Olivier POCH

 

 

Research Director, CNRS

 

Institut de Génétique et de Biologie Moléculaire et Cellulaire

1 rue Laurent Fries

Illkirch

France

Phone: 33 3 88 65 32 94 

Fax:33 3 88 65 32 01

e-mail:poch@igbmc.u-strasbg.fr

 


 

Research interest

 

Bioinformatics and genomics: The aim of my research group is to develop validated high throughput computational biology to study the behaviour of biological systems ranging from protein families to relational systems such as “hyperstructures” (macromolecular complex, organelles, viruses…) or biological networks (metabolosome, transcriptional, developmental or disease-related networks…).

 

To tackle these objectives, two complementary strategies are developed in our laboratory :

 

i) bioinformatics involved in the development of original algorithms and in the construction of an integrated platform

 

ii) bioanalysis dedicated to in depth analysis of specialized biological systems to identify interesting biological targets and better define efficient algorithms or computational strategies

 

In this context, the functional genomics of the informational proteins and complexes (replication, transcriptional and translation) constitute invaluable systems in modern human comparative genomics combining the availability of numerous experimental genomic and functional data with major fundamental and therapeutical aspects.

 

 

Biography

 


Scientific Distinctions

 

Thesis prize A. D. R. E. R. U. S. Jun. 1987

Dr Darolles Prize from National Académie of Medecine for the determination of the Primary structure determination of the Rabies genome Nov. 1987

 

Membership

           

Member of the ARVO (Association for Research in Vision and Ophthalmology)

           

 

PUBLICATIONS


A)    Articles

 

0.    Tibayrenc M., Echalar L., Dujardin J.P., Poch O. and Desjeux P. (1984) The microdistribution of isoenzymic strains of Trypanosoma cruzi in southern Bolivia; new isoenzyme profiles and further arguments against Mendelian sexuality.

            Trans. R. Soc. Trop. Med. Hyg., 78(4): 519-525.

 

1.    Breniere S.F., Poch O., Selaes H., Tibayrenc M., Lemesre J.L., Antezana G. and Desjeux P. (1984) Specific humoral depression in chronic patients infected by Trypanosoma cruzi.

            Rev. Inst. Med. Trop. Sao Paulo, 26(5): 254-258.

 

2.    Tibayrenc M., Cariou M.L., Solignac M., Delet J.P., Poch O. and Desjeux P. (1985) New electrophoretic evidence of genetic variation and diploidy in Trypanosoma cruzi, the causative agent of Chagas’ disease.

            Genetica, 67(3): 223-230.

 

3.    Carrasco R.L., Breniere S.F., Poch O., Miguez H.V., Selaes H., Antezana G., Desjeux P., Carlier Y. (1985) Chagas serology and its problems.

            Ann. Soc. Belg. Med. Trop., 65(1): 79-84.

 

4.    Tibayrenc M., Hoffmann A., Poch O., Echalar L., Le pont F., Lemesre J.L., Desjeux P. and Ayala F.J. (1986) Additional data on Trypanosoma cruzi isozymic strains encountered in Bolivian domestic transmission cycles.

            Trans. R. Soc. Trop. Med. Hyg., 80(3): 442-447.

 

5.    Tordo N., Poch O., Ermine A. and Keith G. (1986) Primary structure of leader RNA and nucleoprotein genes of the rabies genome: segmented homology with VSV.

            Nucleic Acids Res., 14(6): 2671-2683.

 

6.    Tordo N., Poch O., Ermine A., Keith G. and Rougeon F. (1986) Walking along the rabies genome: is the large G-L intergenic region a remnant gene?

            Proc. Natl. Acad. Sci. U S A., 83(11): 3914-3918.

 

7.    Poch O., Tordo N. and Keith G. (1988) Sequence of the 3386 3' nucleotides of the genome of the AVO1 strain rabies virus : structural similarities in the protein regions involved in transcription.

            Biochimie, 70(8): 1019-1029.

 

8.    Tordo N., Poch O., Ermine A., Keith G. and Rougeon F. (1988) Completion of the rabies virus genome sequence determination: highly conserved domains among the L (polymerase) proteins of unsegmented negative-strand RNA viruses.

            Virology, 165(2): 565-576.

 

9.    Poch O., Sauvaget I., Delarue M. and Tordo N. (1989) Identification of four conserved motifs among the RNA-dependent polymerase encoding elements.

