My main scientific interest is focused on biology or life science. Trying to understand biological entities with informatics tool is my daily job. I have learned several programming languages (C, Java...) but my preference is set to Tcl/Tk a wonderful and flexible scripting language. My complete CV is available in english or in french in pdf format.
[Scientific career]
My scientific career started in 2002 during my post-master in advanced specialized studies (DESS) entitled "Complementary Skills in Informatics" where I was involved in comparative analysis of prokaryotic genomes responsible of diarrhea. I continued in the same lab (LBGI in IGBMC, Strasbourg) as a PhD student from 2002 to 2006 combining bioinformatics and microarrays developments implemented to study the different cytoskeletons. My PhD was co-directed by Olivier Poch (LBGI, Strasbourg) and Evelyne Friederich (LBMAGM, Luxembourg). Since the 29th of November 2006, you can download my PhD thesis in pdf format here. I moved then to Heidelberg at EMBL where I did a postdoc in Peer Bork's lab. More information about this fantastic lab can to be found here.
Since september 2009, I am now working as a MCU-PH in Strasbourg (France) jointly in the Laboratoire de Diagnostique Génétique du Nouvel Hopital Civil and the Laboratoire de Bioinformatique et Génomique Intégratives (IGBMC). I mainly take care of the molecular diagnostic (post and prenatal) of the Bardet-Biedl Syndrome in France and partly in Europe and participate in developing methods/tools to better characterize protein families.
[Phd]
My PhD was focused on the applications and the development of bioinformatics methodologies and high throughput technologies aiming at better understanding the cytoskeleton. I first applied comparative genomics and particularly phylogenetic profiling methods. For this, I developped ComIcs to automatically establish the phylogenetic profiles for the complete set of the 1200 cytoskeleton genes in 41 eukaryotic organisms. Results revealed several major limitations of the method linked either to highly similar protein families or the lack of complete proteomes for some organisms. Some of these issues were addressed by an in depth analysis of actin and the Actin-Related Proteins family. This led to the implementation of ARPAnno, a web server dedicated to the identification of protein sequences similar to actin.
In parallel, we developped a new dedicated microarray, named Actichip, to monitor the expression profiles of cytoskeleton genes. For this we implemented Actinome, a collection of sequences related to the cytoskeleton (see details here) and CADO4MI (see details here), a new program dedicated to the automatic design of specific oligonucleotide probes for microarrays. You can also find additional information on Actichip at the CRP-Santé National microarray platform web site (www.microarray.lu).
Finally, one major work achieved during my Phd was the discovery of 2 novel genes, BBS10 and BBS12, involved in the Bardet-Biedl syndrome. This disease (OMIM:209900) is characterized by multiple clinical phenotypes, most prominently a progressive retinal dystrophy, postnatal obesity, polydactyly, cognitive impairment and renal dysplasia. Combining SNP analysis, phenotyping analysis in zebrafish together with bioinformatic analysis (e.g. sequence analysis using multiple alignment of complete sequences and comparative genomics) led to the characterization of 2 vertebrate specific and fast evolving genes. You can find additional information on this website.
[PostDoc]
...
[Publications]
Equal contributors are highlighted with *.
[36] Vasli N., Bohm J.*, Le Gras S.*, Muller J., Pizot C., Jost B., Echaniz-Laguna A., Laugel V., Tranchant C., Bernard R., Plewniak F., Vicaire S., Levy N., Chelly J., Mandel JL., Biancalana V., Laporte J. Next generation sequencing for molecular diagnosis of neuromuscular diseases.
Acta Neuropathologica. April 2012. (10.1007/s00401-012-0982-8)
[35] Cowling BS.*, Toussaint A.*, Muller J., Laporte J. Defective membrane remodeling in neuromuscular diseases: insights from animal models.
PLoS Genet. 2012 Apr;8(4):e1002595. Epub 2012 Apr 5. (doi:10.1371/journal.pgen.1002595)
[34] Luu TD., Rusu AM., Walter V., Ripp R., Moulinier L., Muller J., Toursel T., Thompson JD., Poch O. and Nguyen H. MSV3d: database of human MisSense variants mapped to 3D protein structure.
