Le langage universel du vivant c'est la chimie qui se déroule derrière.

Survol

Bernard OFFMANN

Professeur Université

section 64
Équipe :

Thèmes de recherche

Développements méthodologiques en bioinformatique structurale

  • approches autour d’un alphabet structural (les blocs protéiques) pour l’analyse et la prédiction des structures des protéines
  • approches computationnelles pour l’évolution dirigée et l’ingénierie des protéines
  • caractérisation structurale et fonctionnelle de grandes familles de protéines

Les applications

  • développement de méthodes et logiciels pour la reconnaissance du repliement des protéines à l’échelle des génomes
  • le protein design
  • la caractérisation et l’ingénierie des enzymes actifs sur les sucres
  • les bases structurales de l’olfaction dans le vivant notamment chez le moustique

Mes logiciels et bases de données

  1. iMutate : simulation de mutagénèse dirigée
  2. PB-kPRED : prédiction de squelette cartonnée des protéines à l’aide des blocs protéiques
  3. FORSA : reconnaissance du repliement des protéines à l’aide des blocs protéiques
  4. PENTAPEPT : base de données de pentapeptides constitutifs des structures des protéines
  5. PBE : Protein Block Expert (plateforme d’outils autour des blocs protéiques)
  6. mOBPdb : Mosquito odorant binding proteins database

Mots-clés : , , , , , , ,

Projets

Parcours universitaire

2006 – Habilitation à diriger des recherches. Université de La Réunion. Nouvelles approches en bioinformatique pour l’analyse et la prédiction des structures des protéines.
2000 – Doctorat en biochimie et biologie moléculaire. Université de La Réunion. Caractérisation et analyse génétique de la résistance de la canne à sucre à Xanthomonas albilineans
1997 – DEA en Analyse du Génome et Modélisation Moléculaire. Université Denis Diderot, Paris VII.
1996 – Maîtrise es Sciences et Techniques (MST), Chimie-Biologie : Valorisation chimique et biologique du végétal. Université de La Réunion.
1993 – DEUG SNV Biologie, Biochimie, Chimie. Université d’Avignon et des Pays du Vaucluse.

Publications

5 publications

Dhingra, Surbhi; Sowdhamini, Ramanathan; Sanejouand, Yves-Henri; Cadet, Frédéric; Offmann, Bernard

Customised fragment libraries for ab initio protein structure prediction using a structural alphabet Article

arXiv:2005.01696, 2020.

Résumé | Liens | BibTeX

Ostafe, Raluca; Fontaine, Nicolas; Frank, David; Ng Fuk Chong, Matthieu ; Prodanovic, Radivoje; Pandjaitan, Rudy; Offmann, Bernard; Cadet, Frédéric; Fischer, Rainer

One-shot optimization of multiple enzyme parameters: Tailoring glucose oxidase for pH and electron mediators Article

Biotechnology and Bioengineering, 117 (1), p. 17–29, 2020, ISSN: 10970290.

Résumé | Liens | BibTeX

Nagaraja, Anamya Ajjolli; Charton, Philippe; Cadet, Xavier F; Fontaine, Nicolas; Delsaut, Mathieu; Wiltschi, Birgit; Voit, Alena; Offmann, Bernard; Damour, Cedric; Grondin-Perez, Brigitte; Cadet, Frederic

A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization Article

Catalysts, 10 (3), 2020, ISSN: 2073-4344.

Résumé | Liens | BibTeX

Liu, Guoxia; Xuan, Ning; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François

Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions Article

Genes, 11 (4), p. 413, 2020.

Résumé | Liens | BibTeX

Dhingra, Surbhi; Sowdhamini, Ramanathan; Cadet, Frédéric; Offmann, Bernard

A glance into the evolution of template-free protein structure prediction methodologies Article

Biochimie, 175 , p. 85 - 92, 2020, ISSN: 0300-9084.

Résumé | Liens | BibTeX

6 publications

Ajjolli Nagaraja, Anamya ; Fontaine, Nicolas; Delsaut, Mathieu; Charton, Philippe; Damour, Cedric; Offmann, Bernard; Grondin-Perez, Brigitte; Cadet, Frédéric

Flux prediction using artificial neural network (ANN) for the upper part of glycolysis Article

PLOS ONE, 14 (5), p. e0216178, 2019, ISSN: 1932-6203.

Résumé | Liens | BibTeX

Ghosh, Pritha; Joshi, Adwait; Guita, Niang; Offmann, Bernard; Sowdhamini, Ramanathan

EcRBPome: A comprehensive database of all known E. coli RNA-binding proteins Article

BMC Genomics, 20 (1), p. 1–6, 2019, ISSN: 14712164.