            EMBO J., 8(12): 3867-3874.

 

10.  Poch O., Blumberg B.M., Bougueleret L. and Tordo N. (1990) Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains.

            J. Gen. Virol., 71(5): 1153-1162.

 

11.  Delarue M., Poch O., Tordo N., Moras D. and Argos P. (1990) An attempt to unify the structure of polymerases.

            Protein Eng., 3(6): 461-467.

 

12.  Schmitter D., Poch O., Zeder G., Heinrich G.F., Kocher H.P., Quesniaux V.F. and Van Regenmortel M.H. (1990) Analysis of the structural diversity of monoclonal antibodies to cyclosporine.

            Mol. Immunol., 27(10): 1029-1038.

 

13.  Simonin F., Menissier-de Murcia J., Poch O., Muller S., Gradwohl G., Molinete M., Penning C., Keith G. and de Murcia G. (1990) Expression and site-directed mutagenesis of the catalytic domain of human poly(ADP-ribose)polymerase in Escherichia coli. Lysine 893 is critical for activity.

            J. Biol. Chem., 265(31): 19249-19256.

 

14.  Eriani G., Delarue M., Poch O., Gangloff J. and Moras D. (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs.

            Nature, 347(6289): 203-206.

 

15.  Poch O., L’Hote H., Dallery V., Debeaux F., Fleer R. and Sodoyer R. (1992) Sequence of the Kluyveromyces lactis beta-galactosidase: comparison with prokaryotic enzymes and secondary structure analysis.

            Gene, 118(1): 55-63.

 

16.  Simonin F., Poch O., Delarue M. and de Murcia G. (1993) Identification of potential active-site residues in the human poly(ADP-ribose) polymerase.

            J. Biol. Chem., 268(12): 8529-8535.

 

17.  Muller R., Poch O., Delarue M., Bishop D.H. and Bouloy M. (1994) Rift Valley fever virus L segment: correction of the sequence and possible functional role of newly identified regions conserved in RNA-dependent polymerases.

            J. Gen. Virol., 75(6): 1345-1352.

 

18.  De Murcia G., Schreiber V., Molinete M., Saulier B., Poch O., Masson M., Niedergang C. and Menissier-de Murcia J. (1994) Structure and function of poly(ADP-ribose) polymerase.

            Mol. Cell. Biochem., 138(1-2): 15-24.

 

19.  Poch O., Schwob E., de Fraipont F., Camasses A., Bordonne R. and Martin R.P. (1994) RPK1, an essential yeast protein kinase involved in the regulation of the onset of mitosis, shows homology to mammalian dual-specificity kinases.

            Mol. Gen. Genet., 243(6): 641-653.

 

20.  Madania A., Poch O., Tarassov I., Winsor B. and Martin R. (1996) Analysis of a 22,956 bp region on the right arm of Saccharomyces cerevisiae chromosome XV.

            Yeast, 12(15): 1563-1573.

 

21.  Bordonne R., Camasses A., Madania A., Poch O., Tarassov I., Winsor B. and Martin R. (1997) Analysis of a 35.6 kb region on the right arm of Saccharomyces cerevisiae chromosome XV.

            Yeast, 13(1): 73-83.

 

22.  Dujon B, Albermann K, Aldea M, Alexandraki D, Ansorge W, Arino J, Benes V, Bohn C, Bolotin-Fukuhara M, Bordonne R, Boyer J, Camasses A, Casamayor A, Casas C, Cheret G, Cziepluch C, Daignan-Fornier B, Dang DV, de Haan M, Delius H, Durand P, Fairhead C, Feldmann H, Gaillon L, …Poch O., …and Kleine K, (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.

            Nature, 387(6632 Suppl): 98-102.

 

23.  Friant S., Heyman T., Poch O., Wilhelm M. and Wilhelm F.X. (1997) Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex.

            Yeast, 13(7): 639-645.

 

24.  Poch O. and Winsor B. (1997) Who's who among the Saccharomyces cerevisiae actin-related proteins? A classification and nomenclature proposal for a large family.

            Yeast, 13(11): 1053-1058.

 

25.  Poch O. (1997) Conservation of a putative inhibitory domain in the GAL4 family members.

            Gene, 184(2): 229-235.

 

26.  Poterszman A., Lamour V., Egly J.M., Moras D., Thierry J.C. and Poch O. (1997) A eukaryotic XPB/ERCC3-like helicase in Mycobacterium leprae?