Database. 2012 (10.1093/database/bas018)
[33] Bloch-Zupan A., Jamet X., Etard C., Muller J., Geoffroy V., Strauss JP., Pelletier V., Marion V., Poch O., Strahle U., Stoetzel C. and Dollfus H. Homozygosity Mapping and Candidate Prioritization Identify Mutations, Missed by Whole-Exome Sequencing, in SMOC2, Causing Major Dental Developmental Defects.
American Journal of Human Genetics. 2011 Dec 9;89(6):773-781 (10.1016/j.ajhg.2011.11.002)
[32] Creevey C.J.*, Muller J.*, Doerks T., Thompson J. D., Arendt D., Bork P. Single copy orthologs in Metazoa.
PLoS Computational Biology 2011 Dec;7(12):e1002269 (10.1371/journal.pcbi.1002269)
[31] Powell S., Szklarczyk D., Trachana K., Roth A., Kuhn M., Muller J., Arnold R., Rattei T., Letunic I., Doerks T., Jensen LJ., von Mering C., Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res. 2011 Nov 16. (10.1093/nar/gkr1060)
[30] Trachana K., Larsson TA., Powell S., Chen WH., Doerks T., Muller J. and Bork P. Orthology prediction methods: A quality assessment using curated protein families.
Bioessays. 2011 Aug 19. (10.1002/bies.201100062)
[29] Luu TD., Nguyen NH., Friedrich A., Muller J., Moulinier L., Poch O. Extracting Knowledge from a Mutation Database Related to Human Monogenic Disease Using Inductive Logic Programming.
In International Conference on Bioscience, Biochemistry and Bioinformatics; Singapore 2011. IEEE Catalog Number: CFP1134M-PRT. ISBN: 978-1-4244-9388-3.
[28] Schaefer E. Zaloszyc A., Lauer J., Durand M., Stutzmann F., Perdomo-Trujillo Y., Redin C., Bennouna Greene V., Toutain A., Perrin L., Gerard M., Caillard S., Bei X., Lewis R.A., Christmann D., Letsch J., Kribs M., Mutter C., Muller J., Stoetzel C., Fischbach M., Marion V., Katsanis N., Dollfus H. Mutations in SDCCAG8/NPHP10 Cause Bardet-Biedl Syndrome and Are Associated with Penetrant Renal Disease and Absent Polydactyly.
Molecular Syndromology 2011;1:273-281 (10.1159/000331268)
[27] The MetaHIT Consortium, including Arumugam M., Raes J., Yamada T., Mende DR., Muller J. and Peer Bork Enterotypes of the human gut microbiome.
Nature April 2011. (doi:10.1038/nature09944)
[26] Koscinski I.*, ElInati E.*, Fossard C., Redin C., Muller J., Velez de la Calle J., Schmitt F., Ben Khelifa M., Ray P., Kilani Z., Barratt CL. R., Viville S. DPY19L2 deletion as a major cause of globozoospermia.
American Journal of Human Genetics. 2011 Mar 11;88(3):351-61. (PMID: 21397063)
[25] Colbourne JK., Pfender ME., Gilbert D., Thomas WK., Tucker A., Oakley TH., Tokishita S., Aerts A., Arnold GJ., Basu MK., Bauer DJ., Caceres CE., Carmel L., Casola C., Choi JH., Detter JC., Dong Q., Dusheyko S., Eads BD., Frohlich T., Geiler-Samerotte KA., Gerlach D., Hatcher P., Jogdeo S., Krijgsveld J., Kriventseva EV., Kultz D., Laforsch C., Lindquist E., Lopez J., Manak JR., Muller J., Pangilinan J., Patwardhan1 RP., Pitluck S., Pritham EJ., Rechtsteiner A., Rho M., Rogozin IB., Sakarya O., Salamov A., Schaack S., Shapiro H., Shiga Y., Skalitzky C., Smith Z., Souvorov A., Sung W., Tang Z., Tsuchiya D., Tu H., Vos H., Wang M., Wolf YI., Yamagata H., Yamada T., Ye Y., Shaw JR.,Andrews J., Crease TJ., Tang H., Lucas SM., Robertson HM., Bork P., Koonin EV., Zdobnov EM., Grigoriev IV., Lynch M. and Boore JL. The Ecoresponsive Genome of Daphnia pulex.
Science. February 2011, 331, 6017, 555-561. (doi:10.1126/science.1197761)
[24] Szklarczyk D., Franceschini A., Kuhn M., Simonovic M., Roth A., Minguez P., Doerks T., Starck M., Muller J., Bork P., Jensen L.J. and von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Nucleic Acids Research, 2010 Nov 3. (doi:10.1093/nar/gkq973).
