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Jean Muller, Phd, MCU-PH

Laboratoire Diagnostic Génétique (HUS)
Laboratoire de Génétique Médicale (UMR_S U1112)

Phone: +33 6 27 12 54 57, +33 3 69 55 07 77 (Diagnostic Lab)

Unistra


[Introduction]

My main scientific interest is focused on life science and genetics. 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 Master degree dedicated into learning "Complementary Skills in Informatics" where I was involved in comparative analysis of prokaryotic genomes responsible of diarrhea (report and presentation). I continued in the same lab (LBGI within the 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 Dr Olivier Poch (Laboratoire de Bioinformatique et Génomique Intégratives, Strasbourg) and Dr Evelyne Friederich (LBMAGM, Luxembourg). My PhD thesis is available online since the 29th of November 2006 (report and presentation. In 2006, I moved then to Heidelberg at EMBL where I did a postdoc in the bioinformatics group from Dr Peer Bork. More information about this fantastic lab can to be found here.
Since september 2009, I am working as an assistant professor in Bioinformatics and Genetics (MCU-PH) at the University of Strasbourg and the Academic Strasbourg Hospital. In the Laboratoire de Diagnostique Génétique, I take care of the molecular diagnostic (post and prenatal) of the Bardet-Biedl Syndrome and the Alstrom Syndrome in France and partly in Europe.
My research has been developped jointly in the bioinformatic group co-headed by Drs O. Poch and J. Thompson (LBGI) and in the group of Pr J-L. Mandel (Genetic Mechanism of Neurodevelopmental diseases Laboratory at IGBMC). In 2015, I have joined Pr H. Dollfus' lab (Laboratoire de Génétique Médicale) to further develop my research on eye diseases. This includes retinitis pigmentosum and more syndromic forms (such as BBS and Alstrom syndromes) for which we are developing new diagnotic tests to better characterize patients molecular causes. I specifically focus on the development of assays and tools dedicated to improve the analyses of Next Generation Sequencing applications. As an example, we have developped in the lab VaRank a comprehensive workflow to rank/prioritize variations identified from high throughput sequencing and AnnotSV to annotate structural variations.


[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]

During my postdoc, I joined the Bork group at EMBL in Heidelberg, Germany. In this fantastic collaborative place, I was involved in the development of tools, protocols and databases related to the evolution of Metazoan. Among those, AQUA is a simple automated protocol for the selection of high quality multiple sequence alignment. eggNOG is a database of clusters of orthologs that provide a nice framework for comparative genome analysis. STRING is a database of known and predicted protein interactions. I also participated in some large collaborative analysis such as the sequencing project of 2 insects genomes (Daphnia pulex and Nasonia vitripennis) and the Gut Microbiome.



[Publications] ORCID iD icon Google_scholar iD icon

Equal contributors are highlighted with *.

[74] Ben Rhouma M., Okutman O., Muller J., Benkhalifa M., Bahri H., Ben Rhouma K., Tebourbi O., Viville S.
Aspect génétique de l'infertilité masculine : de la recherche à la clinique.
Gynécologie Obstétrique Fertilité et Sénologie 2018. (10.1016/j.gofs.2018.11.004).

[73] Laugel-Haushalter V.*, Morkmued S*, Stoetzel C., Geoffroy V., Muller J., Boland A., Deleuze JF., Pitiphat W., Dollfus H., Niederreither K., Bloch-Zupan A., Pungchanchaikul P.
Genetic evidence supporting the role of the calcium channel, CACNA1S, in tooth cusp and root patterning.
Frontiers in Physiology 2018. (10.3389/fphys.2018.01329).

[72] Okutman O., Ben Rhouma M., Benkhalifa M., Muller J., Viville S.
Genetic evaluation of patients with non-syndromic male infertility.
Journal of Assisted Reproduction and Genetics 2018. (10.1007/s10815-018-1301-7).

[71] Montagne L.*, Derhourhi M.*, Piton A., Toussaint B., Durand E., Vaillant E., Thuillier D., Gaget S., De Graeve F., Rabearivelo L., Lansiaux A., Lenne B., Sukno S., Desailloud R., Cnop M., Nicolescu R., Cohen L, Zagury JF, Amouyal M., Weill J., Muller J., Sand O., Delobel B., Froguel P.*, Bonnefond A*.
CoDE-seq, an augmented whole-exome sequencing, enables the accurate detection of CNVs and mutations in Mendelian obesity and intellectual disability.
Molecular Metabolism 2018. (10.1016/j.molmet.2018.05.005).

