CSTB team: Complex Systems and Translational Bioinformatics

Olivier Poch

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Research

Our research interests are mainly focused on the development of robust, automated and integrated in silico approaches (analytical / statistical approaches, data integration and mining, extraction and representation of knowledge ...) to study the evolution and behavior of complex biological systems ("hyperstructures", networks) in humans and various animal models. Taking advantage of our integrated computational approaches and in the context of collaborations at the international, national and local level, we participate in the analysis of complex systems involved in various human diseases (ciliopathies, myopathies), including the study of the links between genetic variations and various functional deficiences (retinal, kidney, lung deficiences, obesity, diabetes, etc.).

On-going projects

Sequence analysis and evolutionary inference

  • Workpackage leader, project ANR Infrastructure : BIP BIP: Bayesian inference paradigm: Biology in Processors
  • Partner European project INSTRUCT European Strategy Forum for Research Infrastructures (ESFRI) : Structural Bioinformatics in Strasbourg Node
  • Partner project ANR (FRISBI) : ‘French Infrastructure for Integrated Structural Biology’

Analysis of Complex Systems

  • Partner project FRM : 1000 exomes contre les myopathies: identification et analyse intégrée de nouveaux gènes
  • Workpackage leader project ANR OncoVaccine: Amélioration génétique du virus de la vaccine TG6002 pour le traitement des cancers résistants
  • orkpackage leader project FRM : Novel genes identification in Bardet-Biedl Syndrome

Infrastructure and knowledge extraction

  • Co-leader project FRM : KBaSS-ViSIOn : Base de Connaissances sur le Système Sensoriel - Information Scientifique sur la Vision En ligne
  • Co-leader project Invest.LIFESENSES Labex : Knowledge Base for Sensory Systems

Publications

Publications in peer-reviewed journals

Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson J, Poch O, Lecompte O. (2014) Orthoinspector v 2.0: software and databases updates. Bioinformatics, in press

Ozdemir BC, Hensel J, Secondini C, Wetterwald A, Schwaninger R, Fleischmann A, Raffelsberger W, Poch O, Delorenzi M, Temanni R, Mills IG, van der Pluijm G, Thalmann GN, Cecchini MG. (2014) The molecular signature of the stroma response in prostate cancer-induced osteoblastic bone metastasis highlights expansion of hematopoietic and prostate epithelial stem cell niches. PLoS One, 9(12):e114530.

Chennen K, Scerbo MJ, Dollfus H, Poch O, Marion V.(2014) Bardet-Biedl syndrome: cilia and obesity - From genes to integrative approaches. Med Sci (Paris), 30(11):1034-1039

Khenoussi W, Vanhoutrève R, Poch O, Thompson JD. (2014) SIBIS: A Bayesian model for inconsistent protein sequence estimation Bioinformatics, 30(17): 2432-2439

Bermejo-Das-Neves C, Nguyen HN, Poch O, Thompson JD. (2014) A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). BMC Bioinformatics, 15(1):111.

Neuillé M, El Shamieh S, Orhan E, Michiels C, Antonio A, Lancelot ME, Condroyer C, Bujakowska K, Poch O, Sahel JA, Audo I, Zeitz C. (2014) Lrit3 deficient mouse (nob6): a novel model of complete congenital stationary night blindness (cCSNB). PLoS One, 9(3):e90342.

Nguyen H, Michel L, Thompson J, Poch O. (2014) Heterogeneous Biological Data Integration with Declarative Query Language. IBM Journal of Res. and Dev., 58 (2/3)

Scheidecker S, Etard C, Pierce NW, Geoffroy V, Schaefer E, Muller J, Chennen K, Flori E, Pelletier V, Poch O, Marion V, Stoetzel C, Strähle U, Nachury MV, Dollfus H. (2014) Exome sequencing of Bardet-Biedl syndrome patient identifies a null mutation in the BBSome subunit BBIP1 (BBS18). Med. Genet., 51(2): 132-136

Audo I, Bujakowska K, Orhan E, El Shamieh S, Sennlaub F, Guillonneau X, Antonio A, Michiels C, Lancelot ME, Letexier M, Saraiva JP, Nguyen H, Luu TD, Leveillard T, Poch O, Dollfus H, Paques M, Goureau O, Mohand-Saïd S, Bhattacharya SS, Sahel JA, Zeitz C. (2014) The familial dementia gene revisited: a missense mutation revealed by whole-exome sequencing identifies ITM2B as a candidate gene underlying a novel autosomal dominant retinal dystrophy in a large family. Hum. Mol. Genet., 23(2): 491-501

Schwenzer H, Scheper GC, Zorn N, Moulinier L, Gaudry A, Leize E, Martin F, Florentz C, Poch O, Sissler M. (2013) Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase. Biochimie, 100:18-26

Allot A, Anno YN, Poidevin L, Ripp R, Poch O, Lecompte O. (2013) PARSEC: PAtteRn SEarch and Contextualization. Bioinformatics, 29(20):2643-44

Bruneaux M, Mary J, Verheye M, Lecompte O, Poch O, Jollivet D, Tanguy A. (2013) Detection and characterisation of mutations responsible for allele-specific protein thermostabilities at the Mn-Superoxide Dismutase gene in the deep-sea hydrothermal vent polychaete Alvinella pompejana. J. Mol. Evol., 76(5):295-310

Nguyen H, Luu TD, Poch O, Thompson JD. (2013) Knowledge discovery in variant databases using inductive logic programming Bioinform. Biol. Insights, 7:119-31.

AMD Gene Consortium. (2013) Seven New Loci Associated with Age-Related Macular degeneration. Nat. Genet., 45(4):433-9

Zeitz C, Jacobson SG, Hamel CP, Bujakowska K, Neuille M, Orhan E, Zanlonghi X,Lancelot ME, Michiels C, Schwartz SB, Bocquet B; Congenital Stationary Night Blindness Consortium, Antonio A, Audier C, Letexier M, Saraiva JP, Luu TD, Sennlaub F, Nguyen H, Poch O, Dollfus H, Lecompte O, Kohl S, Sahel JA, Bhattacharya SS, Audo I. (2013) Whole-Exome Sequencing Identifies LRIT3 Mutations as a Cause of Autosomal-Recessive Complete Congenital Stationary Night Blindness. Am. J. Hum. Genet., 92(1):67-75.

Bedez F, Linard B, Brochet X, Ripp R, Thompson JD, Moras D, Lecompte O, Poch O. (2013) Functional insights into the core-TFIIH from a comparative survey. Genomics, 101:178-186.

