genetics Michael Harris Predoc Fellow Anna McGeachy Predoc Fellow Eric Mills Predoc Fellow We are interested in hearing from people interested in joining our lab as postdoctoral scholars to pursue experimental projects or computational analysis of genome scale data Contact ingolia at ciwemb dot edu about opportunities to do research with us Our lab recruits graduate students mainly through the Johns Hopkins CMDB PhD program Carnegie Institution members serve as thesis advisors for Johns Hopkins graduate students Publications NT Ingolia Genome wide translational profiling by ribosome footprinting Methods Enzymol

    Original URL path: http://emb.carnegiescience.edu/labs/nick-ingolia (2013-06-13)
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  • Publications | Department of Embryology
    1 Mammalian microRNAs predominantly act to decrease target mRNA levels Guo H Ingolia NT Weissman JS Bartel DP Nature 2010 Aug 12 466 7308 835 40 Molecular basis of infrared detection by snakes Gracheva EO Ingolia NT Kelly YM Cordero Morales JF Hollopeter G Chesler AT Sánchez EE Perez JC Weissman JS Julius D Nature 2010 Apr 15 464 7291 1006 11 Epub 2010 Mar 14 Rapid creation and quantitative monitoring of high coverage shRNA libraries Bassik MC Lebbink RJ Churchman LS Ingolia NT Patena W LeProust EM Schuldiner M Weissman JS McManus MT Nat Methods 2009 Jun 6 6 443 5 Epub 2009 May 17 Genome wide analysis in vivo of translation with nucleotide resolution using ribosome profiling Ingolia NT Ghaemmaghami S Newman JR Weissman JS Science 2009 Apr 10 324 5924 218 23 Epub 2009 Feb 12 Systems biology Reverse engineering the cell Ingolia NT Weissman JS Nature 2008 Aug 28 454 7208 1059 62 No abstract available Positive feedback loops as a flexible biological module Ingolia NT Murray AW Curr Biol 2007 Apr 17 17 8 668 77 Epub 2007 Mar 29 The ups and downs of modeling the cell cycle Ingolia NT Murray AW Curr Biol

    Original URL path: http://emb.carnegiescience.edu/labs/nick-ingolia/publications (2013-06-13)
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  • Lepper Lab | Department of Embryology
    Joseph G Gall Publications Former Lab Members Jeffrey Han Publications Marnie Halpern Publications Nick Ingolia Publications Christoph Lepper Allan Spradling Publications Frederick Tan Yixian Zheng Publications Research Programs Faculty Resources Seminars Outreach Contact Home Lepper Lab Research Summary to be posted Christoph Lepper Staff Associate Office Telephone 410 246 3069 Lab Telephone 410 246 3089 Department Fax 410 243 6311 Email Lab Members Lakshmi Gorrepati P D Associate Stephanie Kuo

    Original URL path: http://emb.carnegiescience.edu/labs/christoph-lepper (2013-06-13)
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  • Spradling Lab | Department of Embryology
    to provide insight into nuclear and cytoplasmic rejuvenation By studying ovarian stem cells we are learning how cells maintain an undifferentiated state and how cell production is regulated by microenvironments known as niches We have found that epithelial stem cells responsible for follicle cell production compete Replacement of damaged stem cells may be a major mechanism that limits somatic mutation but we hae also found that mutations exist that confer the ability to replace wild type cells Such mutations may be precursors to cellular aging and cancer We also believe that an elaborate system of organelle sorting during the time germ cells are interconnected prior to meiosis contributes to the removal of damaged mitochondrial DNA molecules and possibly also acts on damaged proteins Finally in order to understand better how these complex processes are controlled we are re investigating the role of steroid and prostaglandin hormones in controlling the process of oogenesis from stem cell to laid egg A Drosophila intestinal stem cell ISC was labeled with a lineage marker green revealing that its progeny consist of two distinct cell types enterocytes large green circles and enteroendocrine cells smaller orange circles An internediate the enteroblast EB is also indicated Allan

    Original URL path: http://emb.carnegiescience.edu/labs/allan-spradling (2013-06-13)
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  • Publications | Department of Embryology
    cells and niches Mechanisms that promote tissue maintenance throughout life Cell 132 598 611 Allen A and Spradling A C 2008 The SF 1 like nuclear hormone receptor Hr39 regulates Drosophila female reproductive tract development and function Development 135 311 321 Nystul T and Spradling A C 2007 An epithelial niche in the Drosophila ovary undergoes long range stem cell replacement Cell Stem Cell 1 277 285 Fuller M and Spradling A C 2007 The male and female Drosophila germline stem cell niches two versions of immortality Science 316 402 404 Ohlstein B and A C Spradling 2007 Multipotent Drosophila intestinal stem cells specify daughter cell fates by differential Notch signaling Science 315 988 92 Ohlstein B and A C Spradling 2006 The adult Drosophila posterior midgut is maintained by pluripotent stem cells Nature 439 470 474 Kai T and A C Spradling 2004 Differentiating germ cells can revert into functional stem cells in Drosophila melanogaster ovaries Nature 428 564 9 Allan Spradling Director Office Telephone 410 246 3015 Lab Telephone 410 246 3038 Department Fax 410 243 6311 Email Publications Lab Members Jui Ko Chang Predoc Fellow Carol Davenport Technician HHMI Steven DeLuca P D Assoc HHMI Megha Ghildiyal