Résumé | Liens | BibTeX

Chaaya, Nancy; Shahsavarian, Melody A; Maffucci, Irene; Friboulet, Alain; Offmann, Bernard; Léger, Jean Benoist; Rousseau, Sylvain; è, Bérang; è, Séverine Padiolleau-Lef

Genetic background and immunological status influence B cell repertoire diversity in mice Article

Scientific Reports, 9 (1), p. 1–7, 2019, ISSN: 20452322.

Résumé | Liens | BibTeX

Liu, Guoxia; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François

Pheromone, Natural Odor and Odorant Reception Suppressing Agent (ORSA) for Insect Control incollection

Olfactory Concepts of Insect Control-Alternative to Insecticides, p. 311–345, Springer, Cham, 2019.

Résumé | Liens | BibTeX

Vetrivel, Iyanar; Hoffmann, Lionel; Guegan, Sean; Offmann, Bernard; Laurent, Adele D

PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet Inproceedings

Byska, Jan; Krone, Michael; Sommer, Björn (Ed.): Workshop on Molecular Graphics and Visual Analysis of Molecular Data, The Eurographics Association, 2019, ISBN: 978-3-03868-085-7.

Résumé | Liens | BibTeX

Vetrivel, Iyanar; de Brevern, Alexandre G; Cadet, Frédéric; Srinivasan, Narayanaswamy; Offmann, Bernard

Structural variations within proteins can be as large as variations observed across their homologues Article

Biochimie, 167 , p. 162–170, 2019, ISSN: 61831638.

Résumé | Liens | BibTeX

1 publication

Cadet, Frédéric; Fontaine, Nicolas; Li, Guangyue; Sanchis, Joaquin; Ng Fuk Chong, Matthieu ; Pandjaitan, Rudy; Vetrivel, Iyanar; Offmann, Bernard; Reetz, Manfred T

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes Article

Scientific Reports, 8 (1), p. 1–15, 2018, ISSN: 20452322.

Résumé | Liens | BibTeX

3 publications

Vetrivel, Iyanar; Mahajan, Swapnil; Tyagi, Manoj; Hoffmann, Lionel; Sanejouand, Yves-Henri; Srinivasan, Narayanaswamy; De Brevern, Alexandre G; Cadet, Frédéric; Offmann, Bernard

Knowledge-based prediction of protein backbone conformation using a structural alphabet Article

PLoS ONE, 12 (11), 2017, ISSN: 19326203.

Résumé | Liens | BibTeX

Labbé, Pauline; Faure, Emilie; Lecointe, Simon; Le Scouarnec, Solena ; Kyndt, Florence; Marrec, Marie; Le Tourneau, Thierry ; Offmann, Bernard; Duplaà, Cécile; Zaffran, Stéphane; Schott, Jean Jacques; Merot, Jean

The alternatively spliced LRRFIP1 Isoform-1 is a key regulator of the Wnt/β-catenin transcription pathway Article

Biochimica et Biophysica Acta - Molecular Cell Research, 1864 (7), p. 1142–1152, 2017, ISSN: 18792596.

Résumé | Liens | BibTeX

Shahsavarian, Melody A; Chaaya, Nancy; Costa, Narciso; Boquet, Didier; Atkinson, Alexandre; Offmann, Bernard; Kaveri, Srini V; Lacroix-Desmazes, Sébastien; Friboulet, Alain; Avalle, Bérangère; Padiolleau-Lefèvre, Séverine

Multitarget selection of catalytic antibodies with β-lactamase activity using phage display Article

FEBS Journal, 284 (4), p. 634–653, 2017, ISSN: 17424658.

Résumé | Liens | BibTeX

2 publications

Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean François

Biotype characterization, developmental profiling, insecticide response and binding property of Bemisia tabaci chemosensory proteins: Role of CSP in insect defense Article

PLoS ONE, 11 (5), 2016, ISSN: 19326203.

Résumé | Liens | BibTeX

Verhaeghe, Tom; De Winter, Karel ; Berland, Magali; De Vreese, Rob ; D'Hooghe, Matthias; Offmann, Bernard; Desmet, Tom

Converting bulk sugars into prebiotics: Semi-rational design of a transglucosylase with controlled selectivity Article

Chemical Communications, 52 (18), p. 3687–3689, 2016, ISSN: 1364548X.

