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Publications avant IGFL

Y. GHAVI-HELM - Developmental epigenomics

This folder holds the following references to publications, sorted by year and author.

There are 15 references in this bibliography folder.

Erceg, J, Pakozdi, T, Marco-Ferreres, R, Ghavi-Helm, Y, Girardot, C, Bracken, AP, and Furlong, EEM (2017).
Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements.
Genes Dev, 31(6):590-602.

Schauer, T, Ghavi-Helm, Y, Sexton, T, Albig, C, Regnard, C, Cavalli, G, Furlong, EE, and Becker, PB (2017).
Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation

Ghavi-Helm, Y, Klein, FA, Pakozdi, T, Ciglar, L, Noordermeer, D, Huber, W, and Furlong, EEM (2016).
Corrigendum: Enhancer loops appear stable during development and are associated with paused polymerase.
Nature, 537(7619):254.

Ghavi-Helm, Y, Zhao, B, and Furlong, EEM (2016).
Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila.
Methods Mol Biol, 1478:263-277.

Seyres, D, Ghavi-Helm, Y, Junion, G, Taghli-Lamallem, O, Guichard, C, Roder, L, Girardot, C, Furlong, EEM, and Perrin, L (2016).
Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network.
Development, 143(23):4533-4542.

Klein, FA, Pakozdi, T, Anders, S, Ghavi-Helm, Y, Furlong, EEM, and Huber, W (2015).
FourCSeq: analysis of 4C sequencing data.
Bioinformatics, 31(19):3085-91.

Ghavi-Helm, Y, Klein, FA, Pakozdi, T, Ciglar, L, Noordermeer, D, Huber, W, and Furlong, EEM (2014).
Enhancer loops appear stable during development and are associated with paused polymerase.
Nature, 512(7512):96-100.

Pinskaya, M, Ghavi-Helm, Y, Mariotte-Labarre, S, Morillon, A, Soutourina, J, and Werner, M (2014).
PHD and TFIIS-Like domains of the Bye1 transcription factor determine its multivalent genomic distribution.
PLoS One, 9(7):e102464.

Bonn, S, Zinzen, RP, Girardot, C, Gustafson, EH, Perez-Gonzalez, A, Delhomme, N, Ghavi-Helm, Y, Wilczynski, B, Riddell, A, and Furlong, EEM (2012).
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Nat Genet, 44(2):148-56.

Carriere, L, Graziani, S, Alibert, O, Ghavi-Helm, Y, Boussouar, F, Humbertclaude, H, Jounier, S, Aude, J, Keime, C, Murvai, J, Foglio, M, Gut, M, Gut, I, Lathrop, M, Soutourina, J, Gerard, M, and Werner, M (2012).
Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells.
Nucleic Acids Res, 40(1):270-83.

Ghavi-Helm, Y and Furlong, EEM (2012).
Analyzing transcription factor occupancy during embryo development using ChIP-seq.
Methods Mol Biol, 786:229-45.

Cazalet, C, Jarraud, S, Ghavi-Helm, Y, Kunst, F, Glaser, P, Etienne, J, and Buchrieser, C (2008).
Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species.
Genome Res, 18(3):431-41.

Esnault, C, Ghavi-Helm, Y, Brun, S, Soutourina, J, Van Berkum, N, Boschiero, C, Holstege, F, and Werner, M (2008).
Mediator-dependent recruitment of TFIIH modules in preinitiation complex.
Mol Cell, 31(3):337-46.

Ghavi-Helm, Y, Michaut, M, Acker, J, Aude, J, Thuriaux, P, Werner, M, and Soutourina, J (2008).
Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription.
Genes Dev, 22(14):1934-47.

Kwapisz, M, Wery, M, Despres, D, Ghavi-Helm, Y, Soutourina, J, Thuriaux, P, and Lacroute, F (2008).
Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways.
EMBO J, 27(18):2411-21.

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F. LEULIER - Functional genomics of host/intestinal bacteria interactions

This folder holds the following references to publications, sorted by year and author.

There are 23 references in this bibliography folder.

Meinander, A, Runchel, C, Tenev, T, Chen, L, Kim, CH, Ribeiro, PS, Broemer, M, Leulier, F, Zvelebil, M, Silverman, N, and Meier, P (2012).
Ubiquitylation of the initiator caspase DREDD is required for innate immune signalling
EMBO J, 31(12):2770-83.

Storelli, G, Defaye, A, Erkosar, B, Hols, P, Royet, J, and Leulier, F (2011).
Lactobacillus plantarum promotes Drosophila systemic growth by modulating hormonal signals through TOR-dependent nutrient sensing
Cell Metab, 14(3):403-14.

Defaye, A, Evans, I, Crozatier, M, Wood, W, Lemaitre, B, and Leulier, F (2009).
Genetic ablation of Drosophila phagocytes reveals their contribution to both development and resistance to bacterial infection
J Innate Immun, 1(4):322-34.

Erturk-Hasdemir, D, Broemer, M, Leulier, F, Lane, WS, Paquette, N, Hwang, D, Kim, CH, Stoven, S, Meier, P, and Silverman, N (2009).
Two roles for the Drosophila IKK complex in the activation of Relish and the induction of antimicrobial peptide genes
Proc Natl Acad Sci U S A, 106(24):9779-84.

Geuking, P, Narasimamurthy, R, Lemaitre, B, Basler, K, and Leulier, F (2009).
A non-redundant role for Drosophila Mkk4 and hemipterous/Mkk7 in TAK1-mediated activation of JNK
PLoS One, 4(11):e7709.

Leulier, F (2009).
Tuning down NF-kappaB signaling by DUBs: a fly case
Cell Host Microbe, 6(4):294-6.

Leulier, F and Royet, J (2009).
Maintaining immune homeostasis in fly gut
Nat Immunol, 10(9):936-8.

Leulier, F and Lemaitre, B (2008).
Toll-like receptors–taking an evolutionary approach
Nat Rev Genet, 9(3):165-78.

Lhocine, N, Ribeiro, PS, Buchon, N, Wepf, A, Wilson, R, Tenev, T, Lemaitre, B, Gstaiger, M, Meier, P, and Leulier, F (2008).
PIMS modulates immune tolerance by negatively regulating Drosophila innate immune signaling
Cell Host Microbe, 4(2):147-58.

Ribeiro, PS, Kuranaga, E, Tenev, T, Leulier, F, Miura, M, and Meier, P (2007).
DIAP2 functions as a mechanism-based regulator of drICE that contributes to the caspase activity threshold in living cells
J Cell Biol, 179(7):1467-80.

Leulier, F, Lhocine, N, Lemaitre, B, and Meier, P (2006).
The Drosophila inhibitor of apoptosis protein DIAP2 functions in innate immunity and is essential to resist gram-negative bacterial infection
Mol Cell Biol, 26(21):7821-31.

Leulier, F, Ribeiro, PS, Palmer, E, Tenev, T, Takahashi, K, Robertson, D, Zachariou, A, Pichaud, F, Ueda, R, and Meier, P (2006).
Systematic in vivo RNAi analysis of putative components of the Drosophila cell death machinery
Cell Death Differ, 13(10):1663-74.

Pili-Floury, S, Leulier, F, Takahashi, K, Saigo, K, Samain, E, Ueda, R, and Lemaitre, B (2004).
In vivo RNA interference analysis reveals an unexpected role for GNBP1 in the defense against Gram-positive bacterial infection in Drosophila adults
J Biol Chem, 279(13):12848-53.

Stenbak, CR, Ryu, JH, Leulier, F, Pili-Floury, S, Parquet, C, Herve, M, Chaput, C, Boneca, IG, Lee, WJ, Lemaitre, B, and Mengin-Lecreulx, D (2004).
Peptidoglycan molecular requirements allowing detection by the Drosophila immune deficiency pathway
J Immunol, 173(12):7339-48.

Leulier, F, Marchal, C, Miletich, I, Limbourg-Bouchon, B, Benarous, R, and Lemaitre, B (2003).
Directed expression of the HIV-1 accessory protein Vpu in Drosophila fat-body cells inhibits Toll-dependent immune responses
EMBO Rep, 4(10):976-81.

Leulier, F, Parquet, C, Pili-Floury, S, Ryu, JH, Caroff, M, Lee, WJ, Mengin-Lecreulx, D, and Lemaitre, B (2003).
The Drosophila immune system detects bacteria through specific peptidoglycan recognition
Nat Immunol, 4(5):478-84.