Brants J, Semenchenko K, Wasylyk C, Robert A, Carles A, Zambrano A, Pradeau-Aubreton K, Birck C, Schalken JA, Poch O, de Mey J, Wasylyk B. (2012) Tubulin Tyrosine Ligase Like 12, a TTLL Family Member with SET- and TTL-Like Domains and Roles in Histone and Tubulin Modifications and Mitosis. PLoS One, 7(12):e51258.

Bianchetti L, Kieffer D, Federkeil R, Poch O. (2012) Increased frequency of single base substitutions in a population of transcripts expressed in cancer cells. BMC Cancer, 12(1):509.

Kieffer D, Bianchetti L, Poch O, Wicker N. (2012) Perfect sampling on 2 x ... x 2 x K contingency tables with an application to SAGE data. J. of Stat. Planning and Inference, 142 (4): 896-901

Devignes MD, Benabderrahmane S, Smaïl-Tabbone M, Napoli A, Poch O. (2012) Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis. Int. J. Comput. Biol. Drug Des., 5(3-4):245-60.

Luu TD, Rusu A, Walter V, Linard B, Poidevin L, Ripp R, Moulinier L, Muller J, Raffelsberger W, Wicker N, Lecompte O, Thompson JD, Poch O, Nguyen H. (2012) KD4v: Comprehensible Knowledge Discovery System for Missense Variant. Nucleic Acids Res., 40(Web Server issue):W71-5.

De Craene JO, Ripp R, Poch O, Friant S. (2012) Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism. BMC Genomics, 13(1):297

Levasseur A, Paganini J, Dainat J, Thompson JD, Poch O, Pontarotti P, Gouret P. (2012) The chordate proteome history database. Evol. Bioinform. Online, 8:437-47

Anamika K, Gyenis A, Poidevin L, Poch O, Tora L.(2012) RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts. PLoS One, 7(6):e38769

Luu TD, Rusu AM, Walter V, Ripp R, Moulinier L, Muller J, Toursel T, Thompson JD, Poch O, Nguyen NH. (2012) MSV3d: Database of human MisSense Variants mapped to 3D protein structure. Database (Oxford), bas018

Jaillard C, Mouret A, Niepon ML, Clerin E, Yang Y, Lee-Rivera I, Aït-Ali N, Millet-Puel G, Cronin T, Sedmak T, Raffelsberger W, Kinzel B, Trembleau A, Poch O, Bennett J, Wolfrum U, Lledo PM, Sahel JA, Leveillard T. (2012) Nxnl2 splicing results in dual functions in neuronal cell survival and maintenance of cell integrity. Hum. Mol. Genet., 21(10):2298-311

Jollivet D, Mary J, Gagniere N, Tanguy A, Fontanillas E, Boutet I, Hourdez S, Segurens B, Weissenbach J, Poch O, Lecompte O. (2012) Proteome adaptation to high temperatures in the ectothermic hydrothermal vent pompeii worm. PLoS One, 7(2):e31150

Audo I, Bujakowska K, Orhan E, Poloschek CM, Defoort-Dhellemmes S, Drumare I, Kohl S, Luu TD, Lecompte O, Zrenner E, Lancelot ME, Antonio A, Germain A, Michiels C, Audier C, Letexier M, Saraiva JP, Leroy BP, Munier FL, Mohand-Saïd S, Lorenz B, Friedburg C, Preising M, Kellner U, Renner AB, Moskova-Doumanova V, Berger W, Wissinger B, Hamel CP, Schorderet DF, De Baere E, Sharon D, Banin E, Jacobson SG, Bonneau D, Zanlonghi X, Le Meur G, Casteels I, Koenekoop R, Long VW, Meire F, Prescott K, de Ravel T, Simmons I, Nguyen H, Dollfus H, Poch O, Leveillard T, Nguyen-Ba-Charvet K, Sahel JA, Bhattacharya SS, Zeitz C. (2012) Whole-Exome Sequencing Identifies Mutations in GPR179 Leading to Autosomal-Recessive Complete Congenital Stationary Night Blindness. Am. J. Hum. Genet., 90(2):321-30.

Linard B, Nguyen NH, Prosdocimi F, Poch O, Thompson JD. (2012) EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evol. Bioinform. Online, 8:61-77

Prosdocimi F, Linard B, Pontarotti P, Poch O, Thompson JD. (2012) Controversies in modern evolutionary biology: the imperative for error detection and quality control. BMC Genomics, 13(1):5.

Guerin E, Raffelsberger W, Pencreach E, Maier A, Neuville A, Schneider A, Bachellier P, Rohr S, Petitprez A, Poch O, Moras D, Oudet P, Larsen AK, Gaub MP, Guenot D. (2012) In vivo topoisomerase I inhibition attenuates the expression of hypoxia-inducible factor 1α target genes and decreases tumor angiogenesis. Mol. Med., 18(1):83-94.

Clerin E, Wicker N, Mohand-Saïd S, Poch O, Sahel JA, Leveillard T. (2011) ℮-conome: an automated tissue counting platform of cone photoreceptors for rodent models of retinitis pigmentosa. BMC Ophthalmol., 11:38

Delyfer MN, Raffelsberger W, Mercier D, Korobelnik JF, Gaudric A, Charteris DG, Tadayoni R, Metge F, Caputo G, Barale PO, Ripp R, Muller JD, Poch O, Sahel JA, Leveillard T. (2011) Transcriptomic analysis of human retinal detachment reveals both inflammatory response and photoreceptor death. PLoS One, 6(12):e28791.

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, Dollfus H. (2011) Homozygosity mapping and candidate prioritization identify mutations, missed by whole-exome sequencing, in SMOC2, causing major dental developmental defects. Am. J. Hum. Genet., 89(6):773-81.

Lupberger J, Zeisel MB, Xiao F, Thumann C, Fofana I, Zona L, Davis C, Mee CJ, Turek M, Gorke S, Royer C, Fischer B, Zahid MN, Lavillette D, Fresquet J, Cosset FL, Rothenberg SM, Pietschmann T, Pate AH, Pessaux P, Doffoël M, Raffelsberger W, Poch O, McKeating JA, Brino L, Baumert TF. (2011) EGF receptor and EphA2 are hepatitis C virus host entry factors and targets for antiviral therapy. Nature Medecine, 17(5):585-595

Lalevee S, Anno YN, Chatagnon A, Samarut E, Poch O, Laudet V, Benoit G, Lecompte O, Rochette-Egly C. (2011) Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp). J. Biol. Chem., 286(38):33322-34.

