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References


Caenorhabditis elegans

  • Blacque, O.E. et al. Functional Genomics of the Cilium, a Sensory Organelle. Current Biology 15:935-941 (2005). PMID: 15916950.
  • Cachero S, et al. The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons. PLoS Biol. 4:9 (2011). PMID: 21283833.
  • Chen, N. et al. Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biol. 7:R126 (2006). PMID: 17187676.
  • Efimenko, E. et al. Analysis of xbx genes in C. elegans. Development 132:1923-1934 (2005). PMID: 15790967.
  • Phirke, P. et al. Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport. Dev Biol. 357:235-247 (2011). PMID: 21740898.

Chlamydomonas reinhardtii

  • Boesger J et al. Analysis of flagellar phosphoproteins from Chlamydomonas reinhardtii. Eukaryot Cell. 8:922-32(2009). PMID: 19429781.
  • Hodges, ME. et al. Conservation of ciliary proteins in plants with no cilia. BMC Plant Biol 11:185 (2011). PMID: 22208660.
  • Keller, L.C. et al. Proteomic Analysis of Isolated Chlamydomonas Centrioles Reveals Orthologs of Ciliary-Disease Genes. Current Biology 15:1090-1098 (2005). PMID: 15964273.
  • Li, J.B. et al. Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene. Cell 117:541-552 (2004). PMID: 15137946.
  • Merchant,S.S. et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science, 318:245-250 (2007). PMID: 17932292.
  • Pazour, G.J. et al. Proteomic analysis of a eukaryotic cilium. J Cell Biol. 170:103-113 (2005). PMID: 15998802
  • Stolc, V. et al. Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes. Proc Natl Acad Sci U S A. 102:3703-3707 (2005). PMID: 15738400.

Ciona intestinalis

  • Nakachi, M. et al. Proteomic profiling reveals compartment-specific, novel functions of ascidian sperm proteins. Mol Reprod Dev. 78:529-549 (2011). PMID: 21710637.

Dictyostelium discoideum

  • Reinders,Y. et al. Identification of novel centrosomal proteins in Dictyostelium discoideum by comparative proteomic approaches. J. Proteome Res, 5:589-598 (2006). PMID: 16512674.

Drosophila melanogaster

  • Avidor-Reiss, T. et al. Decoding Cilia Function: Defining Specialized Genes Required for Compartmentalized Cilia Biogenesis. Cell 117:527-539 (2004). PMID: 15137945.
  • Bechstedt, S. et al. A double cortin containing microtubule-associated protein is implicated in mechanotransduction in Drosophila sensory cilia. Nat Commun 1:11 (2010). PMID: 20975667.
  • Cachero, S. et al. The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons. PLoS Biol. 9:e1000568 (2011). PMID: 21283833.
  • Dorus,S. et al. Genomic and functional evolution of the Drosophila melanogaster sperm proteome. Nat. Genet, 38:1440-1445 (2006). PMID: 17099714.
  • Hughes,J.R. et al. A microtubule interactome: complexes with roles in cell cycle and mitosis. PLoS Biol 6:e98 (2008). PMID: 18433294..
  • Laurencon, A. et al. Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species. Genome Biol. 8:R195 (2007). PMID: 17875208.
  • Müller H. et al. Proteomic and functional analysis of the mitotic Drosophila centrosome. EMBO J. 29:3344-3357 (2010). PMID: 20818332.

Giardia lamblia

  • Lauwaet, T. et al. Mining the Giardia genome and proteome for conserved and unique basal body proteins. Int J Parasitol. 41:1079-1092 (2010). PMID: 21723868.

Homo sapiens

  • Andersen, J.S. et al. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426:570-574 (2003). PMID: 14654843.
  • Datta, M. et al. Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: prediction and validation. BMC Genomics 12:463 (2011). PMID: 21943362.
  • Geremek, M. et al. Gene expression studies in cells from primary ciliary dyskinesia patients identify 208 potential ciliary genes. Hum Genet 129:283-293 (2011). PMID: 21136274.
  • Geremek, M. et al. Ciliary genes are down-regulated in bronchial tissue of primary ciliary dyskinesia patients. PLoS One. 9:e88216 (2014). PMID: 24516614.
  • Hoh, R.A. et al. Transcriptional program of ciliated epithelial cells reveals new cilium and centrosome components and links to human disease. PLoS One. 7:e35618 (2012). PMID: 23300604.
  • Ivliev, A.E. et al. Exploring the transcriptome of ciliated cells using in silico dissection of human tissues. PLoS One. 7:e52166 (2012). PMID: 22558177.
  • Jakobsen, L. et al. Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods. EMBO J. 30:1520-35 (2011). PMID: 21399614.
  • Kim J. et al. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature 464:1048-51 (2010). PMID: 20393563.
  • Kubo,A. et al. Sentan: a novel specific component of the apical structure of vertebrate motile cilia. Mol. Biol. Cell, 19:5338-5346 (2008). PMID: 18829862.
  • Martínez-Heredia,J. et al. Proteomic identification of human sperm proteins. Proteomics 6:4356-4369 (2006). PMID: 16819732..
  • Nogales-Cadenas,R. et al. CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Res, 37:D175-D180 (2006). PMID: 18971254.
  • Ostrowski, L.E. et al. A Proteomic Analysis of Human Cilia: Identification of Novel Components. Mol Cell Proteomics 1:451-465 (2002). PMID: 12169685.
  • Ross,A.J. et al. Transcriptional profiling of mucociliary differentiation in human airway epithelial cells. Am. J. Respir. Cell Mol. Biol, 37:169-185 (2007). PMID: 17413031.
  • Sauer,G. et al. Proteome analysis of the human mitotic spindle . Mol. Cell Proteomics, 4:35-43 (2005). PMID: 15561729.