Khush, RS, Leulier, F, and Lemaitre, B (2002).
Immunology. Pathogen surveillance–the flies have it
Science, 296(5566):273-5.

Leulier, F and Lemaitre, B (2002).
Les récepteurs de la famille TOLL et l’activation de la réponse immunitaire innée
Bulletin de l'association des anciens élèves de l'Institut Pasteur, 171(mai-juin):78-83.

Leulier, F, Vidal, S, Saigo, K, Ueda, R, and Lemaitre, B (2002).
Inducible expression of double-stranded RNA reveals a role for dFADD in the regulation of the antibacterial response in Drosophila adults
Curr Biol, 12(12):996-1000.

Imboden, M, De Saint Jan, D, Leulier, F, Korn, H, Goblet, C, and Bregestovski, P (2001).
Isolation and characterization of an alpha 2-type zebrafish glycine receptor subunit
Neuroscience, 103(3):799-810.

Khush, RS, Leulier, F, and Lemaitre, B (2001).
Drosophila immunity: two paths to NF-kappaB
Trends Immunol, 22(5):260-4.

Vidal, S, Khush, RS, Leulier, F, Tzou, P, Nakamura, M, and Lemaitre, B (2001).
Mutations in the Drosophila dTAK1 gene reveal a conserved function for MAPKKKs in the control of rel/NF-kappaB-dependent innate immune responses
Genes Dev, 15(15):1900-12.

Leulier, F, Rodriguez, A, Khush, RS, Abrams, JM, and Lemaitre, B (2000).
The Drosophila caspase Dredd is required to resist gram-negative bacterial infection
EMBO Rep, 1(4):353-8.

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J. ENRIQUEZ - Development and function of the neuromuscular system

This folder holds the following references to publications, sorted by year and author.

There are 8 references in this bibliography folder.

Enriquez, J, Rio, LQ, Blazeski, R, Bellemin, S, Godement, P, Mason, C, and Mann, RS (2018).
Differing Strategies Despite Shared Lineages of Motor Neurons and Glia to Achieve Robust Development of an Adult Neuropil in Drosophila

Enriquez, J, Venkatasubramanian, L, Baek, M, Peterson, M, Aghayeva, U, and Mann, RS (2015).
Specification of individual adult motor neuron morphologies by combinatorial transcription factor codes
Neuron, 86(4):955-970.

Baek, M, Enriquez, J, and Mann, RS (2013).
Dual role for Hox genes and Hox co-factors in conferring leg motoneuron survival and identity in Drosophila
Development, 140(9):2027-38.

Boukhatmi, H, Frendo, JL, Enriquez, J, Crozatier, M, Dubois, L, and Vincent, A (2012).
Tup/Islet1 integrates time and position to specify muscle identity in Drosophila
Development, 139(19):3572-82.

Enriquez, J, de Taffin, M, Crozatier, M, Vincent, A, and Dubois, L (2012).
Combinatorial coding of Drosophila muscle shape by Collier and Nautilus
Dev Biol, 363(1):27-39.

Enriquez, J and Vincent, A (2010).
Segmental variations in the patterns of somatic muscles: what roles for Hox?
Fly (Austin), 4(3):249-52.

Enriquez, J, Boukhatmi, H, Dubois, L, Philippakis, AA, Bulyk, ML, Michelson, AM, Crozatier, M, and Vincent, A (2010).
Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo
Development, 137(3):457-66.

Dubois, L, Enriquez, J, Daburon, V, Crozet, F, Lebreton, G, Crozatier, M, and Vincent, A (2007).
Collier transcription in a single Drosophila muscle lineage: the combinatorial control of muscle identity
Development, 134(24):4347-55.

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N. GOUDEMAND - Biomodelling

This folder holds the following references to publications, sorted by year and author.

There are 36 references in this bibliography folder.

Brosse, M, Bucher, H, Bagherpour, B, Baud, A, Frisk, AM, Guodun, K, and Goudemand, N (2015).
Conodonts from the Early Triassic Microbialite of Guangxi (South China): Implications for the Definition of the Base of the Triassic System
Palaeontology, 58(3):563-584.

Hautmann, M, Bagherpour, B, Brosse, M, Frisk, A, Hofmann, R, Baud, A, Nutzel, A, Goudemand, N, and Bucher, H (2015).
Competition in slow motion: the unusual case of benthic marine communities in the wake of the end-Permian mass extinction
Palaeontology, 58(5):871-901.

Ovtcharova, M, Goudemand, N, Hammer, O, Guodun, K, Cordey, F, Galfetti, T, Schaltegger, U, and Bucher, H (2015).
Developing a strategy for accurate definition of a geological boundary through radio-isotopic and biochronological dating: The Early-Middle Triassic boundary (South China)
Earth-Science Reviews, 146:65-76.

Goudemand, N, Romano, C, Brayard, A, Hochuli, PA, and Bucher, H (2013).
Comment on "Lethally Hot Temperatures During the Early Triassic Greenhouse"
Science, 339(6123).

Romano, C, Goudemand, N, Vennemann, TW, Ware, D, Schneebeli-Hermann, E, Hochuli, PA, Bruhwiler, T, Brinkmann, W, and Bucher, H (2013).
Climatic and biotic upheavals following the end-Permian mass extinction
Nature Geoscience, 6(1):57-60.

Schneebeli-Hermann, E, Kurschner, WM, Hochuli, PA, Ware, D, Weissert, H, Bernasconi, SM, Roohi, G, ur-Rehman, K, Goudemand, N, and Bucher, H (2013).
Evidence for atmospheric carbon injection during the end-Permian extinction
Geology, 41(5):579-582.

Bruhwiler, T, Bucher, H, Goudemand, N, and Galfetti, T (2012).
Smithian (Early Triassic) ammonoid faunas from Exotic Blocks from Oman: taxonomy and biochronology
Palaeontographica Abteilung a-Palaozoologie-Stratigraphie, 296(1-4):3-107.

Goudemand, N, Orchard, MJ, Bucher, H, and Jenks, J (2012).
The elusive origin of Chiosella timorensis (Conodont Triassic)
Geobios, 45(2):199-207.

Goudemand, N, Orchard, MJ, Tafforeau, P, Urdy, S, Bruhwiler, T, Brayard, A, Galfetti, T, and Bucher, H (2012).
Early Triassic conodont clusters from South China: revision of the architecture of the 15 element apparatuses of the superfamily Gondolelloidea
Palaeontology, 55:1021-1034.

Schneebeli-Hermann, E, Hochuli, PA, Bucher, H, Goudemand, N, Bruhwiler, T, and Galfetti, T (2012).
Palynology of the Lower Triassic succession of Tulong, South Tibet - Evidence for early recovery of gymnosperms
Palaeogeography Palaeoclimatology Palaeoecology, 339:12-24.

Schneebeli-Hermann, E, Kurschner, WM, Hochuli, PA, Bucher, H, Ware, D, Goudemand, N, and Roohi, G (2012).
Palynofacies analysis of the Permian-Triassic transition in the Amb section (Salt Range, Pakistan): Implications for the anoxia on the South Tethyan Margin
Journal of Asian Earth Sciences, 60:225-234.

Brayard, A, Vennin, E, Olivier, N, Bylund, KG, Jenks, J, Stephen, DA, Bucher, H, Hofmann, R, Goudemand, N, and Escarguel, G (2011).
Transient metazoan reefs in the aftermath of the end-Permian mass extinction
Nature Geoscience, 4(10):693-697.

Forel, MB, Crasquin, S, Bruhwiler, T, Goudemand, N, Bucher, H, Baud, A, and Randon, C (2011).
Ostracod recovery after Permian-Triassic boundary mass-extinction: The south Tibet record
Palaeogeography Palaeoclimatology Palaeoecology, 308(1-2):160-170.

Goudemand, N, Orchard, MJ, Urdy, S, Bucher, H, and Tafforeau, P (2011).
Synchrotron-aided reconstruction of the conodont feeding apparatus and implications for the mouth of the first vertebrates
Proceedings of the National Academy of Sciences of the United States of America, 108(21):8720-8724.

Hautmann, M, Bucher, H, Bruhwiler, T, Goudemand, N, Kaim, A, and Nutzel, A (2011).
An unusually diverse mollusc fauna from the earliest Triassic of South China and its implications for benthic recovery after the end-Permian biotic crisis
Geobios, 44(1):71-85.

Hofmann, R, Goudemand, N, Wasmer, M, Bucher, H, and Hautmann, M (2011).
New trace fossil evidence for an early recovery signal in the aftermath of the end-Permian mass extinction
Palaeogeography Palaeoclimatology Palaeoecology, 310(3-4):216-226.