[23] Fradin M., Stoetzel C., Muller J., Koob M., Christmann D., Debry C., Kohler M., Isnard M., Astruc D., Desprez P., Zorres C., Flori E., Dollfus H., Doray B. Osteosclerotic bone dysplasia in siblings with a Fam20C mutation.
Clinical Genetics. 2010 Jul 23. (doi:10.1111/j.1399-0004.2010.01516.x).
[22] Muller J.*, Stoetzel C.*, Vincent MC., Leitch CC., Laurier V., Danse JM., Hellé S., Marion V., Bennouna-Greene V., Vicaire S., Megarbane A., Kaplan J., Drouin-Garraud V., Hamdani M., Sigaudy S., Francannet C., Roume J., Bitoun P., Goldenberg A., Philip N., Odent S., Green J., Cossée M., Davis EE., Katsanis N., Bonneau D., Verloes A., Poch O., Mandel JL., Dollfus H. Identification of 28 novel mutations in the Bardet-Biedl syndrome (BBS) genes: the burden of private mutations in an extensively heterogeneous disease.
Human Genetics. 2010 Feb 23. (PMID: 20177705).
[21] The Nasonia Genome Working Group, including Muller J., Yamada T. and Bork P. Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species.
Science. January 2010: 343-348. (doi:10.1126/science.1178028)
[20] Muller J.*, Creevey CJ.*, Thompson JD., Arendt D., Bork P. AQUA: Automated quality improvement for multiple sequence alignments.
Bioinformatics. 2009 Nov 19. (PMID: 19926669)
[19] Friedrich A.*, Garnier N.*, Gagnière N., Nguyen H., Albou LP., Biancalana V., Bettler E., Deléage G., Lecompte O., Muller J., Moras D., Mandel JL., Toursel T., Moulinier L., Poch O. SM2PH-db: an interactive system for the integrated analysis of phenotypic consequences of missense mutations in proteins involved in human genetic diseases.
Human Mutation, 2009 Nov 17. (PMID: 19921752)
[18] Muller J., Szklarczyk D., Julien P., Letunic I., Roth A., Kuhn M., Powell S., von Mering C., Doerks T., Jensen L.J. and Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Nucleic Acids Research 2009. (doi:10.1093/nar/gkp951)
[17] Vetter G*, Le Béchec A*, Muller J., Muller A, Moes M, Yatskou M, Altanoury Z, Poch O, Vallar L, Friederich E. Time-resolved analysis of transcriptional events during SNAI1-triggered epithelial to mesenchymal transition.
Biochem Biophys Res Commun. 2009 May 11. (PMID:19442650)
[16] Foerstner K.U., Doerks T., Muller J., Raes J., Bork P. A Nitrile Hydratase in the Eukaryote Monosiga brevicollis.
PLoS ONE 3(12): e3976 (doi:10.1371/journal.pone.0003976)
[15] Jensen L.J.*, Kuhn M.*, Stark M., Chaffron S., Creevey C., Muller J., Doerks T., Julien P., Roth A., Simonovic M., Bork P. and von Mering C. STRING 8: a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Research, 2008. (PMID: 18940858)
[14] Becker J.A., Befort K., Blad C., Filliol D., Ghate A., Dembele D., Thibault C., Koch M., Muller J., Lardenois A., Poch O. and Kieffer BL. Transcriptome analysis identifies genes with enriched expression in the mouse central extended amygdala.
Neuroscience 2008 Aug 14. (PMID: 18786617)
[13] Befort K., Filliol D., Ghate A., Darcq E., Matifas A., Muller J., Lardenois A., Thibault C., Dembele D., Le Merrer J., Becker J.A., Poch O. and Kieffer B.L. Mu-opioid receptor activation induces transcriptional plasticity in the central extended amygdala.
European Journal of Neuroscience, 2008 Jun;27(11):2973-84. (PMID: 18588537)
[12] Befort K., Filliol D., Darcq E., Ghate A., Matifas A., Lardenois A., Muller J., Thibault C., Dembele D., Poch O. and Kieffer B.L. Gene Expression Is Altered in the Lateral Hypothalamus upon Activation of the mu Opioid Receptor.