Thompson JD, Linard B, Lecompte O, Poch O (2011) A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives. PLoS One, 6(3):e18093

Luu TD, Nguyen NH, Friedrich A, Muller J, Moulinier L, Poch O. (2011) Extracting knowledge from a mutation database related to human monogenic disease using inductive logic programming. International Conference on Bioscience, Biochemistry and Bioinformatics; Singapore. IACSIT Press 5: 83-100

Linard B, Thompson JD, Poch O, Lecompte O. (2011) OrthoInspector: comprehensive orthology analysis and visual exploration BMC Bioinformatics; 12:11

Beau-Faller M, Guennegues M, Guerin E, Raffelsberger W, Poch O, Le Pretre F, Figeac M, Baudrin L , De Fraipont F, Oudet P, Zalcman G. (2011) Prognostic and predictive values of high-resolution molecular DNA markers in non-small cell lung cancers (NSCLC) of IFCT-00-02 trial J. of Thoracic Oncology; 6(6): S616

Anno YN, Myslinski E, Ngondo-Mbongo RP, Krol A, Poch O, Lecompte O, Carbon P. (2011) Genome-wide evidence for an essential role of the Human Staf/ZNF143 transcription factor in bidirectional transcription. Nucleic Acids Res. 39(8):3116-27

Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD. (2010) IntelliGO: a new vector-based semantic similarity measure including annotation origin. BMC Bioinformatics;11(1):588.

Gagniere N, Jollivet D, Boutet I, Brelivet Y, Busso D, Da Silva C, Gaill F, Higuet D, Hourdez S, Knoops B, Lallier F, Leize-Wagner E, Mary J, Moras D, Perrodou E, Rees JF, Segurens B, Shillito B, Tanguy A, Thierry JC, Weissenbach J, Wincker P, Zal F, Poch O, Lecompte O. (2010) Insights into metazoan evolution from Alvinella pompejana cDNAs. BMC Genomics, 11:634.

Anamika K, Krebs AR, Thompson J, Poch O, Devys D, Tora L. (2010) Lessons from genome-wide studies: an integrated definition of the co-activator function of histone acetyl transferases. Epigenetics Chromatin, 3(1):18.

Albou LP, Poch O, Moras D. (2010) M-ORBIS: Mapping of mOleculaR Binding sItes and Surfaces. Nucleic Acids Res., 39(1):30-43

Audo I, Friedrich A, Mohand-Saïd S, Lancelot ME, Antonio A, Moskova-Doumanova V, Poch O, Bhattacharya S, Sahel JA, Zeitz C. (2010) An unusual retinal phenotype associated with a novel mutation in RHO. Arch. Ophthalmol., 128(8):1036-45.

Aniba MR, Poch O, Thompson JD. (2010) Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res., 38(21):7353-68.

Bard N, Bolze R, Caron E, Desprez F, Heymann M, Friedrich A, Moulinier L, Nguyen NH, Poch O, Toursel T. (2010) Decrypthon grid - grid resources dedicated to neuromuscular disorders. Stud. Health Technol. Inform., 159:124-33.

Aniba MR, Poch O, Marchler-Bauer A, Thompson JD. (2010) AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res., 38(19):6338-49.

Muller J, Stoetzel C, Vincent MC, Leitch CC, Laurier V, Danse JM, Helle 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, Cossee M, Davis EE, Katsanis N, Bonneau D, Verloes A, Poch O, Mandel JL, Dollfus H. (2010) Identification of 28 novel mutations in the Bardet-Biedl syndrome genes: the burden of private mutations in an extensively heterogeneous disease. Hum. Genet., 127(5):583-93.

Berge C, Froloff N, Kalathur RK, Maumy M, Poch O, Raffelsberger W, Wicker N. (2010) Multidimensional fitting for multivariate data analysis. J. Comput. Biol., 17(5):723-32.

Audo I, Manes G, Mohand-Saïd S, Friedrich A, Lancelot ME, Antonio A, Moskova-Doumanova V, Poch O, Zanlonghi X, Hamel CP, Sahel JA, Bhattacharya SS, Zeitz C. (2010) Spectrum of rhodopsin mutations in French autosomal dominant rod-cone dystrophy patients. Invest. Ophthalmol. Vis. Sci., 51(7):3687-700.

Cronin T, Raffelsberger W, Lee-Rivera I, Jaillard C, Niepon ML, Kinzel B, Clerin E, Petrosian A, Picaud S, Poch O, Sahel JA, Leveillard T. (2010) The disruption of the rod-derived cone viability gene leads to photoreceptor dysfunction and susceptibility to oxidative stress. Cell Death Differ., 17(7):1199-210.

Friedrich A, Garnier N, Gagniere N, Nguyen H, Albou LP, Biancalana V, Bettler E, Deleage G, Lecompte O, Muller J, Moras D, Mandel JL, Toursel T, Moulinier L, Poch O. (2010) SM2PH-db: an interactive system for the integrated analysis of phenotypic consequences of missense mutations in proteins involved in human genetic diseases. Hum. Mutat., 31(2):127-35.

Delacroix L, Moutier E, Altobelli G, Legras S, Poch O, Choukrallah MA, Bertin I, Jost B, Davidson I. (2010) Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic fibroblasts and embryonic stem cells. Mol. Cell. Biol., 30(1):231-44.

Reichman S, Kalathur RK, Lambard S, Aït-Ali N, Yang Y, Lardenois A, Ripp R, Poch O, Zack DJ, Sahel JA, Leveillard T. (2010) The homeobox gene CHX10/VSX2 regulates RdCVF promoter activity in the inner retina. Hum. Mol. Genet., 19(2):250-61

Gazdag E, Santenard A, Ziegler-Birling C, Altobelli G, Poch O, Tora L, Torres-Padilla ME. (2009) TBP2 is essential for germ cell development by regulating transcription and chromatin condensation in the oocyte. Genes Dev., 23(18):2210-23.

Fridlich R, Delalande F, Jaillard C, Lu J, Poidevin L, Cronin T, Perrocheau L, Millet-Puel G, Niepon ML, Poch O, Holmgren A, Van Dorsselaer A, Sahel JA, Leveillard T. (2009) The thioredoxin-like protein RdCVFL interacts with Tau and inhibits its phosphorylation in the retina. Mol. Cell. Proteomics, 8(6):1206-18.

Ruano-Rubio V, Poch O, Thompson JD. (2009) Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods. BMC Bioinformatics, 10:383.