Monnet, C, Klug, C, Goudemand, N, De Baets, K, and Bucher, H (2011).
Quantitative biochronology of Devonian ammonoids from Morocco and proposals for a refined unitary association method
Lethaia, 44(4):469-489.

Bruhwiler, T, Bucher, H, and Goudemand, N (2010).
Smithian (Early Triassic) ammonoids from Tulong, South Tibet
Geobios, 43(4):403-431.

Bruhwiler, T, Bucher, H, Brayard, A, and Goudemand, N (2010).
High-resolution biochronology and diversity dynamics of the Early Triassic ammonoid recovery: The Smithian faunas of the Northern Indian Margin
Palaeogeography Palaeoclimatology Palaeoecology, 297(2):491-501.

Bruhwiler, T, Ware, D, Bucher, H, Krystyn, L, and Goudemand, N (2010).
New Early Triassic ammonoid faunas from the Dienerian/Smithian boundary beds at the Induan/Olenekian GSSP candidate at Mud (Spiti, Northern India)
Journal of Asian Earth Sciences, 39(6):724-739.

Kaim, A, Nutzel, A, Bucher, H, Bruhwiler, T, and Goudemand, N (2010).
Early Triassic (Late Griesbachian) gastropods from South China (Shanggan, Guangxi)
Swiss Journal of Geosciences, 103(1):121-128.

Urdy, S, Goudemand, N, Bucher, H, and Chirat, R (2010).
Allometries and the Morphogenesis of the Molluscan Shell: A Quantitative and Theoretical Model
Journal of Experimental Zoology Part B-Molecular and Developmental Evolution, 314b(4):280-302.

Urdy, S, Goudemand, N, Bucher, H, and Chirat, R (2010).
Growth-Dependent Phenotypic Variation of Molluscan Shells: Implications for Allometric Data Interpretation
Journal of Experimental Zoology Part B-Molecular and Developmental Evolution, 314b(4):303-326.

Brayard, A, Escarguel, G, Bucher, H, Monnet, C, Bruhwiler, T, Goudemand, N, Galfetti, T, and Guex, J (2009).
Good Genes and Good Luck: Ammonoid Diversity and the End-Permian Mass Extinction
Science, 325(5944):1118-1121.

Bruhwiler, T, Goudemand, N, Galfetti, T, Bucher, H, Baud, A, Ware, D, Hermann, E, Hochuli, PA, and Martini, R (2009).
The Lower Triassic sedimentary and carbon isotope records from Tulong (South Tibet) and their significance for Tethyan palaeoceanography
Sedimentary Geology, 222(3-4):314-332.

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A. KHILA - Developmental genomics and evolution

This folder holds the following references to publications, sorted by year and author.

There are 16 references in this bibliography folder.

Khila, A, Abouheif, E, and Rowe, L (2014).
Comparative functional analyses of ultrabithorax reveal multiple steps and paths to diversification of legs in the adaptive radiation of semi-aquatic insects
Evolution, 68(8):2159-70.

Khila, A, Abouheif, E, and Rowe, L (2012).
Function, developmental genetics, and fitness consequences of a sexually antagonistic trait
Science, 336(6081):585-9.

Rajakumar, R, San Mauro, D, Dijkstra, MB, Huang, MH, Wheeler, DE, Hiou-Tim, F, Khila, A, Cournoyea, M, and Abouheif, E (2012).
Ancestral developmental potential facilitates parallel evolution in ants
Science, 335(6064):79-82.

Khila, A, Abouheif, E, and Rowe, L (2011).
Eco-Evo-Devo: Lessons from Semi-Aquatic Bugs
Developmental Biology, 356(1):107-107.

Lynch, JA, Ozuak, O, Khila, A, Abouheif, E, Desplan, C, and Roth, S (2011).
The phylogenetic origin of oskar coincided with the origin of maternally provisioned germ plasm and pole cells at the base of the Holometabola
PLoS Genet, 7(4):e1002029.

Smith, CD, Zimin, A, Holt, C, Abouheif, E, Benton, R, Cash, E, Croset, V, Currie, CR, Elhaik, E, Elsik, CG, Fave, MJ, Fernandes, V, Gadau, J, Gibson, JD, Graur, D, Grubbs, KJ, Hagen, DE, Helmkampf, M, Holley, JA, Hu, H, Viniegra, AS, Johnson, BR, Johnson, RM, Khila, A, Kim, JW, Laird, J, Mathis, KA, Moeller, JA, Munoz-Torres, MC, Murphy, MC, Nakamura, R, Nigam, S, Overson, RP, Placek, JE, Rajakumar, R, Reese, JT, Robertson, HM, Smith, CR, Suarez, AV, Suen, G, Suhr, EL, Tao, S, Torres, CW, van Wilgenburg, E, Viljakainen, L, Walden, KK, Wild, AL, Yandell, M, Yorke, JA, and Tsutsui, ND (2011).
Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)
Proc Natl Acad Sci U S A, 108(14):5673-8.

Smith, CR, Smith, CD, Robertson, HM, Helmkampf, M, Zimin, A, Yandell, M, Holt, C, Hu, H, Abouheif, E, Benton, R, Cash, E, Croset, V, Currie, CR, Elhaik, E, Elsik, CG, Fave, MJ, Fernandes, V, Gibson, JD, Graur, D, Gronenberg, W, Grubbs, KJ, Hagen, DE, Viniegra, AS, Johnson, BR, Johnson, RM, Khila, A, Kim, JW, Mathis, KA, Munoz-Torres, MC, Murphy, MC, Mustard, JA, Nakamura, R, Niehuis, O, Nigam, S, Overson, RP, Placek, JE, Rajakumar, R, Reese, JT, Suen, G, Tao, S, Torres, CW, Tsutsui, ND, Viljakainen, L, Wolschin, F, and Gadau, J (2011).
Draft genome of the red harvester ant Pogonomyrmex barbatus
Proc Natl Acad Sci U S A, 108(14):5667-72.

Khila, A and Abouheif, E (2010).
Evaluating the role of reproductive constraints in ant social evolution
Philos Trans R Soc Lond B Biol Sci, 365(1540):617-30.

Shbailat, SJ, Khila, A, and Abouheif, E (2010).
Correlations between spatiotemporal changes in gene expression and apoptosis underlie wing polyphenism in the ant Pheidole morrisi
Evol Dev, 12(6):580-91.

Khila, A and Abouheif, E (2009).
In situ hybridization on ant ovaries and embryos
Cold Spring Harb Protoc, 2009(7):pdb prot5250.

Khila, A, Abouheif, E, and Rowe, L (2009).
Evolution of a novel appendage ground plan in water striders is driven by changes in the Hox gene Ultrabithorax
PLoS Genet, 5(7):e1000583.

Khila, A and Abouheif, E (2008).
Reproductive constraint is a developmental mechanism that maintains social harmony in advanced ant societies
Proc Natl Acad Sci U S A, 105(46):17884-9.

Grbic, M, Khila, A, Lee, KZ, Bjelica, A, Grbic, V, Whistlecraft, J, Verdon, L, Navajas, M, and Nagy, L (2007).
Mity model: Tetranychus urticae, a candidate for chelicerate model organism
Bioessays, 29(5):489-96.

Khila, A and Grbic, M (2007).
Gene silencing in the spider mite Tetranychus urticae: dsRNA and siRNA parental silencing of the Distal-less gene
Dev Genes Evol, 217(3):241-51.

El Haidani, AKAHAHAVA and K.S., I (2005).
Study of the olive fruits infestation by Bactrocera oleae in the area of fez in Morocco and their fertility in the laboratory.
Mor. J. Biol., 1:19-29.

Khila, A, El Haidani, A, Vincent, A, Payre, F, and Souda, SI (2003).
The dual function of ovo/shavenbaby in germline and epidermis differentiation is conserved between Drosophila melanogaster and the olive fruit fly Bactrocera oleae
Insect Biochem Mol Biol, 33(7):691-9.

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M. AVEROF - Biologie comparative du développement et de la régénération

This folder holds the following references to publications, sorted by year and author.

There are 32 references in this bibliography folder.

El-Sherif, E, Averof, M, and Brown, SJ (2012).
A segmentation clock operating in blastoderm and germband stages of Tribolium development
Development, 139(23):4341-6.

Sarrazin, AF, Peel, AD, and Averof, M (2012).
A segmentation clock with two-segment periodicity in insects
Science, 336(6079):338-41.