Annals of New York Academy of Sciences. 1129: 175-184 (2008). (PMID: 18591478)
[11] Wicker N., Muller J., Kiran Reddy Kalathur R. and Poch O. A maximum likelihood approximation method for Dirichlet's parameter estimation.
Computational Statistics & Data Analysis 2008 Jan 1, Volume 52, Issue 3. (doi:10.1016/j.csda.2007.07.011)
[10] Jensen L.J.*, Julien P.*, Kuhn M., von Mering C., Muller J, Doerks T., Bork P. eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic Acids Research, 2007 Oct 16. (PMID: 17942413)
[9] Muller J., Mehlen A., Vetter G., Yatskou M., Muller A., Chalmel F., Poch O., Friederich E., Vallar L. Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton.
BMC Genomics. 2007 Aug 29;8(1):294. (PMID: 17727702)
[8] Stoetzel C.*, Muller J.*, Laurier V., Davis EE., Zaghloul NA., Vicaire S., Jacquelin C., Plewniak F., Leitch CC., Sarda P., Hamel C., de Ravel TJ., Lewis RA., Friederich E., Thibault C., Danse JM., Verloes A., Bonneau D., Katsanis N., Poch O., Mandel JL., Dollfus H. Identification of a Novel BBS gene (BBS12) Highlights the Major Role of a Vertebrate-Specific Branch of Chaperonin-Related Proteins in Bardet-Biedl Syndrome.
American Journal of Human Genetics. Jan 2007. (PMID: 17160889)
[7] V. Laurier*, C. Stoetzel*, J. Muller, C. Thibault, S. Corbani, N. Jalkh, S. Nabiha, E. Chouery, O. Poch, JM. Danse, P. Amati-Bonneau, D. Bonneau, A. Mégarbané, JL. Mandel and H. Dollfus. Pitfalls of homozygosity mapping: an extended consanguineous Bardet-Biedl syndrome family with two mutant genes (BBS2, BBS10), three mutations, but no triallelism.
European Journal of Human Genetics. Jul 5 2006. (PMID: 16823392)
[6] Dollfus H., Muller J., Stoetzel C., Laurier V., Bonneau D., Mégarbané A., Poch O., Mandel JL. Bardet-Biedl syndrome: a unique family for a major gene (BBS10).
Médecine Sciences (Paris). 2006 Nov;22(11):901-4. (PMID: 17101080)
[5] Stoetzel C*, Laurier V*, Davis EE*, Muller J*, Rix S, Badano JL, Leitch CC, Salem N, Chouery E, Corbani S, Jalk N, Vicaire S, Sarda P, Hamel C, Lacombe D, Holder M, Odent S, Holder S, Brooks AS, Elcioglu NH, Da Silva E, Rossillion B, Sigaudy S, de Ravel TJ, Alan Lewis R, Leheup B, Verloes A, Amati-Bonneau P, Megarbane A, Poch O, Bonneau D, Beales PL, Mandel JL, Katsanis N, Dollfus H. BBS10 encodes a vertebrate-specific chaperonin-like protein and is a major BBS locus.
Nature Genetics. Apr 2 2006. (PMID: 16582908)
[4] Perrodou E., Deshayes C., Muller J., Schaeffer C., Van Dorsselaer A., Ripp R., Poch O., Reyrat JM. and Lecompte O. ICDS database: interrupted CoDing sequences in prokaryotic genomes.
Nucleic Acids Research 34: D338-D343 (2006). (PMID: 16381882)
[3] Muller J., Oma Y., Vallar L., Friederich E., Poch O., and Winsor B. Sequence and Comparative Genomic Analysis of Actin-related Proteins.
Molecular Biology Cell (2005). (PMID: 16195354)
[2] Chalmel F., Lardenois A., Thompson J.D., Muller J., Sahel J.A., Leveillard T., and Poch O. GOAnno: GO annotation based on multiple alignment.
Bioinformatics 21, 2095-2096 (2005). (PMID: 15647299)
[1] Plewniak F., Bianchetti L., Brelivet Y., Carles A., Chalmel F., Lecompte O., Mochel T., Moulinier L., Muller A., Muller J., Prigent V., Ripp R., Thierry J.C., Thompson J.D., Wicker N., and Poch O. PipeAlign: A new toolkit for protein family analysis.
Nucleic Acids Research 31, 3829-3832 (2003). (PMID: 12824430)