Résumé | Liens | BibTeX

2 publications

Mahajan, Swapnil; De Brevern, Alexandre G; Sanejouand, Yves-Henri; Srinivasan, Narayanaswamy; Offmann, Bernard

Use of a structural alphabet to find compatible folds for amino acid sequences Article

Protein Science, 24 (1), p. 145–153, 2015, ISSN: 1469896X.

Résumé | Liens | BibTeX

Fontaine, Nicolas; Grondin-perez, Brigitte; Cadet, Frédéric; Offmann, Bernard; Fontaine, Nicolas; Grondin-perez, Brigitte; Cadet, Frédéric; Offmann, Bernard; Fontaine, Nicolas; Grondin-perez, Brigitte; Cadet, Frédéric; Offmann, Bernard

Modeling of a Cell-Free Synthetic System for Biohydrogen Production Article

Journal of Computer Science & Systems Biology, 8 (3), 2015, ISSN: 09747230.

Résumé | Liens | BibTeX

2014

Berland, Magali; Offmann, Bernard; André, Isabelle; Remaud-Siméon, Magali; Charton, Philippe

A web-based tool for rational screening of mutants libraries using ProSAR Article

Protein Eng Des Sel, 27 (10), p. 375-81, 2014.

Résumé | Liens | BibTeX

Mahajan, Swapnil; de Brevern, Alexandre G; Offmann, Bernard; Srinivasan, Narayanaswamy

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure Article

J Biomol Struct Dyn, 32 (5), p. 751-8, 2014.

Résumé | Liens | BibTeX

Manoharan, Malini; Fuchs, Patrick F J; Sowdhamini, Ramanathan; Offmann, Bernard

Insights on pH-dependent conformational changes of mosquito odorant binding proteins by molecular dynamics simulations Article

J Biomol Struct Dyn, 32 (11), p. 1742-51, 2014.

Résumé | Liens | BibTeX

2013

Mahajan, Swapnil; Agarwal, Garima; Iftekhar, Mohammed; Offmann, Bernard; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

DoSA: Database of Structural Alignments Article

Database (Oxford), 2013 , p. bat048, 2013.

Résumé | Liens | BibTeX

Manoharan, Malini; Chong, Matthieu Ng Fuk; Vaïtinadapoulé, Aurore; Frumence, Etienne; Sowdhamini, Ramanathan; Offmann, Bernard

Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus Article

Genome Biol Evol, 5 (1), p. 163-80, 2013.

Résumé | Liens | BibTeX

Manoharan, Malini; Sankar, Kannan; Offmann, Bernard; Ramanathan, Sowdhamini

Association of putative members to family of mosquito odorant binding proteins: scoring scheme using fuzzy functional templates and cys residue positions Article

Bioinform Biol Insights, 7 , p. 231-51, 2013.

Résumé | Liens | BibTeX

2011

Chilamakuri, Chandra Sekhar Reddy; Joshi, Adwait; Rani, Sane Sudha; Offmann, Bernard; Sowdhamini, R

Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species Article

Comparative and Functional Genomics, 2011 , 2011.

Résumé | Liens | BibTeX

2010

Joseph, Agnel Praveen; Agarwal, Garima; Mahajan, Swapnil; Gelly, Jean-Christophe; Swapna, Lakshmipuram S; Offmann, Bernard; Cadet, Frédéric; Bornot, Aurélie; Tyagi, Manoj; Valadié, Hélène; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

A short survey on protein blocks Article

Biophys Rev, 2 (3), p. 137-147, 2010.

Résumé | Liens | BibTeX

Reddy, Chilamakuri Cs; Rani, Sane Sudha; Offmann, Bernard; Sowdhamini, R

Systematic search for putative new domain families in Mycoplasma gallisepticum genome Article

BMC Res Notes, 3 , p. 98, 2010.

Résumé | Liens | BibTeX

Groben, René; Kaloudas, Dimitrios; Raines, Christine A; Offmann, Bernard; Maberly, Stephen C; Gontero, Brigitte

Comparative sequence analysis of CP12, a small protein involved in the formation of a Calvin cycle complex in photosynthetic organisms Article

Photosynth Res, 103 (3), p. 183-94, 2010.

Résumé | Liens | BibTeX

2009

Tyagi, Manoj; Bornot, Aurélie; Offmann, Bernard; de Brevern, Alexandre G

Analysis of loop boundaries using different local structure assignment methods Article

Protein Sci, 18 (9), p. 1869-81, 2009.

Résumé | Liens | BibTeX

Tyagi, Manoj; Bornot, Aurélie; Offmann, Bernard; de Brevern, Alexandre G

Protein short loop prediction in terms of a structural alphabet Article

Comput Biol Chem, 33 (4), p. 329-33, 2009.