Kontarakis, Z, Konstantinides, N, Pavlopoulos, A, and Averof, M (2011).
Reconfiguring gene traps for new tasks using iTRAC
Fly (Austin), 5(4):352-5.

Kontarakis, Z, Pavlopoulos, A, Kiupakis, A, Konstantinides, N, Douris, V, and Averof, M (2011).
A versatile strategy for gene trapping and trap conversion in emerging model organisms
Development, 138(12):2625-30.

Douris, V, Telford, MJ, and Averof, M (2010).
Evidence for multiple independent origins of trans-splicing in Metazoa
Mol Biol Evol, 27(3):684-93.

Lynch, JA, Peel, AD, Drechsler, A, Averof, M, and Roth, S (2010).
EGF signaling and the origin of axial polarity among the insects
Curr Biol, 20(11):1042-7.

Peel, AD and Averof, M (2010).
Early asymmetries in maternal transcript distribution associated with a cortical microtubule network and a polar body in the beetle Tribolium castaneum
Dev Dyn, 239(11):2875-87.

Schinko, JB, Weber, M, Viktorinova, I, Kiupakis, A, Averof, M, Klingler, M, Wimmer, EA, and Bucher, G (2010).
Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters
BMC Dev Biol, 10:53.

Liubicich, DM, Serano, JM, Pavlopoulos, A, Kontarakis, Z, Protas, ME, Kwan, E, Chatterjee, S, Tran, KD, Averof, M, and Patel, NH (2009).
Knockdown of Parhyale Ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology
Proc Natl Acad Sci U S A, 106(33):13892-6.

Pavlopoulos, A, Kontarakis, Z, Liubicich, DM, Serano, JM, Akam, M, Patel, NH, and Averof, M (2009).
Probing the evolution of appendage specialization by Hox gene misexpression in an emerging model crustacean
Proc Natl Acad Sci U S A, 106(33):13897-902.

Copf, T, Rabet, N, and Averof, M (2006).
Knockdown of spalt function by RNAi causes de-repression of Hox genes and homeotic transformations in the crustacean Artemia franciscana
Dev Biol, 298(1):87-94.

Franch-Marro, X, Martin, N, Averof, M, and Casanova, J (2006).
Association of tracheal placodes with leg primordia in Drosophila and implications for the origin of insect tracheal systems
Development, 133(5):785-90.

Kontarakis, Z, Copf, T, and Averof, M (2006).
Expression of hunchback during trunk segmentation in the branchiopod crustacean Artemia franciscana
Dev Genes Evol, 216(2):89-93.

Pavlopoulos, A and Averof, M (2005).
Establishing genetic transformation for comparative developmental studies in the crustacean Parhyale hawaiensis
Proc Natl Acad Sci U S A, 102(22):7888-93.

Copf, T, Schroder, R, and Averof, M (2004).
Ancestral role of caudal genes in axis elongation and segmentation
Proc Natl Acad Sci U S A, 101(51):17711-5.

Pavlopoulos, A, Berghammer, AJ, Averof, M, and Klingler, M (2004).
Efficient transformation of the beetle Tribolium castaneum using the Minos transposable element: quantitative and qualitative analysis of genomic integration events
Genetics, 167(2):737-46.

Copf, T, Rabet, N, Celniker, SE, and Averof, M (2003).
Posterior patterning genes and the identification of a unique body region in the brine shrimp Artemia franciscana
Development, 130(24):5915-27.

Averof, M (2002).
Arthropod Hox genes: insights on the evolutionary forces that shape gene functions
Curr Opin Genet Dev, 12(4):386-92.

Damen, WG, Saridaki, T, and Averof, M (2002).
Diverse adaptations of an ancestral gill: a common evolutionary origin for wings, breathing organs, and spinnerets
Curr Biol, 12(19):1711-6.

Pavlopoulos, A and Averof, M (2002).
Developmental evolution: Hox proteins ring the changes
Curr Biol, 12(8):R291-3.

Ligoxygakis, P, Strigini, M, and Averof, M (2001).
Specification of left-right asymmetry in the embryonic gut of Drosophila
Development, 128(7):1171-4.

Averof, M, Rokas, A, Wolfe, KH, and Sharp, PM (2000).
Evidence for a high frequency of simultaneous double-nucleotide substitutions
Science, 287(5456):1283-6.

Averof, M (1998).
Evolutionary biology. Origin of the spider's head
Nature, 395(6701):436-7.

Averof, M (1997).
Arthropod evolution: same Hox genes, different body plans
Curr Biol, 7(10):R634-6.

Averof, M and Cohen, SM (1997).
Evolutionary origin of insect wings from ancestral gills
Nature, 385(6617):627-30.

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S. MERABET - Ontogenesis and molecular interactions

This folder holds the following references to publications, sorted by year and author.

There are 21 references in this bibliography folder.

Boube, M, Hudry, B, Immarigeon, C, Carrier, Y, Bernat-Fabre, S, Merabet, S, Graba, Y, Bourbon, HM, and Cribbs, DL (2014).
Drosophila melanogaster Hox transcription factors access the RNA polymerase II machinery through direct homeodomain binding to a conserved motif of mediator subunit Med19
PLoS Genet, 10(5):e1004303.

Merabet, S and Hudry, B (2013).
Hox transcriptional specificity despite a single class of cofactors: are flexible interaction modes the key? Plasticity in Hox/PBC interaction modes as a common molecular strategy for shaping Hox transcriptional activities
Bioessays, 35(2):88-92.

Rivas, ML, Espinosa-Vazquez, JM, Sambrani, N, Greig, S, Merabet, S, Graba, Y, and Hombria, JC (2013).
Antagonism versus cooperativity with TALE cofactors at the base of the functional diversification of Hox protein function
PLoS Genet, 9(2):e1003252.

Sambrani, N, Hudry, B, Maurel-Zaffran, C, Zouaz, A, Mishra, R, Merabet, S, and Graba, Y (2013).
Distinct molecular strategies for Hox-mediated limb suppression in Drosophila: from cooperativity to dispensability/antagonism in TALE partnership
PLoS Genet, 9(3):e1003307.

Hudry, B, Remacle, S, Delfini, MC, Rezsohazy, R, Graba, Y, and Merabet, S (2012).
Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors
PLoS Biol, 10(6):e1001351.

Hudry, B, Viala, S, Graba, Y, and Merabet, S (2011).
Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay
BMC Biol, 9:5.

Merabet, S and Hudry, B (2011).
On the border of the homeotic function: re-evaluating the controversial role of cofactor-recruiting motifs: the role of cofactor-recruiting motifs in conferring Hox evolutionary flexibility may critically depend on the protein environment
Bioessays, 33(7):499-507.

Merabet, S, Litim-Mecheri, I, Karlsson, D, Dixit, R, Saadaoui, M, Monier, B, Brun, C, Thor, S, Vijayraghavan, K, Perrin, L, Pradel, J, and Graba, Y (2011).
Insights into Hox protein function from a large scale combinatorial analysis of protein domains
PLoS Genet, 7(10):e1002302.

Saadaoui, M, Merabet, S, Litim-Mecheri, I, Arbeille, E, Sambrani, N, Damen, W, Brena, C, Pradel, J, and Graba, Y (2011).
Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity
Proc Natl Acad Sci U S A, 108(6):2276-81.

Merabet, S, Sambrani, N, Pradel, J, and Graba, Y (2010).
Regulation of Hox activity: insights from protein motifs
Adv Exp Med Biol, 689:3-16.

Merabet, S, Hudry, B, Saadaoui, M, and Graba, Y (2009).
Classification of sequence signatures: a guide to Hox protein function
Bioessays, 31(5):500-11.

Merabet, S, Saadaoui, M, Sambrani, N, Hudry, B, Pradel, J, Affolter, M, and Graba, Y (2007).
A unique Extradenticle recruitment mode in the Drosophila Hox protein Ultrabithorax
Proc Natl Acad Sci U S A, 104(43):16946-51.

Ebner, A, Cabernard, C, Affolter, M, and Merabet, S (2005).
Recognition of distinct target sites by a unique Labial/Extradenticle/Homothorax complex
Development, 132(7):1591-600.

Merabet, S, Ebner, A, and Affolter, M (2005).
The Drosophila Extradenticle and Homothorax selector proteins control branchless/FGF expression in mesodermal bridge-cells
EMBO Rep, 6(8):762-8.

Merabet, S, Hombria, JC, Hu, N, Pradel, J, and Graba, Y (2005).
Hox-controlled reorganisation of intrasegmental patterning cues underlies Drosophila posterior spiracle organogenesis
Development, 132(13):3093-102.