    Original URL path: http://emb.carnegiescience.edu/labs/allan-spradling/publications (2013-06-13)
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  • Tan Lab | Department of Embryology
    naturally occurring repeats In addition to spontaneous recombination events recombination machinery can also be harnessed as a powerful tool to precisely modify genomes I am using genetic screens to identify rate limiting steps during genome modification PUBLICATIONS Tan FJ Hoang ML and Koshland D 2012 DNA resection at chromosome breaks promotes genome stability by constraining non allelic homologous recombination PLoS Genetics pmid 22479212 Hoang ML Tan FJ Lai DC Celniker SE Hoskins RA Dunham MJ Zheng Y and Koshland D 2010 Competitive repair by naturally dispersed repetitive DNA during non allelic homologous recombination PLoS Genetics pmid 21151956 Tan FJ Zuckerman JE Wells RC and Hill RB 2011 The C elegans B cell lymphoma 2 Bcl 2 homolog cell death abnormal 9 CED 9 associates with and remodels lipid membranes Protein Science pmid 21031486 Tan FJ Husain M Manlandro CM Koppenol M Fire AZ and Hill RB 2008 CED 9 and mitochondrial homeostasis in C elegans muscle J Cell Science pmid 18827010 Tan FJ Fire AZ and Hill RB 2007 Regulation of apoptosis by C elegans CED 9 in the absence of the C terminal transmembrane domain Cell Death Differentiation pmid 17703231 Wells RC Picton LK Williams SC Tan FJ and

    Original URL path: http://emb.carnegiescience.edu/labs/frederick-tan (2013-06-13)
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  • Zheng Lab | Department of Embryology
    the Small GTPase Ran Science 284 1359 1362 5 Wiese C Zheng Y 2000 A New Function for the γ tubulin Ring Complex as a Microtubule Minus end Cap Nature Cell Biology 2 358 364 6 Wilde A Lizarraga S Zhang L Wiese C Gliksman N Walczak C Zheng Y 2001 Ran stimulates spindle assembly by changing microtubule dynamics and the balance of motor activities Nature Cell Biology 3 221 227 7 Wiese C Wilde A Adam S Moore M Merdes A Zheng Y 2001 Role of Importin bin Coupling Ran to Downstream Targets in Microtubule Assembly Science 291 653 656 8 Tsai MY Wiese C Cao K Martin OC Donovan P Ruderman J Prigent C Zheng Y 2003 A Ran signaling pathway mediated by the mitotic kinase Aurora A in spindle assembly Nature Cell Biology 5 242 248 9 Cao K Nakajima R Meyer HH Zheng Y 2003 The AAA ATPase Cdc48 p97 regulates spindle disassembly at the end of mitosis Cell 115 355 367 10 Li HY ZhengY 2004 Mitotic phosphorylation of RCC1 is essential for RanGTP gradient production and spindle assembly in mammalian cells Genes and Development 18 512 527 11 Zheng Y 2004 G Protein Control of Microtubule Assembly Annual Review of Cell and Developmental Biology 20 867 894 12 Tsai M Y Zheng Y 2005 Aurora A Kinase Coated Beads Function as Microtubule Organizing Centers and Enhance RanGTP Induced Spindle Assembly Current Biology 15 2156 2163 13 Vong QP Cao K Li HY Iglesias PA Zheng Y 2005 Chromosome Alignment and Segregation Regulated by Ubiquitination of Survivin Science 310 1499 1504 14 Tsai M Y Wang S Heidinger JM Shumaker D Adam SA Goldman RD Zheng Y 2006 A Mitotic Lamin B Matrix Induced by RanGTP Required for Spindle Assembly Science 311 1887 1893 15 Wiese C Zheng Y 2006 Microtubule nucleation γ tubulin and beyond Journal of Cell Science 119 4143 4153 16 Li M Tsai MY Lu B Chen R Yates III JR Zhu X Zheng Y 2009 A Requirement of Nudel and Dynein for Spindle Matrix Assembly during Spindle Morphogenesis Nature Cell Biology 11 247 256 17 Liu Z Zheng Y 2009 A Requirement for Epsin in Mitotic Membrane and Spindle Organization Journal of Cell Biology 186 473 480 18 Bembenek JN White JG Zheng Y 2010 A Role for Separase in the Regulation of RAB 11 positive Vesicles at the Cleavage Furrow and Midbody Current Biology 20 259 264 19 Zheng Y 2010 Mitotic spindle matrix may hold the answer to orchestrating cell division Nature Reviews Molecular Cell Biology 11 529 535 20 Goodman B Channels W Qiu M Iglesias P Yang G Zheng Y 2010 Lamin B3 counteracts the kinesin Eg5 to restrain spindle pole separation during spindle assembly J Biol Chem 285 35238 44 21 Poirier CC Zheng Y Iglesias PA 2010 Mitotic Membrane Helps to Focus and Stabilize the Mitotic Spindle Biophys J 99 3182 3190 22 Wang S Zheng Y 2011 Identification of a novel dynein binding

    Original URL path: http://emb.carnegiescience.edu/labs/yixian-zheng (2013-06-13)
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