Latest Publication:

  • FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development.

    Köstler SA, Alaybeyoğlu B, Weichenberger C, Çelik A.

    F1000Research 2015, 4:1484-9.
    Understanding the regulatory mechanisms governing eye development of the model organism Drosophila melanogaster (D. m.) requires structured knowledge of the involved genes and proteins, their interactions, and dynamic expression patterns. Especially the latter information is however to a large extent scattered throughout the literature. FlyOde is an online platform for the systematic assembly of data on D.m. eye development. It consists of data on eye development obtained from the literature, and a web interface for users to interactively display these data as a gene regulatory network. Our manual curation process provides high standard structured data, following a specifically designed ontology. Visualization of gene interactions provides an overview of network topology, and filtering according to user-defined expression patterns makes it a versatile tool for daily tasks, as demonstrated by usage examples. Users are encouraged to submit additional data via a simple online form.

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    Fly lab - Publications


    Selected Publications:

    • Çevrim BÇ, Mika K, Callaerts P, and Çelik A (2017) The cell adhesion molecule Unzipped mediates neuron-neuron and neuron-glia interactions to control mushroom body development. submitted to Scientific Reports
    • Köstler S, Alaybeyoğlu B, Weichenberger CX, and Çelik A (2015) FlyOde – a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. F1000Research 4:1484-9
    • Potier D, Davie K, Hulselmans G, Sanchez MN, Haagen L, Huynh-Thu VA, Koldere D, Çelik A, Geurts P, Christiaens V, and Aerts S (2014) Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. Cell Reports 9:1-14.
    • Tsachaki M, Mishra AK, Rister J, Shy D, Ng J, Çelik A, and Sprecher SG (2013) Interplay of Sens and Php13 controls photoreceptor development, differentiation and transformation in Drosophila. PLoS Genetics 9(12):e1004027.
    • Li X, Erclik T, Chen Z, Venkatesh S, Morante J, Çelik A, and Desplan C, (2013) Temporal specification of neuroblasts controls neuronal diversity in the Drosophila medulla. Nature 498(7455):456-62.
    • Vasiliauskas D, Mazzoni EO, Sprecher SG, Johnston RJ Jr, Lidder P, Vogt N, Çelik A, and Desplan C (2011) Feedback from Rhodopsin controls Rhodopsin exclusion in Drosophila R8 photoreceptors. Nature 479(7371):108-12.
    • Mazzoni EO, Çelik A, Wernet MF, Vasiliauskas D, Cook TA, Johnston RJ, Pichaud F, and Desplan C (2008) Iroquois-Complex genes induce co-expression of visual pigments in Drosophila. PLoS Biology 6(4):e9.
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      Primer:
      Stavenga DG, and Arikawa K (2008) One Rhodopsin per Photoreceptor: Iro-C Genes Break the Rule. PLoS Biology 6(4):e115.
    • Wernet MF, Çelik A, Mikeladze-Dvali T, and Desplan C (2007) Generation of uniform fly retinas. Current Biology 17(23):r1002-3.
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    • Wernet MF*, Mazzoni EO*, Çelik A*, Duncan DM, Duncan I, and Desplan C (2006) Stochastic spineless expression creates the retinal mosaic for colour vision. Nature 440(7081):174-180. *equal contribution
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      Featured in
      Faculty1000 ("9") and
      Hummel T, and Klaembt C (2006) Eye development: random precision in color vision. Current Biology 16(10):R361-R363.




    REVIEWS

    • Şahin HB, and Çelik A (2013) Drosophila eye development and photoreceptor specification eLS, John Wiley & Sons, Ltd: Chichester. DOI:10.1002/9780470015902.a0001147.pub2.
    • Morante J, Desplan C, and Çelik A (2007) Generating patterned arrays of photoreceptors. Current Opinion in Developmental Genetics 17(4):314-9. Review
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    • Fuss S, Çelik A, and Desplan C (2007) Olfactory identity kicked up a Notch. Nature Neuroscience 10(2):138-140. News&Views
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    • Mazzoni EO, Desplan C, and Çelik A (2004) 'One receptor' rules in sensory neurons. Developmental Neuroscience 26(5-6):388-95. Review
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    BOOK CONTRIBUTIONS

    • Çelik A (2012) Amphibians and Fish Developmental Biology

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