Olivier Lespinet
Professeur de Bioinformatique, Université Paris-Saclay

Institut de Biologie Intégrative de la Cellule, UMR CNRS 9198
Equipe Bioinformatique Moléculaire

Bâtiment 22
91190 Gif-sur-Yvette

Tél : +33 (0) 1 69 82 62 21
E-mail : olivier.lespinet at universite-paris-saclay.fr

Liste des Publications :

CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes.
(2023) L Oliveira, N Chevrollier, JF Dallery, RJ O'Connell, MH Lebrun, M Viaud, O Lespinet. - Scientific Reports; Jan 25:13(1):1417

A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data.
(2023) P Bastide, C Soneson, DB Stern, O Lespinet, M Gallopin. - Molecular Biology and Evolution; Jan 4:40(1)

On the predictibility of A-minor motifs from their local contexts.
(2022) C Gianfrotta, V Reinharz, O Lespinet, D Barth, A Denise. - RNA Biology; Jan:19(1):1208-1227

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.
(2021) C Papadopoulos, I Callebaut, JC Gelly, I Hatin, O Namy, M Renard, O Lespinet, A Lopes. - Genome Research; Nov 22:31(21):2303-2315

Dynamics of the compartimentalized Streptomyces chromosome during metabolic differentiation.
(2021) VS Lioy, JN Lorenzi, S Najah, T Poinsignon, H Leh, C Saulnier, B Aigle, S Lautru, A Thibessard, O Lespinet, P Leblond, Y Jaszczyszyn, K Gorrichon, N Varoquaux, I Junier, F Boccard, JL Pernodet, S Bury-Moné. - Nature Communication; Sep 1 :12(1)

Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome.
(2019) JN Lorenzi, O Lespinet, P Leblond, A Thibessard. - Microbial Genomics; Sep :7(6)

Genome Sequences of 11 Conspecific Streptomyces sp. Strains.
(2019) AR Tidjani, JN Lorenzi, M Toussaint, E van Dijk, D Naquin, O Lespinet, C Bontemps, P Leblond. - Microbiology Resource Announcements; Sep 19:8(38)

Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.
(2019) AR Tidjani, JN Lorenzi, M Toussaint, E van Dijk, D Naquin, O Lespinet, C Bontemps, P Leblond. - mBio; Sep 3;10(5)

Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity.
(2018) CM Vicente, A Thibessard, JN Lorenzi, M Benhadj, L Hôtel, D Gacemi-Kirane, O Lespinet, P Leblond, B Aigle. - Antibiotics; Oct 2;7(4):86

Meet-U: Educating through research immersion.
(2018) N Abdollahi, A Albani, E Anthony, A Baud, M Cardon, R Clerc, D Czernecki, R Conte, L David, A Delaune, S Djerroud, P Fourgoux, N Guiglielmoni, J Laurentie, N Lehmann, C Lochard, R Montagne, V Myrodia, V Opuu, E Parey, L Polit, S Privé, C Quignot, M Ruiz-Cuevas, M Sissoko, N Sompairac, A Vallerix, V Verrecchia, M Delarue , R Guérois , Y Ponty, S Sacquin-Mora, A Carbone, C Froidevaux, S Le Crom, O Lespinet, M Weigt, S Abboud, J Bernardes, G Bouvier, C Dequeker, A Ferré, P Fuchs, G Lelandais, P Poulain, H Richard, H Schweke, E Laine, A Lopes. - PLoS Computational Biology; Mar 15;14(3):667

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters.
(2017) JF Dallery, N Lapalu, A Zampounis, S Pigne, I Luyten, J Amselem, AHJ Wittenberg, S Zhou, MV de Queiroz, GP Robin, A Auger, M Hainaut, B Henrissat, KT Kim, YH Lee, O Lespinet, DC Schwartz, MR Thon, RJ O'Connell. - BMC Genomics; Aug 28;18(1):667

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi.
(2016) S Hacquard, B Kracher, K Hiruma, PC Münch, R Garrido-Oter, MR Thon, A Weimann, U Damm, JF Dallery, M Hainaut, B Henrissat, Lespinet O, S Sacristan, E Ver Loren van Themaat, E Kemen, AC McHardy, P Schulze-Lefert, RJ O'Connell. - Nature Communication; Sept 29;7:13072

A meta-approach for improving the prediction and the functional annotation of ortholog groups.
(2014) C Pereira, A Denise, O Lespinet. - BMC Genomics;15 Suppl 6:S16.