Résumé | Liens | BibTeX

Sandhya, Sankaran; Rani, Saane Sudha; Pankaj, Barah; Govind, Madabosse Kande; Offmann, Bernard; Srinivasan, Narayanaswamy; Sowdhamini, Ramanathan

Length variations amongst protein domain superfamilies and consequences on structure and function Article

PLoS One, 4 (3), p. e4981, 2009.

Résumé | Liens | BibTeX

2008

Thangudu, Ratna R; Manoharan, Malini; Srinivasan, N; Cadet, Frédéric; Sowdhamini, R; Offmann, Bernard

Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families Article

BMC Struct Biol, 8 , p. 55, 2008.

Résumé | Liens | BibTeX

Reddy, Chilamakuri C S; Shameer, Khader; Offmann, Bernard; Sowdhamini, Ramanathan

PURE: a webserver for the prediction of domains in unassigned regions in proteins Article

BMC Bioinformatics, 9 , p. 281, 2008.

Résumé | Liens | BibTeX

Sandhya, Sankaran; Pankaj, Barah; Govind, Madabosse Kande; Offmann, Bernard; Srinivasan, Narayanaswamy; Sowdhamini, Ramanathan

CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations Article

BMC Struct Biol, 8 , p. 28, 2008.

Résumé | Liens | BibTeX

Tyagi, M; de Brevern, A G; Srinivasan, N; Offmann, Bernard

Protein structure mining using a structural alphabet Article

Proteins, 71 (2), p. 920-37, 2008.

Résumé | Liens | BibTeX

2007

Chilamakuri, Sekhar Reddy C; Khader, Shameer; Offmann, Bernard; Sowdhamini, Ramanathan

PURE: a web server for querying the relationship between pre-existing domains and unassigned regions in proteins Article

Nature Protocols, 2007.

Résumé | Liens | BibTeX

Thangudu, Ratna R; Sharma, Priyanka; Srinivasan, N; Offmann, Bernard

Analycys: a database for conservation and conformation of disulphide bonds in homologous protein domains Article

Proteins, 67 (2), p. 255-61, 2007.

Résumé | Liens | BibTeX

Bornot, Aurélie; Offmann, Bernard; de Brevern, Alexandre

How flexible protein structures are? New questions on the protein structure plasticity. Article

Bioforum Europe, (11), p. 24, 2007.

BibTeX

Swapna, LS; Offmann, Bernard; Srinivasan, N

Evolutionary dynamics of protein-protein interactions. A case study using the DJ-1/PfpI family of enzyme. Livre

John Wiley & Sons, Inc., 2007.

BibTeX

Offmann, Bernard; Tyagi, Manoj; de Brevern, Alexandre G

Local Protein Structures Article

Current Bioinformatics, 2 (3), p. 165-202, 2007, ISSN: 1574-8936/2212-392X.

Résumé | Liens | BibTeX

2006

Gardebien, Fabrice; Thangudu, Rajesh R; Gontero, Brigitte; Offmann, Bernard

Construction of a 3D model of CP12, a protein linker Article

J Mol Graph Model, 25 (2), p. 186-95, 2006.

Résumé | Liens | BibTeX

Tyagi, Manoj; Gowri, Venkataraman S; Srinivasan, Narayanaswamy; de Brevern, Alexandre G; Offmann, Bernard

A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications Article

Proteins, 65 (1), p. 32-9, 2006.

Résumé | Liens | BibTeX

Tyagi, M; Sharma, P; Swamy, C S; Cadet, F; Srinivasan, N; de Brevern, A G; Offmann, Bernard

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet Article

Nucleic Acids Res, 34 (Web Server issue), p. W119-23, 2006.

Résumé | Liens | BibTeX

2005

Thangudu, Ratna Rajesh; Vinayagam, A; Pugalenthi, G; Manonmani, A; Offmann, Bernard; Sowdhamini, R

Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides Article

Proteins, 58 (4), p. 866-79, 2005.

Résumé | Liens | BibTeX

2003

Besnard, G; Pinçon, G; D'Hont, A; Hoarau, J-Y; Cadet, Frédéric; Offmann, Bernard

Characterisation of the phosphoenolpyruvate carboxylase gene family in sugarcane (Saccharum spp.) Article

Theoretical and Applied Genetics, 107 (3), p. 470-8, 2003.

Résumé | Liens | BibTeX

Offmann, Bernard; Raboin, Louis Marie; Notaise, Julien

Segregation of resistance to Xanthomonas albilineans in a sugarcane progeny Inproceedings

p. 113–124, Bourbon sciences, 2003.