            Trends Biochem. Sci., 22(11): 418-419.

 

27.  Birck C., Poch O., Romier C., Ruff M., Mengus G., Lavigne A.C., Davidson I. and Moras D. (1998) Human TAFII28 and TAFII18 interact through a canonical histone fold encoded by atypical evolutionary conserved sequence motifs also found in the SPT3 TAFII family.

            Cell, 94(2): 239-249.

 

28.  Thompson J.D., Plewniak F. and Poch O. (1999) BAliBASE: A benchmark alignment database for the evaluation of multiple sequence alignment programs.

            BioInformatics, 15(1): 87-88.

 

29.  Thompson J.D., Plewniak F. and Poch O. (1999) A comprehensive comparison of protein sequence alignment programs.

            Nucleic Acids Res., 27(13): 2682-2690.

 

30.  Lavigne A.C., Gangloff Y.-G., Carré L., Mengus G., Birck C., Poch O., Romier C., Moras D. and Davidson I. (1999) Asynergistic transcriptional activation by TATA-binding protein and hTAFII28 requirs specific amino acids of the hTAFII28 histone fold.

            Mol. Cell. Biol., 19(7): 5050-5060.

 

31.  Dantonel J.C., Wurtz J.M., Poch O., Moras D. and Tora L. (1999) The TBP-like factor : an alternative transcription factor in metazoa ?

            Trends Biochem. Sci., 24(9): 335-9.

 

32.  Gangloff Y.-G., Werten S., Romier C., Carré L., Poch O., Moras D. and Davidson I. (2000) The human TFIID components TAFII135-TAFII20 and the yeast SAGA components ADA1-TAFII68 heterodimerise to form histone-like pairs.

            Mol. Cell. Biol., 20(1): 340-351.

 

33.   Plewniak F, Thompson JD, Poch O. (2000) Ballast : blast post-processing based on locally conserved segments.

            Bioinformatics, 16(9): 750-759.

 

34.  Thompson J.D., Plewniak F. and Poch O. (2000) DbClustal : rapid and reliable global multiple alignments of protein sequences detected by database searches.

            Nucleic Acids Res., 28(15): 2919-2926.

 

35.  Bahr A., Thompson J.D., Thierry J.C., Poch O. (2001) BAliBASE (Benchmark alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.

                Nucleic Acids Res., 29 (1): 323-326.

 

36.  Mayer C., Suck D. and Poch O. (2001) A new component of the U3 snoRNP in Archaea: the U3 specific Imp4-related protein.

      Trends Biochem. Sci., 26 (3):143-4.

 

37.  Lecompte O., Thompson J.D., Plewniak F., Thierry J.C. and Poch O. (2001) Multiple alignment of complete sequences (MACS) in the post-genomic era.

      Gene, 270:17-30.

 

38.  Lecompte O., Ripp R., Puzos-Barbe V., Duprat S., Heilig R., Dietrich J., Thierry J.C. and Poch O. (2001) Genome evolution at the genus level : comparison of three complete genomes of hyperthermophilic Archaea.

      Genome Research, 11 (6): 981-993.

 

39.  Wicker N., Perrin G.R., Thierry J.C. and Poch O. (2001) Secator: a program for inferring protein subfamilies from phylogenetic trees.

      Mol. Biol. Evol., 18 (8): 1435-41.

 

40.  Thompson J.D., Plewniak F., Ripp R., J-C Thierry J.C. and Poch O. (2001) Towards A Reliable Measure for Multiple Sequence Alignments

      J. Mol. Biol., 314 (4): 937-951.

 

41.  Bianchetti L., Oudet C. and Poch O. (2002) M13 Endopeptidases : New Conserved Motifs correlated with Structure, and Simultaneous Phylogenetic Occurence of PHEX and the Bony Fish

      Proteins, 47 (4): 481-8.

 

42.  Wicker N., Dembele D., Raffelsberger W. and Poch O.(2002) Density of points clustering, application to transcriptomic data analysis.

        Nucleic Acids Res., 30(18):3992-4000.

 

43.  Lecompte O., Ripp R., Thierry J.C., Moras D. and Poch O. (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain-scale.

        Nucleic Acids Res., 30(24): 5382-5390.