Vetter G, Bechec AL, Muller J, Muller A, Moes M, Yatskou M, Altanoury Z, Poch O, Vallar L, Friederich E. (2009) Time-resolved analysis of transcriptional events during SNAI1-triggered epithelial to mesenchymal transition. Biochem. Biophys. Res. Commun., 385(4):485-91.

Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C. (2009) Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family. PLoS One, 4(3):e4712

Aniba MR, Siguenza S, Friedrich A Plewniak F, Poch O, Marchler-Bauer A, Thompson JD. (2009) Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis. Brief Bioinfo., 10(1):11-23.

Gallien S, Perrodou E, Carapito C, Deshayes C, Reyrat JM, Van Dorsselaer A, Poch O, Schaeffer C, Lecompte O. (2009) Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res., 19(1):128-35.

Albou LP, Schwarz B, Poch O, Wurtz JM, Moras D. (2009) Defining and characterizing protein surface using alpha shapes. Proteins, 76(1):1-12

Becker JA, Befort K, Blad C, Filliol D, Ghate A, Dembele D, Thibault C, Koch M, Muller J, Lardenois A, Poch O, Kieffer BL. (2008) Transcriptome analysis identifies genes with enriched expression in the mouse central extended amygdala. Neuroscience, 156(4):950-65.

Levasseur A, Pontarotti P, Poch O, Thompson JD. (2008) Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Evol. Bioinform. Online, 4:121-37.

Lecompte O, Poch O, Laporte J. (2008) PtdIns5P regulation through evolution: roles in membrane trafficking? Trends Biochem. Sci., 33(10):453-60

Befort K, Filliol D, Darcq E, Ghate A, Matifas A, Lardenois A, Muller J, Thibault C, Dembele D, Poch O, Kieffer BL. (2008) Gene expression is altered in the lateral hypothalamus upon activation of the mu opioid receptor. Ann. N. Y. Acad. Sci., 1129:175-84.

Befort K, Filliol D, Ghate A, Darcq E, Matifas A, Muller J, Lardenois A, Thibault C, Dembele D, Le Merrer J, Becker JA, Poch O, Kieffer BL. (2008) Mu-opioid receptor activation induces transcriptional plasticity in the central extended amygdala. Eur. J. Neurosci., 27(11):2973-84.

Kalathur RK, Gagniere N, Berthommier G, Poidevin L, Raffelsberger W, Ripp R, Leveillard T, Poch O. (2008) RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina. BMC Genomics, 9:208.

Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD. (2008) A new protein linear motif benchmark for multiple sequence alignment software. BMC Bioinformatics, 9:213.

Deshayes C, Perrodou E, Euphrasie D, Frapy E, Poch O, Bifani P, Lecompte O, Reyrat JM. (2008) Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences. BMC Evol. Biol., 6(8):78

Lagier-Tourenne C, Tazir M, López LC, Quinzii CM, Assoum M, Drouot N, Busso C, Makri S, Ali-Pacha L, Benhassine T, Anheim M, Lynch DR, Thibault C, Plewniak F, Bianchetti L, Tranchant C, Poch O, DiMauro S, Mandel JL, Barros MH, Hirano M, Koenig M. (2008) ADCK3, an ancestral kinase, is mutated in a form of recessive ataxia associated with coenzyme Q10 deficiency. Am. J. Hum. Genet., 82(3):661-72.

Thiersch M, Raffelsberger W, Frigg R, Samardzija M, Wenzel A, Poch O, Grimm C. (2008) Analysis of the retinal gene expression profile after hypoxic preconditioning identifies candidate genes for neuroprotection. BMC Genomics, 9:73.

Thiersch M, Raffelsberger W, Frigg E, Samardzija M, Blank P, Poch O, Grimm C. (2008) The hypoxic transcriptome of the retina: identification of factors with potential neuroprotective activity. Adv. Exp. Med. Biol., 613:75-85.

Raffelsberger W, Krause Y, Moulinier L, Kieffer D, Morand AL, Brino L, Poch O. (2008) RReportGenerator: automatic reports from routine statistical analysis using R. Bioinformatics, 24(2):276-8.

Bianchetti L, Wu Y, Guerin E, Plewniak F, Poch O. (2007) SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. Nucleic Acids Res., 35(18):e122

Schluter A, Fourcade S, Domenech-Estevez E, Gabaldon T, Huerta-Cepas J, Berthommier G, Ripp R, Wanders RJ, Poch O, Pujol A. (2007) PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. Nucleic Acids Res., 35(Database issue):D815-22.

Zrenner E, Wilke R, Troeger E, Ayuso C, Vallespin E, Silva E, Scholl H, Bellmann C, Ripp R, Poch O, Cunha-Vaz J, Sahel J, Chakravarthy U, Moore T. (2007) The EVI-genoret phenotype / genotype patient database: a pan-European tool for retinal dystrophies and age related macular degeneration. Acta Ophthalmologica Scandinavica, 85: S240.

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. (2007) Identification of a novel BBS gene (BBS12) highlights the major role of a vertebrate-specific branch of chaperonin-related proteins in Bardet-Biedl syndrome. Am. J. Hum. Genet., 80(1):1-11.

Deshayes C, Perrodou E, Gallien S, Euphrasie D, Schaeffer C, Van-Dorsselaer A, Poch O, Lecompte O, Reyrat JM. (2007) Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors? Genome Biol., 8(2):R20

Friedrich A, Ripp R, Garnier N, Bettler E, Deleage G, Poch O, Moulinier L. (2007) Blast sampling for structural and functional analyses. BMC Bioinformatics, 8:62.

Wicker N, Carles A, Mills IG, Wolf M, Veerakumarasivam A, Edgren H, Boileau F, Wasylyk B, Schalken JA, Neal DE, Kallioniemi O, Poch O. (2007) A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics, 8(1):84

Brulliard M, Lorphelin D, Collignon O, Lorphelin W, Thouvenot B, Gothie E, Jacquenet S, Ogier V, Roitel O, Monnez JM, Vallois P, Yen FT, Poch O, Guenneugues M, Karcher G, Oudet P, Bihain BE. (2007) Nonrandom variations in human cancer ESTs indicate that RNA heterogeneity increases during carcinogenesis. Proc. Natl. Acad. Sci. U S A, 104(18):7522-7.