[70] Geoffroy V.*, Stoetzel C.*, Scheidecker S., Schaefer E., Perrault I., Bär S., Kröll A., Delbarre M., Antin M., Leuvrey AS., Henry C., Blanché H., Decker E., Kloth K., Klaus G., Mache C., Martin-Coignard D., McGinn S., Boland A., Deleuze JF., Friant S., Saunier S., Rozet JM., Bergmann C., Dollfus H., Muller J.
Whole Genome Sequencing in patients with ciliopathies uncovers a novel recurrent tandem duplication in IFT140.
Human Mutation 2018. (10.1002/humu.23539).

[69] Geoffroy V., Hérenger Y., Kress A., Stoetzel C., Piton A., Dollfus H., Muller J.
AnnotSV: An integrated tool for Structural Variations annotation.
Bioinformatics 2018. (10.1093/bioinformatics/bty304).

[68] Rimessi A.*, Bezzerri V.*, Salvatori F.*, Tamanini A., Nigro F., Dechecchi MC., Santanglo A., Prandini P., Munari S., Provezza L., Garreau de Loubresse N., Muller J., Ribeiro MPC., Lippi G., Gambari R.*, Pinton P.*, and Cabrini G.*
PLCB3 loss-of-function reduces P. aeruginosa-dependent IL-8 release in cystic fibrosis.
American Journal of Respiratory Cell and Molecular Biology 2018. (10.1165/rcmb.2017-0267OC).

[67] Okutman O., Muller J., Skory V., Garnier JM., Gaucherot A., Baert Y., Rombaut C., Lamour V., Serdarogullari M., Gultomruk M., Roepke A., Kliesch S., Herbepin V., Aknin I., Teletin M., Bakircioglu E., Goossens E., Charlet-Berguerand N., Bahceci M., Tüttelmann F., Viville S.
A no-stop mutation in MAGEB4 is a possible cause of rare X-linked azoospermia and oligozoospermia in a consanguineous Turkish family.
Journal of Assisted Reproduction and Genetics 2017. (10.1007/s10815-017-0900-z).

[66] Montaut S., Apartis E., Chanson JB., Ewenczyk C., Renaud M., Guissart C., Muller J., Legrand AP., Durr, A., Laugel V., Koenig M., Tranchant C., Anheim M.
SCA13 causes dominantly inherited non-progressive myoclonus ataxia.
Parkinsonism & Related Disorders 2017. (10.1016/j.parkreldis.2017.02.012)

[65] Quartier A.*, Poquet H.*, Gilbert-Dussardier B., Rossi M., Casteleyn AS., Portes VD., Feger C., Nourisson E., Kuentz P., Redin C., Thevenon J., Mosca-Boidron AL., Callier P., Muller J., Lesca G., Huet F., Geoffroy V., El Chehadeh S., Jung M., Trojak B., Le Gras S., Lehalle D., Jost B., Maury S., Masurel A., Edery P., Thauvin-Robinet C., Gérard B., Mandel JL., Faivre L, Piton A.
Intragenic FMR1 disease-causing variants: a significant mutational mechanism leading to Fragile-X syndrome.
European Journal of Human Genetics 2017. (10.1038/ejhg.2016.204)

[64] Renaud M.*, Guissart C.*, Mallaret M., Ferdinandusse S., Cheillan D., Drouot N., Muller J., Claustres M., Tranchant C., Anheim M., Koenig M.
Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia.
Journal of Neurology 2016. (10.1007/s00415-016-8167-3)

[63] Mallaret M., Renaud M., Redin C., Drouot N., Muller J., Severac F., Mandel JL., Hamza W., Benhassine T., Ali-Pacha L., Tazir M., Durr A., Monin ML., Mignot C., Charles P., Van Maldergem L., Chamard L., Thauvin C., Laugel V., Burglen B., Fleury MC., Tranchant C., Anheim M.*, Koenig M*.
Validation of a clinical practice-based algorithm for the diagnosis of autosomal recessive cerebellar ataxias.
Journal of Neurology 2016. (10.1007/s00415-016-8112-5)

[62] Calmels N., Greff G., Obringer C., Kempf N., Gasnier C., Tarabeux J., Miguet M., Bessis D, Bretones P., Cavau A., Digeon B., Doco-Fenzy M., Doray B., Feillet F., Gardeazabal J., Gener B., Julia S., Llano-Rivas I., Mazur A., Michot C., Renaldo-Robin F., Rossi M., Sabouraud P., Keren B., Depienne C., Muller J., Mandel JL., Laugel V.
Unexpected nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing.
Orphanet Journal of Rare Diseases 2016. (10.1186/s13023-016-0408-0)