Mus musculus

  • Baker,M.A. et al. The mouse sperm proteome characterized via IPG strip prefractionation and LC-MS/MS identification. Proteomics, Apr;8(8):1720-30 (2008) PMID: 18340633. .
  • Cao,W. et al. Proteomic profiling of accessory structures from the mouse sperm flagellum. Mol. Cell Proteomics, 5:801-810 (2006). PMID: 16452089.
  • Guo,X. et al. Proteomic analysis of proteins involved in spermiogenesis in mouse. J Proteome Res. 9:1246-1256 (2010). PMID: 20099899.
  • Huang,X. et al. Construction of a proteome profile and functional analysis of the proteins involved in the initiation of mouse spermatogenesis. J. Proteome Res 7:3435-3446 (2008). PMID: 18582094.
  • Ishikawa,H. et al. Proteomic analysis of mammalian primary cilia. Curr Biol 22:414-419 (2012). PMID: 22326026.
  • Liu, Q. et al. The Proteome of the Mouse Photoreceptor Sensory Cilium Complex. Mol Cell Proteomics. 6:1299-317 (2007). PMID: 17494944.
  • McClintock,T.S. et al. Tissue expression patterns identify mouse cilia genes. Physiol. Genomics, 32, 198-206 (2008). PMID: 17971504.

Naegleria gruberi

  • Fritz-Laylin,L.K. et Cande, W.Z. Ancestral centriole and flagella proteins identified by analysis of Naegleria differentiation. J Cell Sci., 123:4024-4031 (2010). PMID: 21045110.

Paramecium tetraurelia

  • Arnaiz,O. et al. Cildb: a knowledgebase for centrosomes and cilia. Database Vol. 2009:bap022;doi:10.1093 (2009). PMID: 20428338.
  • Arnaiz,O. et al. Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia BMC Genomics 11:547 (2010) PMID: 20932287.
  • Yano,J. et al. Proteomic analysis of the cilia membrane of Paramecium tetraurelia. J Proteomics 78:113-122 (2013) PMID: 23146917.

Rattus norvegicus

  • Mayer, U. et al. Proteomic Analysis of a Membrane Preparation from Rat Olfactory Sensory Cilia. Chem. Senses 33:145-162 (2008). PMID: 18032372.
  • Mayer U. et al. The proteome of rat olfactory sensory cilia. Proteomics 9:322-34 (2009). PMID: 19086097.
  • Baker,M.A. et al. The rat sperm proteome characterized via IPG strip prefractionation and LC-MS/MS identification. Proteomics, 8:2312-2321 (2008). PMID: 18528845..
  • Sakamoto,T. et al. Mass spectrometric analysis of microtubule co-sedimented proteins from rat brain. Genes Cells, 13:295-312 (2008). PMID: 18363962.

Saccharomyces cerevisiae

  • Wigge,P.A. et al. Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. J. Cell Biol, 141:967-977 (1998). PMID: 9585415.

Schmidtea mediterranea

  • Azimzadeh, J. et al. Centrosome loss in the evolution of planarians. Science 335:461-463 (2012). PMID: 22223737.

Trypanosoma brucei

  • Broadhead, R. et al. Flagellar motility is required for the viability of the bloodstream trypanosome. Nature 440:224-227 (2006). PMID: 16525475.

    Tetrahymena thermophila

    • Kilburn, C.L. et al. New Tetrahymena basal body protein components identify basal body domain structure. J Cell Biol. 178, 905-912(2007). PMID: 17785518.
    • Smith, J. et al. Robust Method for Proteome Analysis by MS/MS Using an Entire Translated Genome: Demonstration on the Ciliome of Tetrahymena thermophila. J. Proteome Res. 4, 909-919(2005). PMID: 15952738.

    Xenopus laevis

    • Stubbs,J.L. et al. The forkhead protein Foxj1 specifies node-like cilia in Xenopus and zebrafish embryos. Nat. Genet, 40, 1454-1460(2008). PMID: 19011629.

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