Profiling the orphan enzymes.
(2014) M Sorokina, M Stam, C Médigue, O Lespinet, D Vallenet. - Biology Direct; Jun 6;9:10

Comparative genomics of emerging pathogens in the Candida glabrata clade.
(2013) T Gabaldón, T Martin, M Marcet-Houben, P Durrens, M Bolotin-Fukuhara, O Lespinet, S Arnaise, S Boisnard, G Aguileta, R Atanasova, C Bouchier, A Couloux, S Creno, J Almeida Cruz, H Devillers, A Enache-Angoulvant, J Guitard, L Jaouen, L Ma , C Marck, C Neuvéglise, E Pelletier, A Pinard, J Poulain, J Recoquillay, E Westhof, P Wincker, B Dujon, C Hennequin, C Fairhead. - BMC Genomics; Sept;14:6233

Comparative analysis of phylogenetic profiles for the enzymatic characterization of fungal groups.
(2013) C Pereira, J Azé, A Denise, C Drevet, C Froidevaux, P Silar, O Lespinet - JOBIM, Toulouse 1-4 Juillet, Editeurs C Gaspin, N Lindley, C NotreDame.

Genome-wide comparative analysis of pogo-like transposable elements in different Fusarium species.
(2011) M Dufresne M, O Lespinet, MJ Daboussi, A Hua-Van - Journal of Molecular Evolution; Oct;73(3-4):230-43

Evolution des Génomes et du Métabolisme : Annotation, Analyse et Exploration des données.
(2010) O Lespinet - Habilitation à Diriger des Recherches de l'université Paris-Sud 11.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina.
(2010) F Bidard, S Imbeaud, N Reymond, O Lespinet, P Silar, C Clavé, H Delacroix, V Berteaux-Lecellier and R Debuchy. BMC Research Notes; Jun 18;3(1):171.

FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology.
(2010) S Grossetête, B Labedan and O Lespinet - BMC Genomics; Feb 1;11(1):81.

Fast and accurate multiple sequence alignment of large and diversified sets of distant homologues.
(2010) M Barba, O Lespinet and B Labedan - JOBIM, Montpellier 7-8 Septembre

Assessment of phylogenetic diversity of bacterial microflora in drinking water using serial analysis of ribosomal sequence tags.
(2009) JB Poitelon, M Joyeux, B Welté, JP Duguet, E Prestel, O Lespinet and MS DuBow - Water Research; Sep;43(17):4197-206.

FUNGIpath: a new tool for analysing the evolution of fungal metabolic pathways.
(2009) S Grossetête, B Labedan and O Lespinet - JOBIM, Nantes 9-11 Juin, Editeurs E Rivals, I Rusu.

Darwin et l'arbre du vivant.
(2009) O Lespinet, B Labedan, N Glansdorff et Y Xu - Plein Sud, Le magazine d'information de l'université Paris-Sud; 73:14-15

SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.
(2008) F Lemoine, B Labedan and O Lespinet - BMC Bioinformatics; Dec 16;9:536.

Genome-wide analysis of the Fusarium oxysporum mimp family of MITEs and mobilization of both native and de novo created mimps.
(2008) M Bergemann, O Lespinet, SB M'Barek, MJ Daboussi and M Dufresne - Journal of Molecular Evolution; Dec;67(6):631-42.

The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species.
(2008) S Descorps-Declère, F Lemoine, Q Sculo, O Lespinet and B Labedan - Biochimie; Apr;90(4):595-608.