Muller J, Mehlen A, Vetter G, Yatskou M, Muller A, Chalmel F, Poch O, Friederich E, Vallar L. (2007) Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton. BMC Genomics, 8(1):294

Chalmel F, Leveillard T, Jaillard C, Lardenois A, Berdugo N, Morel E, Koehl P, Lambrou G, Holmgren A, Sahel JA, Poch O. (2007) Rod-derived Cone Viability Factor-2 is a novel bifunctional-thioredoxin-like protein with therapeutic potential. BMC Mol. Biol., 8(1):74

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, Silva ED, Rossillion B, Sigaudy S, de Ravel TJ, Lewis RA, Leheup B, Verloes A, Amati-Bonneau P, Megarbane A, Poch O, Bonneau D, Beales PL, Mandel JL, Katsanis N, Dollfus H. (2006) BBS10 encodes a vertebrate-specific chaperonin-like protein and is a major BBS locus. Nat. Genet., 38(5):521-4. Erratum in: Nat Genet. 2006 Jun;38(6):727.

Gaillard E, Bruck N, Brelivet Y, Bour G, Lalevee S, Bauer A, Poch O, Moras D, Rochette-Egly C. (2006) Phosphorylation by PKA potentiates retinoic acid receptor alpha activity by means of increasing interaction with and phosphorylation by cyclin H/cdk7. Proc. Natl. Acad. Sci. U S A., 103(25):9548-53.

Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, Plewniak F, Poch O. (2006) MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics, 7:318.

Garnier N, Friedrich A, Bolze R, Bettler E, Moulinier L, Geourjon C, Thompson JD, Deleage G, Poch O. (2006) MAGOS: multiple alignment and modelling server. Bioinformatics, 22(17):2164-5.

Laurier V, Stoetzel C, Muller J, Thibault C, Corbani S, Jalkh N, Salem N, Chouery E, Poch O, Licaire S, Danse JM, Amati-Bonneau P, Bonneau D, Megarbane A, Mandel JL, Dollfus H. (2006) Pitfalls of homozygosity mapping: an extended consanguineous Bardet-Biedl syndrome family with two mutant genes (BBS2, BBS10), three mutations, but no triallelism. Eur. J. Hum. Genet., 14(11):1195-203.

Lardenois A, Chalmel F, Bianchetti L, Sahel JA, Leveillard T, Poch O. (2006) PromAn: an integrated knowledge-based web server dedicated to promoter analysis. Nucleic Acids Res., 34(Web Server issue):W578-83.

Dollfus H, Muller J, Stoetzel C, Laurier V, Bonneau D, Megarbane A, Poch O, Mandel JL. (2006) [Bardet-Biedl syndrome: a unique family for a major gene (BBS10)] Med. Sci. (Paris), 22(11):901-4.

Carles A, Millon R, Cromer A, Ganguli G, Lemaire F, Young J, Wasylyk C, Muller D, Schultz I, Rabouel Y, Dembele D, Zhao C, Marchal P, Ducray C, Bracco L, Abecassis J, Poch O, Wasylyk B. (2006) Head and neck squamous cell carcinoma (HNSCC) transcriptome analysis by comprehensive validated differential display. Oncogene, 25 (12):1821-1831.

Perrodou E, Deshayes C, Muller J, Schaeffer C, Van Dorsselaer A, Ripp R, Poch O, Reyrat JM, Lecompte O. (2006) ICDS database: interrupted CoDing sequences in prokaryotic genomes. Nucleic Acids Res., 34(Database issue):D338-43.

Abou-Sleymane G, Chalmel F, Helmlinger D, Lardenois A, Thibault C, Weber C, Merienne K, Mandel JL, Poch O, Devys D, Trottier Y. (2006) Polyglutamine expansion causes neurodegeneration by altering the neuronal differentiation program. Hum. Mol. Genet., 15(5):691-703.

Schluter A, Fourcade S, Ripp R, Mandel JL, Poch O, Pujol A. (2006) The evolutionary origin of peroxisomes: an ER-peroxisome connection. Mol. Biol. Evol., 23(4):838-45.

Leveillard T, Mohand-Said S, Poch O, Sahel JA. (2005) [Rod-derived cone viability factor : a clue for therapy of retinitis pigmentosa?] French. Med. Sci. (Paris), 21(1):22-24.

Chalmel F, Lardenois A, Thompson JD, Muller J, Sahel JA, Leveillard T, Poch O. (2005) GOAnno: GO annotation based on multiple alignment. Bioinformatics, 21(9):2095-6.

Thompson JD, Holbrook SR, Katoh K, Koehl P, Moras D, Westhof E, Poch O. (2005) MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res., 33(13):4164-71.

Thompson JD, Koehl P, Ripp R, Poch O. (2005) BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins, 61(1):127-136.

Bianchetti L, Thompson JD, Lecompte O, Plewniak F, Poch O. (2005) vALId: validation of protein sequence quality based on multiple alignment data. Bioinform. Comput. Biol., 3(4):929-947.

Muller J, Oma Y, Vallar L, Friederich E, Poch O, Winsor B. (2005). Sequence and comparative genomic analysis of Actin Related Proteins. Mol. Biol. Cell., 16(12):5736-5748.

Uhring M, Bey G, Lecompte O, Cavarelli J, Moras D, Poch O. (2005) Cloning, purification and crystallization of a Walker-type Pyrococcus abyssi ATPase family member. Acta Crystallograph Sect F Struct Biol Cryst Commun., 61(Pt 10):925-7.

Thompson J, Prigent V, Poch O. (2004) LEON: multiple aLignment Evaluation Of Neighbours. Nucleic Acids Res., 32(4): 1298-1307.

Cromer A, Carles A, Millon R, Ganguli G, Chalmel F, Lemaire F, Young J, Dembele D, Thibault C, Diemunsch F, Poch O, Abecassis J, Wasylyk B. (2004) Identification of genes associated with hypopharyngeal cancer and metastatic potential by microarray analysis. Oncogene, 23(14):2484-2498.

Leveillard T, Mohand-Saïd S, Lorentz O, Hicks D, Fintz AC, Clerin E, Simonutti M, Forster V, Cavusoglu N, Chalmel F, Dolle P, Poch O, Lambrou G, Sahel JA. (2004) Identification and characterization of rod-derived cone viability factor. Nat. Genetics, 36(7):755-759

Brelivet Y, Kammerer S, Rochel N, Poch O, Moras D. (2004) Signature of the oligomeric behaviour of nuclear receptors at the sequence and structural level. EMBO reports, 5(4):423-429

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):14420-14430.

Prigent V, Thierry JC, Poch O, Plewniak F. (2004) DbW: automatic update of a functional family-specific multiple alignment. Bioinformatics, 21(8):1437-42.