[61] Schaefer E., Stoetzel C., Scheidecker S., Geoffroy V., Prasad MK., Redin C., Missotte I., Lacombe D., Mandel JL., Muller J., Dollfus H.
Identification of a novel mutation confirms the implication of IFT172 (BBS20) in Bardet-Biedl syndrome.
Journal of Human Genetics 2016. (10.1038/jhg.2015.162)

[60] Guissart C., Drouot N., Oncel I., Leheup B., Gershoni-Barush R., Muller J., Ferdinandusse S., Larrieu L., Anheim M., Arslan EA., Claustres M., Tranchant C., Topaloglu H., Koenig M.
Genes for spinocerebellar ataxia with blindness and deafness (SCABD/SCAR3, MIM# 271250 and SCABD2).
European Journal of Human Genetics 2015. (10.1038/ejhg.2015.259)

[59] Braun JJ., Noblet V., Kremer S., Molière S., Dollfus H., Marion V., Goetz N., Muller J., Riehm S.
Value of MRI Olfactory Bulb evaluation in the assessment of olfactory dysfunction in Bardet Biedl syndrome.
Clinical Genetics 2015. (10.1111/cge.12697)

[58] Okutman O., Muller J., Baert Y., Serdarogullari M., Gultomruk M., Piton A., Rombaut C., Benkhalifa M., Teletin M., Skory V., Bakircioglu E., Goossens E., Bahceci M., Viville S.
Exome sequencing reveals a nonsense mutation in Tex15 causing spermatogenic failure in a Turkish family.
Human Molecular Genetics 2015. (10.1093/hmg/ddv290)

[57] Farrugia A., Keyser C., Hollard C., Raul J.S., Muller J., Ludes B.
Targeted next generation sequencing application in cardiac channelopathies: Analysis of a cohort of autopsy-negative sudden unexplained deaths.
Forensic Science International 2015. (10.1016/j.forsciint.2015.06.023)

[56] Hamza W., Pacha L.A., Hamadouche T., Muller J., Drouot N., Ferrat F., Makri S., Chaouch M., Tazir M., Koenig M., Benhassine T.
Molecular and clinical study of a cohort of 110 Algerian patients with autosomal recessive ataxia.
BMC Medical Genetics 2015. (10.1186/s12881-015-0180-3)

[55] Scheidecker S., Hull S., Perdomo Y., Studer F., Pelletier V., Muller J., Stoetzel C., Schaefer E., Defoort-Dhellemmes S., Drumare I., Holder G., Hamel C., Webster A., Moore A., Puech B., Dollfus H.
Predominantly cone-system dysfunction as rare form of retinal degeneration in patients with molecularly confirmed Bardet-Biedl Syndrome.
American Journal of Ophthalmology 2015. (10.1016/j.ajo.2015.05.007)

[54] Marshall JD.*, Muller J.*, Collin GB.*, Milan G., Kingsmore S.F., Dinwiddie D., Farrow E. G., Miller N.A., Favaretto F., Maffei P., Dollfus H., Vettor R., Naggert J.K.
Alström Syndrome: Mutation spectrum of ALMS1.
Human Mutation 2015. (10.1002/humu.22796)

[53] Geoffroy V.*, Pizot C.*, Redin C., Piton A., Vasli N., Stoetzel C., Blavier A., Laporte J. and Muller J.
VaRank: a simple and powerful tool for ranking genetic variants.
PeerJ 2015.(10.7717/peerj.796)

[52] Huckert M.*, Stoetzel C.*, Morkmued S., Laugel-Haushalter V., Geoffroy V., Muller J., Clauss F., Prasad MK., Obry F., Raymond JL., Switala M., Alembik Y., Soskin S., Mathieu E., Hemmerlé J., Weickert JL., Dabovic B., Rifkin DB., Dheedene A., Boudin E., Caluseriu O., Cholette MC., McLeod R., Antequera R., Gellé MP., Coeuriot JL., Jacquelin LF., Bailleul-Forestier I., Manière MC., Van Hul W., Bertola D., Dollé P., Verloes A., Mortier G., Dollfus H., Bloch-Zupan A.
Mutations in the Latent TGF-beta Binding Protein 3 (LTBP3) gene cause brachyolmia with amelogenesis imperfecta.
Human Molecular Genetics 2015.(10.1093/hmg/ddv053)

[51] Ozantürk A.*, Marshall JD.*, Collin GB., Düzenli S., Marshall RP., Candan S., Tos T., Esen I., Taskesen M., Cayir A., Oztürk S., Ustün I., Ataman E., Karaca E., Ozdemir TR., Erol I., Eroglu FK., Torun D., Pariltay E., Yilmaz-Güleç E., Karaca E., Atabek ME., Elçioglu N., Satman I., Möller C., Muller J., Naggert JK., Ozgül RK.
The phenotypic and molecular genetic spectrum of Alström syndrome in 44 Turkish kindreds and a literature review of Alström syndrome in Turkey.
Journal of Human Genetics 2014. (10.1038/jhg.2014.85)