Merabet, S, Pradel, J, and Graba, Y (2005).
Getting a molecular grasp on Hox contextual activity
Trends Genet, 21(9):477-80.

Grienenberger, A, Merabet, S, Manak, J, Iltis, I, Fabre, A, Berenger, H, Scott, MP, Pradel, J, and Graba, Y (2003).
Tgfbeta signaling acts on a Hox response element to confer specificity and diversity to Hox protein function
Development, 130(22):5445-55.

Merabet, S, Kambris, Z, Capovilla, M, Berenger, H, Pradel, J, and Graba, Y (2003).
The hexapeptide and linker regions of the AbdA Hox protein regulate its activating and repressive functions
Dev Cell, 4(5):761-8.

Merabet, S, Catala, F, Pradel, J, and Graba, Y (2002).
A green fluorescent protein reporter genetic screen that identifies modifiers of Hox gene function in the Drosophila embryo
Genetics, 162(1):189-202.

Merabet, S, Grienenberger, A, Pradel, J, and Graba, Y (2001).
Modes d'action des protéines Hox: des interrogations nouvelles.
Médecine/Sciences, 7(17):781-786.

Chauvet, S, Merabet, S, Bilder, D, Scott, MP, Pradel, J, and Graba, Y (2000).
Distinct hox protein sequences determine specificity in different tissues
Proc Natl Acad Sci U S A, 97(8):4064-9.

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K. PADMANABHAN - Molecular and epigenetic regulation of biological clocks

This folder holds the following references to publications, sorted by year and author.

There are 10 references in this bibliography folder.

Ors, A, Papin, C, Favier, B, Roulland, Y, Dalkara, D, Ozturk, M, Hamiche, A, Dimitrov, S, and Padmanabhan, K (2017).
Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts
Biochem Cell Biol, 95(4):491-499.

Padmanabhan, K and Billaud, M (2017).
Desynchronization of Circadian Clocks in Cancer: A Metabolic and Epigenetic Connection
Front Endocrinol (Lausanne), 8:136.

Roulland, Y, Ouararhni, K, Naidenov, M, Ramos, L, Shuaib, M, Syed, SH, Lone, IN, Boopathi, R, Fontaine, E, Papai, G, Tachiwana, H, Gautier, T, Skoufias, D, Padmanabhan, K, Bednar, J, Kurumizaka, H, Schultz, P, Angelov, D, Hamiche, A, and Dimitrov, S (2016).
The Flexible Ends of CENP-A Nucleosome Are Required for Mitotic Fidelity
Mol Cell, 63(4):674-85.

Obri, A, Ouararhni, K, Papin, C, Diebold, ML, Padmanabhan, K, Marek, M, Stoll, I, Roy, L, Reilly, PT, Mak, TW, Dimitrov, S, Romier, C, and Hamiche, A (2014).
ANP32E is a histone chaperone that removes H2A.Z from chromatin
Nature, 505(7485):648-53.

Padmanabhan, K, Robles, MS, Westerling, T, and Weitz, CJ (2012).
Feedback regulation of transcriptional termination by the mammalian circadian clock PERIOD complex
Science, 337(6094):599-602.

Cao, Q, Padmanabhan, K, and Richter, JD (2010).
Pumilio 2 controls translation by competing with eIF4E for 7-methyl guanosine cap recognition
RNA, 16(1):221-7.

Robles, MS, Boyault, C, Knutti, D, Padmanabhan, K, and Weitz, CJ (2010).
Identification of RACK1 and protein kinase Calpha as integral components of the mammalian circadian clock
Science, 327(5964):463-6.

Tung, JJ, Padmanabhan, K, Hansen, DV, Richter, JD, and Jackson, PK (2007).
Translational unmasking of Emi2 directs cytostatic factor arrest in meiosis II
Cell Cycle, 6(6):725-31.

Padmanabhan, K and Richter, JD (2006).
Regulated Pumilio-2 binding controls RINGO/Spy mRNA translation and CPEB activation
Genes Dev, 20(2):199-209.

Padmanabhan, K and Smith, TJ (2002).
A preliminary investigation of modified alginates as a matrix for gene transfection in a HeLa cell model
Pharm Dev Technol, 7(1):97-101.

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F. RUGGIERO - Matrix biology and pathology

This folder holds the following references to publications, sorted by year and author.

There are 38 references in this bibliography folder.

Baas, D, Malbouyres, M, Haftek-Terreau, Z, Le Guellec, D, and Ruggiero, F (2009).
Craniofacial cartilage morphogenesis requires zebrafish col11a1 activity
Matrix Biol, 28(8):490-502.

Bader, HL, Keene, DR, Charvet, B, Veit, G, Driever, W, Koch, M, and Ruggiero, F (2009).
Zebrafish collagen XII is present in embryonic connective tissue sheaths (fascia) and basement membranes
Matrix Biol, 28(1):32-43.

Faye, C, Moreau, C, Chautard, E, Jetne, R, Fukai, N, Ruggiero, F, Humphries, MJ, Olsen, BR, and Ricard-Blum, S (2009).
Molecular interplay between endostatin, integrins, and heparan sulfate
J Biol Chem, 284(33):22029-40.

Tristan, A, Benito, Y, Montserret, R, Boisset, S, Dusserre, E, Penin, F, Ruggiero, F, Etienne, J, Lortat-Jacob, H, Lina, G, Bowden, MG, and Vandenesch, F (2009).
The signal peptide of Staphylococcus aureus panton valentine leukocidin LukS component mediates increased adhesion to heparan sulfates
PLoS One, 4(4):e5042.

Pagnon-Minot, A, Malbouyres, M, Haftek-Terreau, Z, Kim, HR, Sasaki, T, Thisse, C, Thisse, B, Ingham, PW, Ruggiero, F, and Le Guellec, D (2008).
Collagen XV, a novel factor in zebrafish notochord differentiation and muscle development
Dev Biol, 316(1):21-35.

Ruggiero, F and Koch, M (2008).
Making recombinant extracellular matrix proteins
Methods, 45(1):75-85.

Bonod-Bidaud, C, Beraud, M, Vaganay, E, Delacoux, F, Font, B, Hulmes, DJ, and Ruggiero, F (2007).
Enzymatic cleavage specificity of the proalpha1(V) chain processing analysed by site-directed mutagenesis
Biochem J, 405(2):299-306.

Roulet, M, Ruggiero, F, Karsenty, G, and LeGuellec, D (2007).
A comprehensive study of the spatial and temporal expression of the col5a1 gene in mouse embryos: a clue for understanding collagen V function in developing connective tissues
Cell Tissue Res, 327(2):323-32.

Torbet, J, Malbouyres, M, Builles, N, Justin, V, Roulet, M, Damour, O, Oldberg, A, Ruggiero, F, and Hulmes, DJ (2007).
Orthogonal scaffold of magnetically aligned collagen lamellae for corneal stroma reconstruction
Biomaterials, 28(29):4268-76.

Torbet, J, Malbouyres, M, Builles, N, Justin, V, Roulet, M, Damour, O, Oldberg, A, Ruggiero, F, and Hulmes, DJ (2007).
Tissue engineering of the cornea: orthogonal scaffold of magnetically aligned collagen lamellae for corneal stroma reconstruction
Conf Proc IEEE Eng Med Biol Soc, 2007:6400.

Vrana, NE, Builles, N, Kocak, H, Gulay, P, Justin, V, Malbouyres, M, Ruggiero, F, Damour, O, and Hasirci, V (2007).
EDC/NHS cross-linked collagen foams as scaffolds for artificial corneal stroma
J Biomater Sci Polym Ed, 18(12):1527-45.

Ricard-Blum, S, Beraud, M, Raynal, N, Farndale, RW, and Ruggiero, F (2006).
Structural requirements for heparin/heparan sulfate binding to type V collagen
J Biol Chem, 281(35):25195-204.

Ricard-Blum, S, Peel, LL, Ruggiero, F, and Freeman, NJ (2006).
Dual polarization interferometry characterization of carbohydrate-protein interactions
Anal Biochem, 352(2):252-9.

Colige, A, Ruggiero, F, Vandenberghe, I, Dubail, J, Kesteloot, F, Van Beeumen, J, Beschin, A, Brys, L, Lapiere, CM, and Nusgens, B (2005).
Domains and maturation processes that regulate the activity of ADAMTS-2, a metalloproteinase cleaving the aminopropeptide of fibrillar procollagens types I-III and V
J Biol Chem, 280(41):34397-408.