Cohen G, Barbe V, Flament D, Galperin M, Heilig R, Ripp R, Lecompte O, Prieur D, Poch O, Querellou J, Thierry JC, Van der Oost J, Weissenbach J, Zivanovic Y, Forterre P. (2003) An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol. 47(6):1495-1512.

Gozuacik D, Chami M, Murakami Y, Faivre J, Lagorce D, Poch O, Biermann E, Knippers R, Brechot C, Paterlini-Brechot P. (2003) Identification and functional characterization of a new member of the human Mcm protein family: hMcm8. Nucleic Acids Res., 31(2): 570-579.

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 JC, Thompson J, Wicker N, Poch O. (2003) PipeAlign : a new toolkit for protein family analysis. Nucleic Acids Res., 31(13): 3829-3832.

Thompson JD, Thierry JC, Poch O. (2003) RASCAL: Rapid scanning and correction of multiple sequence alignment programs. Bioinformatics, 19(9):1155-1161.

Cavusoglu N, Thierse D, Mohand-Said S, Chalmel F, Poch O, Van Dorsselaer A, Sahel JA, 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.

Duval D, Duval G, Kedinger C, Poch O, 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.

Bianchetti L, Oudet C, 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.

Wicker N, Dembele D, Raffelsberger W, Poch O. (2002) Density of points clustering, application to transcriptomic data analysis. Nucleic Acids Res., 30(18):3992-4000.

Lecompte O, Ripp R, Thierry JC, Moras D, 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.

Bahr A, Thompson JD, Thierry JC, Poch O. (2001) BAliBASE (Benchmark alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res., 29 (1): 323-326.

Mayer C, Suck D, 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.

Lecompte O, Ripp R, Puzos-Barbe V, Duprat S, Heilig R, Dietrich J, Thierry JC, Poch O. (2001) Genome evolution at the genus level : comparison of three complete genomes of hyperthermophilic Archaea. Genome Research, 11 (6): 981-993.

Lecompte O, Thompson JD, Plewniak F, Thierry JC, Poch O. (2001) Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene, 270:17-30.

Wicker N, Perrin GR, Thierry JC, Poch O. (2001) Secator: a program for inferring protein subfamilies from phylogenetic trees. Mol. Biol. Evol., 18 (8): 1435-41.

Thompson JD, Plewniak F, Ripp R, Thierry JC, Poch O. (2001) Towards A Reliable Measure for Multiple Sequence Alignments J. Mol. Biol., 314 (4): 937-951.

Plewniak F, Thompson JD, Poch O. (2000) Ballast : blast post-processing based on locally conserved segments. Bioinformatics, 16(9): 750-759.

Thompson JD, Plewniak F, Poch O. (2000) DbClustal : rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res., 28(15): 2919-2926.

Gangloff YG, Werten S, Romier C, Carre L, Poch O, Moras D, 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.

Thompson JD, Plewniak F, Poch O. (1999) BAliBASE: A benchmark alignment database for the evaluation of multiple sequence alignment programs. BioInformatics, 15(1): 87-88.

Thompson JD, Plewniak F, Poch O. (1999) A comprehensive comparison of protein sequence alignment programs. Nucleic Acids Res., 27(13): 2682-2690.

Lavigne AC, Gangloff YG, Carre L, Mengus G, Birck C, Poch O, Romier C, Moras D, 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.

Dantonel JC, Wurtz JM, Poch O, Moras D, Tora L. (1999) The TBP-like factor : an alternative transcription factor in metazoa ? Trends Biochem. Sci., 24(9): 335-9.

Birck C, Poch O, Romier C, Ruff M, Mengus G, Lavigne AC, Davidson I, 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.

Poterszman A, Lamour V, Egly JM, Moras D, Thierry JC, Poch O. (1997) A eukaryotic XPB/ERCC3-like helicase in Mycobacterium leprae? Trends Biochem. Sci., 22(11): 418-419.

Bordonne R, Camasses A, Madania A, Poch O, Tarassov I, Winsor B, Martin R. (1997) Analysis of a 35.6 kb region on the right arm of Saccharomyces cerevisiae chromosome XV. Yeast, 13(1): 73-83.

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., … Kleine K. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature, 387(6632 Suppl): 98-102.

Friant S, Heyman T, Poch O, Wilhelm M, Wilhelm FX. (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.

Poch O, 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.

Poch O. (1997) Conservation of a putative inhibitory domain in the GAL4 family members. Gene, 184(2): 229-235.

Madania A, Poch O, Tarassov I, Winsor B, Martin R. (1996) Analysis of a 22,956 bp region on the right arm of Saccharomyces cerevisiae chromosome XV. Yeast, 12(15): 1563-1573.

Poch O, Schwob E, de Fraipont F, Camasses A, Bordonne R, Martin R. (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.

Muller R, Poch O, Delarue M, Bishop DH, 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.

De Murcia G, Schreiber V, Molinete M, Saulier B, Poch O, Masson M, Niedergang C, Menissier-de Murcia J. (1994) Structure and function of poly(ADP-ribose) polymerase. Mol. Cell. Biochem., 138(1-2): 15-24.

Simonin F, Poch O, Delarue M, de Murcia G. (1993) Identification of potential active-site residues in the human poly(ADP-ribose) polymerase. J. Biol. Chem., 268(12): 8529-8535.

Poch O, L’Hote H, Dallery V, Debeaux F, Fleer R, Sodoyer R. (1992) Sequence of the Kluyveromyces lactis beta-galactosidase: comparison with prokaryotic enzymes and secondary structure analysis. Gene, 118(1): 55-63.

Delarue M, Poch O, Tordo N, Moras D, Argos P. (1990) An attempt to unify the structure of polymerases. Protein Eng., 3(6): 461-467.

Schmitter D, Poch O, Zeder G, Heinrich GF, Kocher HP, Quesniaux VF, Van Regenmortel MH. (1990) Analysis of the structural diversity of monoclonal antibodies to cyclosporine. Mol. Immunol., 27(10): 1029-1038.

Simonin F, Menissier-de Murcia J, Poch O, Muller S, Gradwohl G, Molinete M, Penning C, Keith G, 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.

Eriani G, Delarue M, Poch O, Gangloff J, Moras D. (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature, 347(6289): 203-206.

Poch O, Blumberg BM, Bougueleret L, 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.

Poch O, Sauvaget I, Delarue M, Tordo N. (1989) Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J., 8(12): 3867-3874.

Poch O, Tordo N, 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. ochimie, 70(8): 1019-1029.