[50] Redin C., Gérard B., Lauer J., Herenger Y., Muller J., Quartier A., Masurel-Paulet A., Willems M., Lesca G., El-Chehadeh S., Le Gras S., Vicaire S., Philipps M., Dumas M., Geoffroy V., Feger C., Haumesser N., Alembik Y., Barth M., Bonneau D., Colin E., Dollfus H., Doray B., Delrue MA., Drouin-Garraud V., Flori E., Fradin M., Francannet C., Goldenberg A., Lumbroso S., Mathieu-Dramard M., Martin-Coignard D., Lacombe D., Morin G., Polge A., Sukno S., Thauvin-Robinet C., Thevenon J., Doco-Fenzy M., Genevieve D., Sarda P., Edery P., Isidor B., Jost B., Olivier-Faivre L., Mandel JL., Piton A.
Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing.
Journal of Medical Genetics 2014. (10.1136/jmedgenet-2014-102554)

[49] Huckert M., Mecili H., Laugel-Haushalter V., Stoetzel C., Muller J., Flori E., Laugel V., Maniere M., Dollfus H., Bloch-Zupan A.
A novel mutation in the ROGDI gene in a patient with Kohlschütter-Tönz Syndrome.
Molecular Syndromology 2014. (10.1159/000366252)

[48] Renaud M.*, Anheim M.*, Kamsteeg E.J., Mallaret M., Mochel F., Vermeer S, Drouot N., Pouget J., Redin C., Salort-Campana E., Kremer H.P.H, Corien C., Verschuuren-Bemelmans C.C., Muller J., Scheffer H., Durr A., Tranchant C., Koenig M.
ARCA3 due to ANO10 mutations: delineation and genotype/phenotype correlation study.
JAMA Neurology. 2014 (10.1001/jamaneurol.2014.193)

[47] Braun JJ.*, Noblet V.*, Durand M., Scheidecker S., Zinetti Bertschy A., Foucher J., Marion V., Muller J., Riehm S., Dollfus H., Kremer S.
Olfaction evaluation and correlation with brain atrophy in Bardet Biedl syndrome.
Clinical Genetics 2014.(10.1111/cge.12391)

[46] Piton A.*, Poquet H.*, Redin C., Masurel A., Lauer J., Muller J., Thevenon J., Herenger Y., Chancenotte S., Bonnet M., Pinoit JM., Huet F., Thauvin-Robinet C., Jaeger AS., Le Gras S., Jost B., Gérard B., Peoc'h K., Launay JM., Faivre L.*, Mandel JL*.
20 ans après: a second mutation in MAOA identified by targeted high-throughput sequencing in a family with altered behavior and cognition.
European Journal Human Genetics 2013. (10.1038/ejhg.2013.243)

[45] Scheidecker S.*, Etard C.*, Pierce NW.*, Geoffroy V., Schaefer E., Muller J., Chennen K., Flori E., Pelletier V., Poch O., Marion V., Stoetzel C., Strahle U., Nachury MV., Dollfus H.
Exome sequencing of Bardet-Biedl syndrome patient identifies a null mutation in the BBSome subunit BBIP1 (BBS18).
Journal of Medical Genetics 2013. (10.1136/jmedgenet-2013-101785)

[44] Bonnefond A.*, Philippe J.*, Durand E., Muller J., Saeed S., Arslan M.D, Martinez S., De Graeve F., Dhennin V., Rabearivelo I., Polak M., Cavé H., Castano L., Vaxillaire M., Mandel JL., Sand O. & Froguel P.
Highly sensitive diagnosis of 43 monogenic forms of diabetes or obesity, through one step PCR-based enrichment in combination with next-generation sequencing.
Diabetes Care 2013. (10.2337/dc13-0698)

[43] Fradin M., Merklen-Djafri C., Perrigouard C., Aral B., Muller J., Stoetzel C., Frouin E., Flori E., Doray B., Dollfus H., Lipsker D.
Long-Term Follow-Up and Molecular Characterization of a Patient with a RECQL4 Mutation Spectrum Disorder.
Dermatology 2013. (10.1159/000351311)