Moali, C, Font, B, Ruggiero, F, Eichenberger, D, Rousselle, P, Francois, V, Oldberg, A, Bruckner-Tuderman, L, and Hulmes, DJ (2005).
Substrate-specific modulation of a multisubstrate proteinase. C-terminal processing of fibrillar procollagens is the only BMP-1-dependent activity to be enhanced by PCPE-1
J Biol Chem, 280(25):24188-94.

Ricard-Blum, S and Ruggiero, F (2005).
The collagen superfamily: from the extracellular matrix to the cell membrane
Pathol Biol (Paris), 53(7):430-42.

Ruggiero, F, Roulet, M, and Bonod-Bidaud, C (2005).
[Dermis collagens: beyond their structural properties]
J Soc Biol, 199(4):301-11.

Chanut-Delalande, H, Bonod-Bidaud, C, Cogne, S, Malbouyres, M, Ramirez, F, Fichard, A, and Ruggiero, F (2004).
Development of a functional skin matrix requires deposition of collagen V heterotrimers
Mol Cell Biol, 24(13):6049-57.

Bernocco, S, Steiglitz, BM, Svergun, DI, Petoukhov, MV, Ruggiero, F, Ricard-Blum, S, Ebel, C, Geourjon, C, Deleage, G, Font, B, Eichenberger, D, Greenspan, DS, and Hulmes, DJ (2003).
Low resolution structure determination shows procollagen C-proteinase enhancer to be an elongated multidomain glycoprotein
J Biol Chem, 278(9):7199-205.

Fichard, A, Chanut-Delalande, H, and Ruggiero, F (2003).
[The Ehlers-Danlos syndrome: the extracellular matrix scaffold in question]
Med Sci (Paris), 19(4):443-52.

Perret, S, Eble, JA, Siljander, PR, Merle, C, Farndale, RW, Theisen, M, and Ruggiero, F (2003).
Prolyl hydroxylation of collagen type I is required for efficient binding to integrin alpha 1 beta 1 and platelet glycoprotein VI but not to alpha 2 beta 1
J Biol Chem, 278(32):29873-9.

Chanut-Delalande, H, Fichard, A, Bernocco, S, Garrone, R, Hulmes, DJ, and Ruggiero, F (2001).
Control of heterotypic fibril formation by collagen V is determined by chain stoichiometry
J Biol Chem, 276(26):24352-9.

Kessler, E, Fichard, A, Chanut-Delalande, H, Brusel, M, and Ruggiero, F (2001).
Bone morphogenetic protein-1 (BMP-1) mediates C-terminal processing of procollagen V homotrimer
J Biol Chem, 276(29):27051-7.

Perret, S, Merle, C, Bernocco, S, Berland, P, Garrone, R, Hulmes, DJ, Theisen, M, and Ruggiero, F (2001).
Unhydroxylated triple helical collagen I produced in transgenic plants provides new clues on the role of hydroxyproline in collagen folding and fibril formation
J Biol Chem, 276(47):43693-8.

Delacoux, F, Fichard, A, Cogne, S, Garrone, R, and Ruggiero, F (2000).
Unraveling the amino acid sequence crucial for heparin binding to collagen V
J Biol Chem, 275(38):29377-82.

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JM VANACKER - Physiopathology of orphan nuclear receptors

This folder holds the following references to publications, sorted by year and author.

There are 29 references in this bibliography folder.

Bardet, PL, Laudet, V, and Vanacker, JM (2006).
Studying non-mammalian models? Not a fool's ERRand!
Trends Endocrinol Metab, 17(4):166-71.

Castet, A, Herledan, A, Bonnet, S, Jalaguier, S, Vanacker, JM, and Cavailles, V (2006).
Receptor-interacting protein 140 differentially regulates estrogen receptor-related receptor transactivation depending on target genes
Mol Endocrinol, 20(5):1035-47.

Bardet, PL, Horard, B, Laudet, V, and Vanacker, JM (2005).
The ERRalpha orphan nuclear receptor controls morphogenetic movements during zebrafish gastrulation
Dev Biol, 281(1):102-11.

Bardet, PL, Schubert, M, Horard, B, Holland, LZ, Laudet, V, Holland, ND, and Vanacker, JM (2005).
Expression of estrogen-receptor related receptors in amphioxus and zebrafish: implications for the evolution of posterior brain segmentation at the invertebrate-to-vertebrate transition
Evol Dev, 7(3):223-33.

Bardet, PL, Obrecht-Pflumio, S, Thisse, C, Laudet, V, Thisse, B, and Vanacker, JM (2004).
Cloning and developmental expression of five estrogen-receptor related genes in the zebrafish
Dev Genes Evol, 214(5):240-9.

Horard, B, Castet, A, Bardet, PL, Laudet, V, Cavailles, V, and Vanacker, JM (2004).
Dimerization is required for transactivation by estrogen-receptor-related (ERR) orphan receptors: evidence from amphioxus ERR
J Mol Endocrinol, 33(2):493-509.

Horard, B, Rayet, B, Triqueneaux, G, Laudet, V, Delaunay, F, and Vanacker, JM (2004).
Expression of the orphan nuclear receptor ERRalpha is under circadian regulation in estrogen-responsive tissues
J Mol Endocrinol, 33(1):87-97.

Safi, R, Bertrand, S, Marchand, O, Duffraisse, M, de Luze, A, Vanacker, JM, Maraninchi, M, Margotat, A, Demeneix, B, and Laudet, V (2004).
The axolotl (Ambystoma mexicanum), a neotenic amphibian, expresses functional thyroid hormone receptors
Endocrinology, 145(2):760-72.

Horard, B and Vanacker, JM (2003).
Estrogen receptor-related receptors: orphan receptors desperately seeking a ligand
J Mol Endocrinol, 31(3):349-57.

Vlaeminck-Guillem, V, Vanacker, JM, Verger, A, Tomavo, N, Stehelin, D, Laudet, V, and Duterque-Coquillaud, M (2003).
Mutual repression of transcriptional activation between the ETS-related factor ERG and estrogen receptor
Oncogene, 22(50):8072-84.

Bardet, PL, Horard, B, Robinson-Rechavi, M, Laudet, V, and Vanacker, JM (2002).
Characterization of oestrogen receptors in zebrafish (Danio rerio)
J Mol Endocrinol, 28(3):153-63.

De Mendonca, RL, Bouton, D, Bertin, B, Escriva, H, Noel, C, Vanacker, JM, Cornette, J, Laudet, V, and Pierce, RJ (2002).
A functionally conserved member of the FTZ-F1 nuclear receptor family from Schistosoma mansoni
Eur J Biochem, 269(22):5700-11.

de Mendonca, RL, Escriva, H, Bouton, D, Zelus, D, Vanacker, JM, Bonnelye, E, Cornette, J, Pierce, RJ, and Laudet, V (2000).
Structural and functional divergence of a nuclear receptor of the RXR family from the trematode parasite Schistosoma mansoni
Eur J Biochem, 267(11):3208-19.

Langlois, MC, Vanacker, JM, Holland, ND, Escriva, H, Queva, C, Laudet, V, and Holland, LZ (2000).
Amphicoup-TF, a nuclear orphan receptor of the lancelet Branchiostoma floridae, is implicated in retinoic acid signalling pathways
Dev Genes Evol, 210(10):471-82.

Soullier, S, Jay, P, Poulat, F, Vanacker, JM, Berta, P, and Laudet, V (1999).
Diversification pattern of the HMG and SOX family members during evolution
J Mol Evol, 48(5):517-27.

Vanacker, JM, Bonnelye, E, Chopin-Delannoy, S, Delmarre, C, Cavailles, V, and Laudet, V (1999).
Transcriptional activities of the orphan nuclear receptor ERR alpha (estrogen receptor-related receptor-alpha)
Mol Endocrinol, 13(5):764-73.

Vanacker, JM, Pettersson, K, Gustafsson, JA, and Laudet, V (1999).
Transcriptional targets shared by estrogen receptor- related receptors (ERRs) and estrogen receptor (ER) alpha, but not by ERbeta
EMBO J, 18(15):4270-9.

Vanacker, JM, Bonnelye, E, Delmarre, C, and Laudet, V (1998).
Activation of the thyroid hormone receptor alpha gene promoter by the orphan nuclear receptor ERR alpha
Oncogene, 17(19):2429-35.

Vanacker, JM, Delmarre, C, Guo, X, and Laudet, V (1998).
Activation of the osteopontin promoter by the orphan nuclear receptor estrogen receptor related alpha
Cell Growth Differ, 9(12):1007-14.