BibTeX

2002

Hoarau, J-Y; Grivet, L; Offmann, Bernard; Raboin, L-M; Diorflar, J-P; Payet, J; Hellmann, M; D'Hont, A; Glaszmann, J-C

Genetic dissection of a modern sugarcane cultivar ( Saccharum spp.).II. Detection of QTLs for yield components Article

Theoretical and Applied Genetics, 105 (6-7), p. 1027-1037, 2002.

Résumé | Liens | BibTeX

Besnard, Guillaume; Offmann, Bernard; Robert, Christine; Rouch, Claude; Cadet, Frédéric

Assessment of the C(4) phosphoenolpyruvate carboxylase gene diversity in grasses (Poaceae) Article

Theoretical and Applied Genetics, 105 (2-3), p. 404-412, 2002.

Résumé | Liens | BibTeX

Offmann, Bernard; Cadet, Frédéric

Enzymes as structural tool in infrared spectroscopy Article

Spectroscopy Letters, 35 (4), p. 523-526, 2002.

Résumé | Liens | BibTeX

Offmann, Bernard; Cadet, Frédéric

Redox-active disulfides in a plant light switch: A Pbl problem* Article

Biochemistry and Molecular Biology Education, 30 (4), p. 249-254, 2002.

Résumé | Liens | BibTeX

2001

Hoarau, J-Y; Offmann, Bernard; D'Hont, Angélique; Risterucci, A-M; Roques, D; Glaszmann, J-C; Grivet, Laurent

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers Article

Theoretical and Applied Genetics, 103 (1), p. 84–97, 2001.

BibTeX

Raboin, Louis-Marie; Offmann, Bernard; Hoarau, Jean-Yves; Notaise, Julien; Costet, Laurent; Telismart, Hugues; Roques, Danièle; Rott, Philippe; Glaszmann, Jean-Christophe; D'Hont, Angélique

Undertaking genetic mapping of sugarcane smut resistance Inproceedings

Proc S Afr Sug Technol Ass, p. 94–98, 2001.

Résumé | BibTeX

Besnard, Guillaume; Offmann, Bernard; Robert, Christine; Baret, Pascal; Rouch, Claude; Cadet, Frédéric

Phosphoenolpyruvate carboxylase cDNA phylogeny to investigate the C4 photosynthetic pathway evolution in grasses Article

Science Access, 3 (1), 2001.

BibTeX

2000

Offmann, Bernard

Caractérisation et analyse génétique de la résistance de la canne à sucre à Xanthomonas albilineans Thèse de doctorat

La Réunion, 2000.

BibTeX

1997

Offmann, Bernard

Cartographie génétique et recherche de QTLs chez un cultivar élite de canne à sucre (Saccharum spp) au moyen de marqueurs AFLP Masters Thesis

Université de Paris VII, 1997.

BibTeX

Cadet, Frédéric; Robert, Christine; Offmann, Bernard

Simultaneous Determination of Sugars by Multivariate Analysis Applied to Mid-Infrared Spectra of Biological Samples Article

Appl. Spectrosc., 51 (3), p. 369–375, 1997.

Résumé | Liens | BibTeX

Cadet, Frédéric; Offmann, Bernard

Direct Spectroscopic Sucrose Determination of Raw Sugar Cane Juices Article

Journal of Agricultural and Food Chemistry, 45 (1), p. 166-171, 1997.

Résumé | Liens | BibTeX

1996

Cadet, Frédéric; Offmann, Bernard

Evidence for Potassium-Sucrose Interaction in Biological Mid-Infrared Spectra by Multidimensional Analysis Article

Spectroscopy letters, 29 (7), p. 1353–1365, 1996.

Résumé | Liens | BibTeX

Cadet, Frédéric; Offmann, Bernard

Baseline correction applied to a biological: Mid-infrared spectra collection Article

Spectroscopy letters, 29 (4), p. 591–607, 1996.

Résumé | Liens | BibTeX

Cadet, Frédéric; Offmann, Bernard

Gram-Schmidt Orthogonalization and Elimination of the Effect of Unwanted Component Spectra Applied to a Biological Mid-infrared Spectra Collection Article

Spectroscopy letters, 29 (5), p. 901–918, 1996.

Résumé | Liens | BibTeX

Cadet, Frédéric; Offmann, Bernard

Extraction of Characteristic Bands of Sugars by Multidimensional Analysis of Their Infrared Spectra. Article

Spectroscopy letters, 29 (3), p. 523–536, 1996.

Résumé | Liens | BibTeX

Liens