 

44.  Cohen G., Barbe V., Flament D., Galperin M., Heilig R., Ripp R., Lecompte O., Prieur D., Poch O, Quérellou J., Thierry J.C., Van der Oost J., Weissenbach J., Zivanovic Y and Forterre P. (2003) An integrated analysis of the genome of the hyperthermophilic azrchaeon Pyrococcus abyssi.

        Mol. Microbiol. 47(6):1495-1512.

 

45.  Gozuacik D., Chami M., Murakami Y., Faivre J., Lagorce D., Poch O., Biermann E., Knippers R., Bréchot C. and Paterlini-Bréchot P. (2003) Identification and functional characterization of a new member of the human Mcm protein family: hMcm8.

        Nucleic Acids Res., 31(2): 570-579.

 

46.  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., Wicker N. and Poch O. (2003) PipeAlign : a new toolkit for protein family analysis.

      Nucleic Acids Res., 31(13): 3829-3832.

 

47.  Thompson J.D., Thierry J.C. and Poch O. (2003) RASCAL: Rapid scanning and correction of multiple sequence alignment programs.

      Bioinformatics, 19(9):1155-1161.

 

48.  Cavusoglu N., Thierse D., Mohand-Said S., Chalmel F., Poch O., Van Dorsselaer A., Sahel J.A. and Leveillard T. (2003) Differential proteomic analysis of the mouse retina: The induction of crystallin proteins by retinal degeneration in the rd1 mouse.

Mol. Cell Proteomics, 2(8): 494-505.

 

49.  Duval D., Duval G., Kedinger C., Poch O. and Boeuf H. (2003) The "PINIT" motif, of a newly identified conserved domain of the PIAS protein family, is essential for nuclear retention of PIAS3L.

FEBS Lett., 554(1-2): 111-118.

 

50.  Thompson J., Prigent V and Poch O. (2004) LEON: multiple aLignment Evaluation Of Neighbours.

      Nucleic Acids Res., 32(4): 1298-1307.

 

51.  Cromer A., Carles A., Millon R., Ganguli G., Chalmel F., Lemaire F., Young J., Dembélé D., Thibault C., Diemunsch F., Poch O., Abecassis J. and Wasylyk B. (2004). Identification of genes associated with hypopharyngeal cancer and metastatic potential by microarray analysis.

Oncogene, 23(14):2484-2498.

 

52.  Léveillard T., Mohand-Saïd S., Lorentz O., Hicks D., Fintz A.C., Chalmel F., Poch O., Lambrou G. and Sahel J.A. (2004) Rod-derived cone viability factor is a thioredoxin-like protein with therapeutic potential.

Nature Genetics, 36(7): 755-759.

 

53.  Brelivet Y., Kammerer S., Rochel N., Poch O. and Moras D. (2004) Signature of the oligomeric behaviour of nuclear receptors at the sequence and structural level.

EMBO reports, 5(4): 423-429.

 

54.  Jawhari A, Boussert S, Lamour V, Atkinson RA, Kieffer B, Poch O, Potier N, van Dorsselaer A, Moras D, Poterszman A. (2004) Domain architecture of the p62 subunit from the human transcription/repair factor TFIIH deduced by limited proteolysis and mass spectrometry analysis.

Biochemistry,. 43(45):14420-30.

 

B) Reviews

 

55.  Poch O., Tordo N., Ermine A., Keith G. and Rougeon F. (1987) Cent ans après…le virus de la rage.

Bull. Acad. Natl. Med., 171(8): 1087-1094.

 

56.  Tordo N., De Haan P., Goldbach R. and Poch O. (1992) Evolution of negative-stranded RNA genomes.

Seminars in Virology, 3(1): 341-357.

 

57.  Poch O. and Delarue M. (1996) Converting sequence block alignments into structural insights.

Methods Enzymol., 266: 662-680.

 

58.  Davidson I., Romier C., Lavigne A.C., Birck C., Mengus G., Poch O. and Moras D. (1998) Functional and structural analysis of the subunits of human transcription factor TFIID.

Cold Spring Harbor Symposia on Quantitative Biology LXIII: 233-241.

C) Book Chapters

 

59.  Tordo N. and Poch O. (1988) Structure of the rabies virus.

in : Rabies (Campbell J.B. and Charlton K.M., eds) Kluwer Academic Publishers: 25-45.

 

60.  Thompson J. and Poch O. Sequence Alignment.

Encyclopedia Human Genome, in press.

 

61.  Thompson J. and Poch O. Multiple Alignment.

Encyclopedia Human Genome, in press.