Tordo N, Poch O, Ermine A, Keith G, 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.

Tordo N, Poch O, Ermine A, Keith G, 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.

Tordo N, Poch O, Ermine A, 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.

Tibayrenc M, Hoffmann A, Poch O, Echalar L, Le pont F, Lemesre JL, Desjeux P, Ayala FJ. (1986) Additional data on Trypanosoma cruzi isozymic strains encountered in Bolivian domestic transmission cycles. Trans. R. Soc. Trop. Med. Hyg., 80(3): 442-447.

Tordo N, Poch O, Keith, G and Ermine A. (1985) Primary structure of the rabies Pasteur virus genome Biological ChemistryHoppe-Seyler; 366 (9): 860-861.

Carrasco RL, Breniere SF, Poch O, Miguez HV, Selaes H, Antezana G, Desjeux P, Carlier Y. (1985) Chagas serology and its problems. Ann. Soc. Belg. Med. Trop., 65(1): 79-84.

Tibayrenc M, Cariou ML, Solignac M, Delet JP, Poch O, 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.

Breniere SF, Poch O, Selaes H, Tibayrenc M, Lemesre JL, Antezana G, Desjeux P. (1984) Specific humoral depression in chronic patients infected by Trypanosoma cruzi. Rev. Inst. Med. Trop. Sao Paulo, 26(5): 254-258.

Tibayrenc M, Echalar L, Dujardin JP, Poch O, 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.


Review articles
Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K. (2006) SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr. 62(Pt 10):1184-95.

Thompson JD, Poch O. (2005) Multiple sequence alignment as a workbench for molecular systems biology. Current Bioinformatics, 1: 95-104.

Davidson I, Romier C, Lavigne AC, Birck C, Mengus G, Poch O, 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.

Poch O, Delarue M. (1996) Converting sequence block alignments into structural insights. Methods Enzymol., 266: 662-680.

Tordo N, De Haan P, Goldbach R, Poch O. (1992) Evolution of negative-stranded RNA genomes. Seminars in Virology, 3(1): 341-357.

Poch O, Tordo N, Ermine A, Keith G, Rougeon F. (1987) One century latter…the rabies virus. Bull. Acad. Natl. Med., 171(8): 1087-1094.


Book chapters
Nguyen H, Thompson JD, Schutz P, Poch O. (2014) Intelligent Integrative Knowledge Bases: Bridging Genomics, Integrative Biology and Translational Medicine. In Interactive Knowledge Discovery and Data Mining in Biomedical Informatics. Lecture Notes in Computer Science, Springer.

Benabderrahmane S, Devignes MD, Tabbone MS, Napoli A, Poch O. (2011) Ontology-based functional classification of genes: Evaluation with reference sets and overlap analysis In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) pp 201-208

Friedrich A, Poch O, Moulinier L. (2009) Strategies for efficient exploitation of the informational content of protein multiple alignments. In SEQUENCE ALIGNMENT: METHODS, MODELS, CONCEPTS, AND STRATEGIES, 271-295 ed. M.S. Rosenberg

Shengyin Gu S, Poch O, Hamann B, Koehl P. (2007) A Geometric Representation of Protein Sequences. Proceedings IEEE International Conference on Bioinformatics & Biomedicine, BIBM 2007, 135-142

Thompson JD, Poch O. (2005) New Challenges and Strategies for Multiple Sequence Alignment in the Proteomics Era. The Proteomics Protocols Handbook, Humana Press, March 2005 pp. 475-492.

Thompson JD, Poch O. (2003) Sequence Alignment. Nature Encylopedia of the human genome, Nature Publishing Group, June 2003

Thompson JD, Poch O. (2003) Multiple Alignment. Nature Encylopedia of the human genome, Nature Publishing Group, June 2003

Tordo N, Poch O. (1988) Structure of the rabies virus. in : Rabies (Campbell J.B. and Charlton K.M., eds) Kluwer Academic Publishers: 25-45.


Conference presentations
Ozdemir B, Secondini C, Wetterwald A, Schwaninger R, Raffelsberger W, Poch O, Delorenzi M, van der Pluijm G, Thalmann GN, Cecchini MG. (2011) Molecular characterization of the stromal response to osteoblastic bone metastasis by tissue-compartment specific transcriptional profiling Bone, 48:p41-10th International Conference on Cancer - Induced Bone Disease Sheffield, England, Sept 22-25, 2010

Lupberger J, Thumann C, Soulier E, Fischer B, Froidevaux L, Zeisel MB, Gorke S, Fofana I, Royer C, Wolf P, Raffelsberger W, Poch O, Brino L, Baumert TF. (2009) A genome-wide RNAI kinase screen identifies kinase networks involved in cell polarity as co-factors for hepatitis C virus entry and targets for antivral therapies. Hepatology, 50: 314A in 60th Annual Meeting of the American-Association-for-the-Study-of-Liver- Diseases; Boston Oct 30-NOV 03, 2009

Nguyen H, Friedrich A, Berthommier G, Poidevin L, Moulinier L, Ripp R, Poch O. (2008) Introduction to the new Biomedical Decrypthon Data Center. CORIA 2008, Hermes Edition.

Tordo N, Poch O, Ermine A, Keith G, Rougeon F. (1988) Genetique moleculaire du virus de la rage, un siecle apres Pasteur. in : Molecular Biology and Infectious Diseases (M. Schartz, ed.) Colloque International du Centenaire de l’Institut Pasteur. Elsevier. Paris: 31-40.


Publications in journals not peer reviewed
Poch O, Thierry J.C. (2000) Bioinformatics: Targets and developments within the Strasbourg, Alsace and Lorraine Genopôle project. BioValley Newsletter, 3-4: 26-27.

