Mongin E, Auer TO, Bourrat F, Gruhl F, Dewar K, Blanchette M, Wittbrodt J, Ettwiller L. Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PLoS ONE (2011) vol. 6 (5) pp. e19747
Castro DS, Martynoga B, Parras C, Ramesh V, Pacary E, Johnston C, Drechsel D, Lebel-Potter M, Garcia LG, Hunt C, Dolle D, Bithell A, Ettwiller L, Buckley N, Guillemot F. A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets. Genes Dev (2011) vol. 25 (9) pp. 930-45.
Ruf S., Symmons O., Vural Uslu V., Dolle D., Hot C., Ettwiller L., Spitz F. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet (2011) vol. 43 (4) pp. 379-86. Faculty of 1000 Recommended paper.
Weger B.D., Sahinbas M., Otto G., Mracek P., Armant O., Dolle D., Lahiri K., Vallone D., Ettwiller L., Geisler R., Foulkes N.S., Dickmeis T. The light responsive transcriptome of the zebrafish: function and regulation. PLoS ONE (2011) vol. 6 (2) pp. e17080
Haudry Y., Ramialison M., Paten B., Wittbrodt J., Ettwiller L. Using Trawler_standalone to discover nucleotide signatures in DNA and RNA sequences. Nature protocol (2010) vol. 5, 323–334.
Ettwiller L., Budd A., Spitz F., Wittbrodt J. Evolutionary Analysis of mammalian Gene batteries reveals both a stable core of target genes and dynamic regulatory sequences. Genome Biol. (2008) vol. 9 (12) pp. R172
Ramialison M, Bajoghli B, Aghaallaei N, Ettwiller L, Gaudan S, Wittbrodt B, Czerny T, Wittbrodt J. Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools. Genome Biol (2008) vol. 9 (10) pp. R145
Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J. In vivo validation of a computationally predicted conserved Ath5 target gene set. PLoS Genet. 2007 Sep;3(9):1661-71. Epub 2007 Aug 1.
Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat Methods. 2007 Jul;4(7):563-5. Epub 2007 Jun 24.
Sakkou M, Wiedmer P, Anlag K, Hamm A, Seuntjens E, Ettwiller L, Tschoep MH, Treier M. A role for brain-specific homeobox factor bsx in the control of hyperphagia and locomotory behavior. Cell Metab. 2007 Jun;5(6):450-63. Faculty of 1000 Recommended paper
Ettwiller L, Veitia RA.Protein coevolution and isoexpression in yeast macromolecular complexes.Comp Funct Genomics. 2007;:58721. Epub 2007 Jan 8.
Potier MC, Rivals I, Mercier G, Ettwiller L, Moldrich RX, Laffaire J, Personnaz L, Rossier J, Dauphinot L.Transcriptional disruptions in Down syndrome: a case study in the Ts1Cje mouse cerebellum during post-natal development. J Neurochem. 2006 Jan 17; [Epub ahead of print]
Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol.2005;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, Potier MC. The cerebellar transcriptome during postnatal development of the Ts1Cje mouse, a segmental trisomy model for Down syndrome. Hum Mol Genet. 2005 Feb 1;14(3):373-84. Epub 2004 Dec 8.
Ettwiller L, Paten B. Functional genomics: Guilt by multiple association. Heredity. 2004 April 92, 481–482.
Ettwiller LM, Rung J, Birney E. Discovering novel cis-regulatory motifs using functional networks.Genome Res. 2003 May;13(5):883-95.
Ureta-Vidal A, Ettwiller L, Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet. 2003 Apr;4(4):251-62. Review.
Bateman A, Birney E, Cerruti L, Durbin R, Ettwiller L, Eddy S, Griffiths-Jones S, Howe K, Marshall M, Sonnhammer ELL. The Pfam protein families database. Nucleic Acids Res. 2002; vol. 30 (1) pp. 276-80
Chiang LW, Grenier JM, Ettwiller L, Jenkins LP, Ficenec D, Martin J, Jin F, DiStefano PS, Wood A. An orchestrated gene expression component of neuronal programmed cell death revealed by cDNA array analysis. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2814-9.