The Genome Sequence of the Model Ascomycete Fungus Podospora anserina.
(2008) E Espagne, O Lespinet, F Malagnac, C Da Silva, O Jaillon, BM Porcel, A Couloux, JM Aury, B Ségurens, J Poulain, V Anthouard, S Grossetête, H Khalili, E Coppin, M Déquard-Chablat, M Picard, V Contamine, S Arnaise, A Bourdais, V Berteaux-Lecellier, D Gautheret, RP de Vries, E Battaglia, PM Coutinho, EGJ Danchin, B Henrissat, R El Khoury, A Sainsard-Chanet, A Boivin, B Pinan-Lucarré, CH Sellem, R Debuchy, P Wincker, J Weissenbach and P Silar - Genome Biology; 9(5):R77.

Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data.
(2007) F Lemoine, O Lespinet and B Labedan - BMC Evolutionary Biology; 7(1):237.

ORENZA: a web resource for studying ORphan ENZyme Activities.
(2006) O Lespinet and B Labedan - BMC Bioinformatics; 7:436.

Orphan enzymes could be an unexplored reservoir of new drug targets.
(2006) O Lespinet and B Labedan - Drug Discovery Today; 11(7-8):300-5.

Interspecies and intraspecies comparison of microbial proteins: learning about gene ancestry, protein function, and species life style.
(2006) B Labedan and O Lespinet - WHILEY, Microbial Proteomics: Functionnal Biology of Whole Organisms. Editeurs Ian Humphery-Smith, Michael Hecker.

Puzzling over orphan enzymes.
(2006) O Lespinet and B Labedan - Cellular and Molecular Life Science; 63(5):517-23.

Orphan enzymes?
(2005) O Lespinet and B Labedan - Science; 307(5706):42.

New approaches to improve the soundness of the deep evolutionary relationships in genomic trees of microorganisms.
(2005) Q Sculo, O Lespinet and B Labedan - JOBIM, Lyon 6-8 Juillet, Editeurs G Perrière, A Guénoche, C Geourjon.

Retrieving the Whole Set of Protein Modules of Campylobacter jejuni and Helicobacter pylori.
(2003) Q Sculo, O Lespinet and B Labedan - Genome Letters; 2, 8–15.

The role of lineage-specific gene family expansion in the evolution of eukaryotes.
(2002) O Lespinet, YL Wolf, EV Koonin and L Aravind - Genome Research; 12(7):1048-59.

A lophotrochozoan twist gene is expressed in the ectomesoderm of the gastropod mollusc Patella vulgata.
(2002) AJ Nederbragt, O Lespinet, S van Wageningen, AE van Loon, A Adoutte, and WJAG Dictus - Evolution & Development; 4(5):334-43.

Characterisation of two Snail genes in the gastropod mollusc Patella vulgata. Implications for understanding the ancestral function of the Snail-related genes in Bilateria.
(2002) O Lespinet, AJ Nederbragt, M Cassan, WJAG Dictus, AE van Loon, and A Adoutte - Development, Gene and Evolution; 212(4):186-95.

Expression pattern of Brachyury in the mollusc Patella vulgata suggests a conserved role in the establishment of the A-P axis in Bilateria.
(2002) N Lartillot, O Lespinet, M Vervoort, JAM van den Biggelaar, and A Adoutte - Development; 129(6):1411-21.

La famille des genes Snail. Caractérisation de deux nouveaux membres chez le mollusque Patella vulgata. Hypothèse sur leur fonction ancestrale chez les Bilateria.
(2001) O Lespinet - Thèse de l'université Paris-Sud 11.

Genome quality control: RIP (repeat-induced point mutation) comes to Podospora.
(2001) F Graïa, O Lespinet, B Rimbault, M Dequard-Chablat, E Coppin, and M Picard - Molecular Microbiology; 40(3):586-95.

The new animal phylogeny: Reliability and Implications.
(2000) A Adoutte, G Balavoine, N Lartillot, O Lespinet, B Prud'homme, and R de Rosa - PNAS USA; 97(9): 4453-4456.