Other activities

Editorial board

  • Since 2014 : BMC Bioinformatics


Journal Referee

  • Since 1996 : Bioinformatics, BMC Bioinformatics, Nucleic Acids Research, Proteins, PLOS Bioinformatics


Organisation of conferences

  • Member of organising committee, 13th European Conference Computational Biology (ECCB’14), Strasbourg 7-10/09/2014.
  • Chair des workshops et tutoriaux, 13th European Conference Computational Biology (ECCB’14); Strasbourg 6-7/09/2014
  • Member of organising committee, 5th international conference on Bioinformatic models, methods and algorithms «Bioinformatics 2014 » Angers - 3-6/3/2014
  • Member of organising committee JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques) 2009-2011


Teaching

  • 1997-2000 Masters Chemistry Biology 9 h/year
  • 1997-2000 DEA Genome analysis and molecular modelling Paris VII 4 h/year
  • 2000-2004 Bioinformatics and Genomics DESS EGOISt Rouen 15 h/year
  • 2000-2012 Bioinformatics and Genomics ESBS Strasbourg 15 h/year
  • 2001-2012 Bioinformatics and Genomics, DEPULP, Strasbourg 15 h/year
  • 2006-2012 Module “Bioinformatics in the post-genomics era”, Doctoral School (Strasbourg) 6 days
  • 2007-2010 Module “Bioinformatics in the post-genomics era”, IGBMC (Strasbourg) 4 days
  • 2010-2010 Introduction to Bioinformatics: Sequence Analysis; Buenos Aires 3 days
  • 2012- Bioinformatics and Genomics, Institut Pasteur, Paris 12 h/year
  • 2014- Double Cursus Medicine-Science Faculty of Medicine Strasbourg 3 h/year


Supervision
PhD supervision : 21

  • 1991-1995 Florence de Fraipont (Moelcular biology)
  • 1999-2002 Odile Lecompte (Bioinformatics)
  • 1999-2002 Nicolas Wicker (Bioinformatics)
  • 2001-2004 Frédérique Chalmel (Bioinformatics)
  • 2002-2004 Jean Muller (Bioinformatics, co-direction E. Freiderich)
  • 2003-2005 Aurélie Lardenois (Bioinformatics)
  • 2004-2008 Ravikiran Reddy (Bioinformatics)
  • 2004-2007 Anne Friedrich (Bioinformatics, puis Post-Doctorat, puis MdC UdS)
  • 2004-2006 Julie Thompson (Bioinformatics, co-direction P. Koehl, puis CR/DR CNRS)
  • 2004-2009 Florence Bedez (Biologie/Bioinformatics, co-direction : Arnaud Poterzman)
  • 2005-2008 Yann Brelivet (Bioinformatics, co-direction D. Moras, puis Post-Doctorat)
  • 2005-2009 Radhouene Aniba (Bioinformatics, co-direction J. Thompson)
  • 2006-2009 David Kieffer (Bioinformatics)
  • 2006-2009 Nicolas Gagnière (Bioinformatics, co-direction O. Lecompte)
  • 2007-2010 Laurent Philippe Albou (Bioinformatics, co-direction D. Moras)
  • 2007-2010 Yannick Anno (Bioinformatics, co-direction O. Lecompte)
  • 2007-2011 Sidahmed Benabderrahmane (Bioinformatics, co-direction M.D. Devignes)
  • 2008-2012 Tien-Dao Luu (Bioinformatics)
  • 2012- Alexis Allot (Bioinformatics, co-direction O. Lecompte)
  • 2012- Kirsley Chennen (Bioinformatics, co-direction H Dollfus)
  • 2013- Carlos Bermejo Das Neves (Bioinformatics, co-direction J. Thompson)


Supervision Post-docs : 10

  • 1999-2000 Anne Bahr
  • 2004-2008 Wolfgang Raffelsberger
  • 2004-2009 Emmanuel Perrodoux
  • 2005-2013 Hoan Nguyen
  • 2007-2009 Anne Friedrich
  • 2008-2009 Francisco Prosdocimi
  • 2008-2009 Valentin Ruano-Rubio
  • 2008-2010 Yann Brelivet
  • 2009-2010 Krishanpal Anamika
  • 2010-2012 Xavier Brochet

Animation Scientifique

  • 2001- PhD Jurys : 17
  • 2001- HDR Jurys : 5
  • 2001- Recruitment committee member University Lecturer / Professor : 11
  • 2001- Committee member AERES : 2
  • 2006- Expertise Projects ANR
  • 2005- Expertise Projects AFM ; AFM-Decrypthon
  • 2013- Expertise Projects FRM, Committee member
  • 2003-2005 Committee member IDRIS
  • 2004-2006 Expertise Procjets, Committee member Horizon Programme on Bioinformatics (Netherland Genomics Initiative)
  • 2004 Expertise CNRS - Programme Proteomics and Protein Engineering
  • 2004 Action Concertée Incitative IMPbio
  • 2005-2006 Comité Génopole-CRNG (National Comity for Genomic Research)
  • 2005-2006 Expertise, Committee member FP6-2005-LIFESCIHEALTH-6 (Life Science Genomics and Biotechnology for Health) Programs: Specific Support Action and Co-ordination Action
  • 2007 Expertise of Projects Brittany Region
  • 2008 Expertise, Committee member Project GENOSCOPE, Institut de Génomique CEA/DSV
  • 2008-2013 Jury of Doctoral School IViV Paris
  • 2010-2011 PhD Program IGBMC
  • 2010 Committee member ANR
  • 2010-2012 Consultant Projects AFM/Société Rhenovia
  • 2012 Committee member Evaluation Project Swiss National Science Foundation
  • 2012-2013 Committee member Evaluation Projects CHU Dijon
  • 2012 Evaluation Research and Development Pilot Projects INSTRUCT
  • 2013-2014 International Program Comittee BIOINFORMATICS 2014
  • International Program Comittee BIOINFORMATICS 2015

Member

  • Department of Genetics, Institut de la Vision, Paris
  • Association for the Research In Vision and Ophtalmology (ARVO).
  • Working group: "GRID’5000 Plate-forme de recherche experimentale en informatique"
  • Working group: Biologie et Santé de l'Institut des Grilles
  • RENABI ; Réseau National des Plateformes de Bioinformatique
  • French Bioinformatics Institute (IFB)

Founder member

  • Startup ALIX RCS Strasbourg
  • Startup BioNext


Patents

  • 1987 DNA sequences derived from the rabies virus genome ; numéro EP0237686
  • 2000 Séquence génomique et polypeptides de Pyrococcus abyssi, numéro 9905034
  • 2005 Séquence RdCVF (Rod derived Cone Viability Factor), fragments et utilisations
  • 2008 Marqueurs biologiques de ‘l’Infidélité de la Transcription’ dans les cancers
  • 2009 Neuronal viability factor and use thereof, USPTO 20100247496

Contact

Dr. Olivier Poch
ICube, UMR CNRS 7357
Faculté de Médecine
Bât. 3 5e étage,
11 rue Humann
F-67000 Strasbourg

Mailing address: Faculté de Médecine, ICube, UMR 7357, LBGI - 4, rue Kirschleger - F-67085 Strasbourg cedex

Tel : +33 (0)3 68 85 32 95
email : olivier.poch@unistra.fr

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