Publications

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Haudry, Y., Ramialison, M., Paten, B., Wittbrodt, J., and Ettwiller, L. (2009). Using Trawler_standalone to discover nucleotide signatures in DNA and RNA sequences. Accepted Nature protocol.

Ettwiller, L., Budd, A., Spitz, F., and Wittbrodt, J. (2008). Evolutionary Analysis of mammalian Gene batteries reveals both a stable core of target genes and dynamic regulatory sequences. Genome Biol. vol. 9 (12) pp. R172

Ramialison, M, Bajoghli, B, Aghaallaei, N, Ettwiller, L, Gaudan, S, Wittbrodt, B, Czerny, T, and Wittbrodt, J. (2008). Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools. Genome Biol vol. 9 (10) pp. R145

Del Bene, F, Ettwiller, L, Skowronska-Krawczyk, D, Baier, H, Matter, JM, Birney, E, and Wittbrodt, J. (2007). In vivo validation of a computationally predicted conserved Ath5 target gene set. PLoS Genet. Sep;3(9):1661-71. Epub 2007 Aug 1.

Ettwiller, L, Paten, B, Ramialison, M, Birney, E, and Wittbrodt, J. (2007). Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat Methods. Jul;4(7):563-5. Epub 2007 Jun 24.

Sakkou, M, Wiedmer, P, Anlag, K, Hamm, A, Seuntjens, E, Ettwiller, L, Tschoep, MH, and Treier, M (2007). A role for brain-specific homeobox factor bsx in the control of hyperphagia and locomotory behavior. Cell Metab. Jun;5(6):450-63.

Ettwiller, L, and Veitia, RA (2007). Protein coevolution and isoexpression in yeast macromolecular complexes. Comp Funct Genomics. ;:58721. Epub 2007 Jan 8.

Potier, MC, Rivals, I, Mercier, G, Ettwiller, L, Moldrich, RX, Laffaire, J, Personnaz, L, Rossier, J, and Dauphinot, L.(2006). Transcriptional disruptions in Down syndrome: a case study in the Ts1Cje mouse cerebellum during post-natal development. J Neurochem. Jan 17; [Epub ahead of print]

Ettwiller, L, Paten, B, Souren, M, Loosli, F, Wittbrodt, J, and Birney, E. (2005). The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol. 6(12):R104. Epub 2005 Dec 2.

Dauphinot, L, Lyle, R, Rivals, I, Dang, MT, Moldrich, RX, Golfier, G, Ettwiller, L, Toyama, K, Rossier, J, Personnaz, L, Antonarakis, SE, Epstein, CJ, Sinet, PM, and Potier, MC. (2005). The cerebellar transcriptome during postnatal development of the Ts1Cje mouse, a segmental trisomy model for Down syndrome. Hum Mol Genet. Feb 1;14(3):373-84. Epub 2004 Dec 8.

Ettwiller, L, Rung, J, and Birney, E. (2003). Discovering novel cis-regulatory motifs using functional networks. Genome Res. May;13(5):883-95.

Bateman, A, Birney, E, Cerruti, L, Durbin, R, Ettwiller, L, Eddy, S, Griffiths-Jones, S, Howe, K, Marshall, M, and Sonnhammer ELL. (2002).The Pfam protein families database. Nucleic Acids Res. vol. 30 (1) pp. 276-80

Chiang, LW, Grenier, JM, Ettwiller, L, Jenkins, LP, Ficenec, D, Martin, J, Jin, F, DiStefano, PS, and Wood, A. (2001). An orchestrated gene expression component of neuronal programmed cell death revealed by cDNA array analysis. Proc Natl Acad Sci U S A. Feb 27;98(5):2814-9.

Ureta-Vidal, A, Ettwiller, L, and Birney, E. (2003). Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet. Apr;4(4):251-62. Review.

Ettwiller, L, and Paten, B. (2004). Functional genomics: Guilt by multiple association. Heredity. April 92, 481–482.