[42] Schaefer E.*, Lauer J.*, Durand M., Pelletier V., Obringer C., Claussmann A., Braun JJ., Redin C., Mathis C., Muller J., Schmidt-Mutter C., Flori E., Marion V., Stoetzel C., Dollfus H.
Mesoaxial Polydactyly is a Major Feature in Bardet-Biedl Syndrome (BBS) patients with LZTFL1 (BBS17) Mutations.
Clinical Genetics 2013. (10.1111/cge.12198)

[41] M'Hamdi O.*, Redin C.*, Stoetzel C.*, Ouertani I., Chaabouni M., Faouzi M., M'rad R., Mandel JL., Dollfus H., Muller J., Chaabouni H.
Clinical and Genetic Characterization of Bardet-Biedl Syndrome in Tunisia: Defining a Strategy for Molecular Diagnosis.
Clinical Genetics 2013. (10.1111/cge.12129)

[40] El Inatia E., Muller J. and Viville S.
Autosomal mutations and human spermatogenic failure.
Biochimica et Biophysica Acta - Molecular Basis of Disease 2012. (10.1016/j.bbadis.2012.07.006)

[39] Redin C., Le Gras S., Mhamdi O., Geoffroy V., Stoetzel C., Vincent MC., Chiurazzi P., Lacombe D., Ouertani I., Petit F, Till M., Verloes A., Jost B., Chaabouni HB., Dollfus H., Mandel JL., Muller J..
Targeted high-throughput sequencing for diagnosis of genetically heterogeneous diseases: efficient mutation detection in Bardet-Biedl and Alstrom Syndromes.
Journal of Medical Genetics 2012. (10.1136/jmedgenet-2012-100875)

[38] Elinati E.*, Kuentz P.*, Redin C., Jaber S., Vanden Meerschaut F., Magarian J., Koscinski I., H Nasr-Esfahani M., Demirol A., Gurgan T., Louanjli N., Iqbal N, Bisharah M, Carré Pigeon F., Gourabi H., De Briel D., Brugnon F., Gitlin S.A., Grillo JM., Deemeh X., Ghaedi K., Tanhee X., Heindryckx B., Benkhalifa M., Nikiforaki D., Oehninger S.C., De Sutter P., Muller J., Viville S.
Globozoospermia is mainly due to DPY19L2 deletion via non allelic homologous recombination involving two recombination hotspots.
Human Molecular Genetics 2012. (10.1093/hmg/dds200)

[37] Luu TD., Rusu AM., Walter V., Linard B., Poidevin L., Ripp R., Moulinier L., Muller J., Raffelsberger W., Wicker N., Lecompte O., Thompson JD., Poch O. and Nguyen H.
KD4v: comprehensible knowledge discovery system for missense variant.
Nucleic Acids Research 2012. (10.1093/nar/gks474)

[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 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 Genetics 2012. (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.*, Laugel V., 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. (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. (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 Research 2011. (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. (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. (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 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. (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 2011. (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. (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. (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. (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 2010. (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. (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. (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 Research Communications 2009. (PMID:19442650)

[16] Foerstner K.U., Doerks T., Muller J., Raes J., Bork P.
A Nitrile Hydratase in the Eukaryote Monosiga brevicollis.
PLoS ONE 2008. (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. (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. (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 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. (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. (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. (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 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 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. (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 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 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 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 2003. (PMID: 12824430)

Publication mentioning supervised members of the lab

[2] Piton A.*, Redin C.*, Mandel JL.
XLID-Causing Mutations and Associated Genes Challenged in Light of Data From Large-Scale Human Exome Sequencing.
American Journal of Human Genetics 2013. (10.1016/j.ajhg.2013.06.013)

[1] Bricker DK.*, Taylor EB.*, Schell JC.*, Orsak T.*, Boutron A., Chen YC., Cox JE., Cardon CM., Van Vranken JG., Dephoure N., Redin C., Boudina S., Gygi SP., Brivet M., Thummel CS., Rutter J.
A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila, and Humans.
Science 2012. (10.1126/science.1218099)

Publication without peer review

[4] Muller J.
Le syndrome d'Alström
Arbre décisionnel de l’ANPGM 2018. Pdf available (here)

[3] Muller J.
Le syndrome de Bardet-Biedl
Arbre décisionnel de l’ANPGM 2017. Pdf available (here)

[2] Le Béchec A., De Tayrac M., Paimparay G., Muller J., Lonchamps E.
Séquençage génétique: l’indispensable collaboration DSI bio-informatique.
DSIH Numéro 22, octobre 2017. Pdf available (here) or online here

[1] Tarabeux J., Muller J.
SureSelect Target Enrichment System for Sequencing on the Ion Torrent PGM.
Application Note by Agilent Technologies 2016. Pdf available (here)


Author: Jean Muller, last update 17.09.2018