Bonnelye, E, Vanacker, JM, Dittmar, T, Begue, A, Desbiens, X, Denhardt, DT, Aubin, JE, Laudet, V, and Fournier, B (1997).
The ERR-1 orphan receptor is a transcriptional activator expressed during bone development
Mol Endocrinol, 11(7):905-16.

Bonnelye, E, Vanacker, JM, Spruyt, N, Alric, S, Fournier, B, Desbiens, X, and Laudet, V (1997).
Expression of the estrogen-related receptor 1 (ERR-1) orphan receptor during mouse development
Mech Dev, 65(1-2):71-85.

Vanacker, JM, Corbau, R, Adelmant, G, Perros, M, Laudet, V, and Rommelaere, J (1996).
Transactivation of a cellular promoter by the NS1 protein of the parvovirus minute virus of mice through a putative hormone-responsive element
J Virol, 70(4):2369-77.

Perros, M, Deleu, L, Vanacker, JM, Kherrouche, Z, Spruyt, N, Faisst, S, and Rommelaere, J (1995).
Upstream CREs participate in the basal activity of minute virus of mice promoter P4 and in its stimulation in ras-transformed cells
J Virol, 69(9):5506-15.

Bonnelye, E, Vanacker, JM, Desbiens, X, Begue, A, Stehelin, D, and Laudet, V (1994).
Rev-erb beta, a new member of the nuclear receptor superfamily, is expressed in the nervous system during chicken development
Cell Growth Differ, 5(12):1357-65.

Perros, M, Spegelaere, P, Dupont, F, Vanacker, JM, and Rommelaere, J (1994).
Cruciform structure of a DNA motif of parvovirus minute virus of mice (prototype strain) involved in the attenuation of gene expression
J Gen Virol, 75 ( Pt 10):2645-53.

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L. VIRIOT - Evo-devo of vertebrate dentition

This folder holds the following references to publications, sorted by year and author.

There are 24 references in this bibliography folder.

Charles, C and Viriot, L (2007).
Abnormal and supernumerary teeth in the dentition of a greater Egyptian jerboa Jaculus orientalis (Dipodoidea, Rodentia)
Mammalia, 71(1-2):95-97.

Charles, C, Jaeger, JJ, Michaux, J, and Viriot, L (2007).
Dental microwear in relation to changes in the direction of mastication during the evolution of Myodonta (Rodentia, Mammalia)
Naturwissenschaften, 94(1):71-75.

Charles, C, Pantalacci, S, Peterkova, R, Peterka, M, Laudet, V, and Viriot, L (2007).
Disruption of the palatal rugae pattern in Tabby (eda) mutant mice
European Journal of Oral Sciences, 115(6):441-448.

Merceron, G, Blondel, C, Viriot, L, Koufos, GD, and de Bonis, L (2007).
Dental microwear analysis of bovids from the Vallesian (late Miocene) of Axios Valley in Greece: reconstruction of the habitat of Ouranopithecus macedoniensis (Primates, Hominoidea)
Geodiversitas, 29(3):421-433.

Viriot, L, Vignaud, P, Boisserie, JR, Fara, E, Guy, F, Lihoreau, F, Lehmann, T, Schuster, M, Blondel, C, Duringer, P, Likius, A, Mackaye, HT, Otero, O, and Brunet, M (2007).
Late Miocene to Early Pliocene Chadian vertebrate faunas: paleoenvironmental and paleobiogeographical implications.
Naturwissenschaften, 94(71-75).

Lihoreau, F, Boisserie, JR, Viriot, L, Coppens, Y, Likius, A, Mackaye, HT, Tafforeau, P, Vignaud, P, and Brunet, M (2006).
Anthracothere dental anatomy reveals a late Miocene Chado-Libyan bioprovince
Proceedings of the National Academy of Sciences of the United States of America, 103(23):8763-8767.

Merceron, G, Blondel, C, De Bonis, L, Koufos, GD, and Viriot, L (2005).
A new method of dental microwear analysis: Application to extant primates and Ouranopithecus macedoniensis (Late Miocene of Greece)
Palaios, 20(6):551-561.

Merceron, G, de Bonis, L, Viriot, L, and Blondel, C (2005).
Dental microwear of the late Miocene bovids of northern Greece: Vallesian/Turolian environmental changes and disappearance of Ouranopithecus macedoniensis?
Bulletin De La Societe Geologique De France, 176(5):475-484.

Merceron, G, de Bonis, L, Viriot, L, and Blondel, C (2005).
Dental microwear of fossil bovids from northern Greece: paleoenvironmental conditions in the eastern Mediterranean during the Messinian
Palaeogeography Palaeoclimatology Palaeoecology, 217(3-4):173-185.

Peterkova, R, Lesot, H, Viriot, L, and Peterka, M (2005).
The supernumerary cheek tooth in tabby/EDA mice - a reminiscence of the premolar in mouse ancestors
Archives of Oral Biology, 50(2):219-225.

Denys, C, Viriot, L, Daams, R, Pelaez-Campomanes, P, Vignaud, P, Andossa, L, and Brunet, M (2003).
A new Pliocene xerine sciurid (rodentia) from Kossom Bougoudi, Chad
Journal of Vertebrate Paleontology, 23(3):676-687.

Guy, F, Brunet, M, Schmittbuhl, M, and Viriot, L (2003).
New approaches in hominoid taxonomy: Morphometrics
American Journal of Physical Anthropology, 121(3):198-218.

Brunet, M, Fronty, P, Sapanet, M, de Bonis, L, and Viriot, L (2002).
Enamel hypoplasia in a Pliocene hominid from Chad
Connective Tissue Research, 43(2-3):94-97.

Brunet, M, Guy, F, Pilbeam, D, Mackaye, HT, Likius, A, Ahounta, D, Beauvilain, A, Blondel, C, Bocherens, H, Boisserie, JR, De Bonis, L, Coppens, Y, Dejax, J, Denys, C, Duringer, P, Eisenmann, VR, Fanone, G, Fronty, P, Geraads, D, Lehmann, T, Lihoreau, F, Louchart, A, Mahamat, A, Merceron, G, Mouchelin, G, Otero, O, Campomanes, PP, De Leon, MP, Rage, JC, Sapanet, M, Schuster, M, Sudre, J, Tassy, P, Valentin, X, Vignaud, P, Viriot, L, Zazzo, A, and Zollikofer, C (2002).
A new hominid from the Upper Miocene of Chad, central Africa
Nature, 418(6894):145-151.

de Bonis, L and Viriot, L (2002).
Teeth and paleoanthropology
Connective Tissue Research, 43(2-3):87-93.

Peterkova, R, Peterka, M, Viriot, L, and Lesot, H (2002).
Development of the vestigial tooth primordia as part of mouse odontogenesis
Connective Tissue Research, 43(2-3):120-128.

Vignaud, P, Duringer, P, Mackaye, HT, Likius, A, Blondel, C, Boisserie, JR, de Bonis, L, Eisenmann, V, Etienne, ME, Geraads, D, Guy, F, Lehmann, T, Lihoreau, F, Lopez-Martinez, N, Mourer-Chauvire, C, Otero, O, Rage, JC, Schuster, M, Viriot, L, Zazzo, A, and Brunet, M (2002).
Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad
Nature, 418(6894):152-155.

Viriot, L, Peterkova, R, Peterka, M, and Lesot, H (2002).
Evolutionary implications of the occurrence of two vestigial tooth germs during early odontogenesis in the mouse lower jaw
Connective Tissue Research, 43(2-3):129-133.

Peterkova, R, Peterka, M, Viriot, L, and Lesot, H (2000).
Dentition development and budding morphogenesis
Journal of Craniofacial Genetics and Developmental Biology, 20(4):158-172.

Viriot, L, Lesot, H, Vonesch, JL, Ruch, JV, Peterka, M, and Peterkova, R (2000).
The presence of rudimentary odontogenic structures in the mouse embryonic mandible requires reinterpretation of developmental control of first lower molar histomorphogenesis
International Journal of Developmental Biology, 44(2):233-240.

Courant, F, Brunet-Lecomte, P, Volobouev, V, Chaline, J, Quere, JP, Nadachowski, A, Montuire, S, Bao, G, Viriot, L, Rausch, R, Erbajeva, M, Shi, D, and Giraudoux, P (1999).
Karyological and dental identification of Microtus limnophilus in a large focus of alveolar echinococcosis (Gansu, China)
C R Acad Sci III, 322(6):473-80.

Lesot, H, Peterkova, R, Schmitt, R, Meyer, JM, Viriot, L, Vonesch, JL, Senger, B, Peterka, M, and Ruch, JV (1999).
Initial features of the inner dental epithelium histo-morphogenesis in the first lower molar in mouse
Int J Dev Biol, 43(3):245-54.

Lesot, H, Peterkova, R, Viriot, L, Vonesch, JL, Tureckova, J, Peterka, M, and Ruch, JV (1998).
Early stages of tooth morphogenesis in mouse analyzed by 3D reconstructions
Eur J Oral Sci, 106 Suppl 1:64-70.

Viriot, L, Peterkova, R, Vonesch, JL, Peterka, M, Ruch, JV, and Lesot, H (1997).
Mouse molar morphogenesis revisited by three-dimensional reconstruction. III. Spatial distribution of mitoses and apoptoses up to bell-staged first lower molar teeth
Int J Dev Biol, 41(5):679-90.

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J.-N. VOLFF - Fish evolutionary genomics

This folder holds the following references to publications, sorted by year and author.

There are 64 references in this bibliography folder.

Bollig, F, Mehringer, R, Perner, B, Hartung, C, Schafer, M, Schartl, M, Volff, JN, Winkler, C, and Englert, C (2006).
Identification and comparative expression analysis of a second wt1 gene in zebrafish
Dev Dyn, 235(2):554-61.

Froschauer, A, Braasch, I, and Volff, JN (2006).
Fish genomes, comparative genomics and vertebrate evolution
Current Genomics, 7(1):43-57.

Renn, J, Schaedel, M, Volff, JN, Goerlich, R, Schartl, M, and Winkler, C (2006).
Dynamic expression of sparc precedes formation of skeletal elements in the Medaka (Oryzias latipes)
Gene, 372:208-18.

Schultheis, C, Zhou, Q, Froschauer, A, Nanda, I, Selz, Y, Schmidt, C, Matschl, S, Wenning, M, Veith, AM, Naciri, M, Hanel, R, Braasch, I, Dettai, A, Bohne, A, Ozouf-Costaz, C, Chilmonczyk, S, Segurens, B, Couloux, A, Bernard-Samain, S, Schmid, M, Schartl, M, and Volff, JN (2006).
Molecular analysis of the sex-determining region of the platyfish Xiphophorus maculatus
Zebrafish, 3(3):299-309.

Veith, AM, Klattig, J, Dettai, A, Schmidt, C, Englert, C, and Volff, JN (2006).
Male-biased expression of X-chromosomal DM domain-less Dmrt8 genes in the mouse
Genomics, 88(2):185-95.

Veith, AM, Schafer, M, Kluver, N, Schmidt, C, Schultheis, C, Schartl, M, Winkler, C, and Volff, JN (2006).
Tissue-specific expression of dmrt genes in embryos and adults of the platyfish Xiphophorus maculatus
Zebrafish, 3(3):325-37.

Volff, JN (2006).
Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes
Bioessays, 28(9):913-22.

Zhou, Q, Froschauer, A, Schultheis, C, Schmidt, C, Bienert, GP, Wenning, M, Dettai, A, and Volff, JN (2006).
Helitron Transposons on the Sex Chromosomes of the Platyfish Xiphophorus maculatus and Their Evolution in Animal Genomes
Zebrafish, 3(1):39-52.

Brandt, J, Schrauth, S, Veith, AM, Froschauer, A, Haneke, T, Schultheis, C, Gessler, M, Leimeister, C, and Volff, JN (2005).
Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals
Gene, 345(1):101-11.

Brandt, J, Veith, AM, and Volff, JN (2005).
A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes
Cytogenet Genome Res, 110(1-4):307-17.

Fischer, C, Bouneau, L, Coutanceau, JP, Weissenbach, J, Ozouf-Costaz, C, and Volff, JN (2005).
Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish Tetraodon nigroviridis
Cytogenet Genome Res, 110(1-4):522-36.

Schafer, M, Kinzel, D, Neuner, C, Schartl, M, Volff, JN, and Winkler, C (2005).
Hedgehog and retinoid signalling confines nkx2.2b expression to the lateral floor plate of the zebrafish trunk
Mech Dev, 122(1):43-56.

Volff, JN (2005).
Genome evolution and biodiversity in teleost fish
Heredity (Edinb), 94(3):280-94.

Elmasri, H, Liedtke, D, Lucking, G, Volff, JN, Gessler, M, and Winkler, C (2004).
her7 and hey1, but not lunatic fringe show dynamic expression during somitogenesis in medaka (Oryzias latipes)
Gene Expr Patterns, 4(5):553-9.

Fischer, C, Bouneau, L, Coutanceau, JP, Weissenbach, J, Volff, JN, and Ozouf-Costaz, C (2004).
Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis
Gene, 336(2):175-83.

Gomez, A, Volff, JN, Hornung, U, Schartl, M, and Wellbrock, C (2004).
Identification of a second egfr gene in Xiphophorus uncovers an expansion of the epidermal growth factor receptor family in fish
Mol Biol Evol, 21(2):266-75.

Jaillon, O, Aury, JM, Brunet, F, Petit, JL, Stange-Thomann, N, Mauceli, E, Bouneau, L, Fischer, C, Ozouf-Costaz, C, Bernot, A, Nicaud, S, Jaffe, D, Fisher, S, Lutfalla, G, Dossat, C, Segurens, B, Dasilva, C, Salanoubat, M, Levy, M, Boudet, N, Castellano, S, Anthouard, V, Jubin, C, Castelli, V, Katinka, M, Vacherie, B, Biemont, C, Skalli, Z, Cattolico, L, Poulain, J, De Berardinis, V, Cruaud, C, Duprat, S, Brottier, P, Coutanceau, JP, Gouzy, J, Parra, G, Lardier, G, Chapple, C, McKernan, KJ, McEwan, P, Bosak, S, Kellis, M, Volff, JN, Guigo, R, Zody, MC, Mesirov, J, Lindblad-Toh, K, Birren, B, Nusbaum, C, Kahn, D, Robinson-Rechavi, M, Laudet, V, Schachter, V, Quetier, F, Saurin, W, Scarpelli, C, Wincker, P, Lander, ES, Weissenbach, J, and Roest Crollius, H (2004).
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
Nature, 431(7011):946-57.

Kazianis, S, Nairn, RS, Walter, RB, Johnston, DA, Kumar, J, Trono, D, Della-Coletta, L, Gimenez-Conti, I, Rains, JD, Williams, EL, Pino, BM, Mamerow, MM, Kochan, KJ, Schartl, M, Vielkind, JR, Volff, JN, Woolcock, B, and Morizot, DC (2004).
The genetic map of Xiphophorus fishes represented by 24 multipoint linkage groups
Zebrafish, 1(3):287-304.

Meierjohann, S, Schartl, M, and Volff, JN (2004).
Genetic, biochemical and evolutionary facets of Xmrk-induced melanoma formation in the fish Xiphophorus
Comp Biochem Physiol C Toxicol Pharmacol, 138(3):281-9.

Volff, JN, Lehrach, H, Reinhardt, R, and Chourrout, D (2004).
Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica
Mol Biol Evol, 21(11):2022-33.

Bouneau, L, Fischer, C, Ozouf-Costaz, C, Froschauer, A, Jaillon, O, Coutanceau, JP, Korting, C, Weissenbach, J, Bernot, A, and Volff, JN (2003).
An active non-LTR retrotransposon with tandem structure in the compact genome of the pufferfish Tetraodon nigroviridis
Genome Res, 13(7):1686-95.

Veith, AM, Froschauer, A, Korting, C, Nanda, I, Hanel, R, Schmid, M, Schartl, M, and Volff, JN (2003).
Cloning of the dmrt1 gene of Xiphophorus maculatus: dmY/dmrt1Y is not the master sex-determining gene in the platyfish
Gene, 317(1-2):59-66.

Volff, JN and Schartl, M (2003).
Evolution of signal transduction by gene and genome duplication in fish
J Struct Funct Genomics, 3(1-4):139-50.

Volff, JN, Bouneau, L, Ozouf-Costaz, C, and Fischer, C (2003).
Diversity of retrotransposable elements in compact pufferfish genomes
Trends Genet, 19(12):674-8.

Volff, JN, Kondo, M, and Schartl, M (2003).
Medaka dmY/dmrt1Y is not the universal primary sex-determining gene in fish
Trends Genet, 19(4):196-9.

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