Maude Pupin

Maître de conférences en Informatique
Univ Lille 1   labo cristal   cnrs inria lne
Bâtiment M3 extension, 59650 Villeneuve d'Ascq
+33 (0)3 28 77 85 55
maude.pupin_at_univ-lille1.fr
on google scholar on researchgate

Current research projets

I'm working on bioinformatics for nonribosomal peptides (NRPs). Those are chemical compounds synthesised by huge enzymes that select not only amino acids, but also lipids or carbohydrates and link them by peptide and non peptide bonds. Few NRPs already serve as drugs, and their capacity to provide new drugs or other industrial products is believed to be under-exploited. In 2006, I initiate a tight collaboration with ProBioGEM lab, a microbial laboratory specialized in that topic, to create bioinformatics database and tools that contribute to the process of discovering new NRPs and better understanding their activity. We are one of the very few teams in the world having an activity dedicated to NRP bioinformatics, for which we gain an international recognition.
We created NORINE, the unique and freely available resource dedicated to NRPs [1]. NORINE contains more than 1100 peptides, coming from the scientific literature or submitted directly by researchers. It receives 130 unique visitors from all continents each month, doing around 10 queries each. The recognition by our peers brought the worldwide Protein Data Bank, that maintains the unique archive of macromolecular structural data, to select our entry identifiers as external references along with the UniProt accession codes for gene product sequences.
Nonribosomal peptides harbor specific properties in comparison with peptides that are produced by the universal pathway (DNA transcribed in RNA then translated in protein/peptide). They can incorporate more than 500 different building blocks, which are amino acids, lipids or carbohydrates among others. We call those building blocks monomers. Their structures are not only linear but also contain cycles and/or branches. So, we choose to represent NRPs as monomeric structures, that are undirected graphs with nodes labeled by monomers names and edges corresponding to the bonds between monomers. We design efficient algorithms based on a variant of the compatibility graph to search for a structural pattern [2] or to compare a NRP to others.
Thanks to NORINE, we performed a large-scale statistical analysis on monomeric diversity that has revealed a correlation between monomeric composition and peptide activity [3]. This work has been highlighted by the American Society for Microbiology. Starting from this observation, we designed a machine learning classifier to predict the activity of a given NRP, represented by a monomeric composition fingerprint [4], that provides very good prediction rates.

Past research projets

I worked on DNA sequence analysis, more precisely on local repeats prediction.

Publications

Articles in international journals, with editorial board

Book chapters

Oral presentations in international conferences

Oral presentations in national conferences

Articles in international journals, with editorial board

[16] Norine: a powerful resource for novel nonribosomal peptide discovery
M. Pupin, Q. Esmaeel, A. Flissi, Y. Dufresne, P. Jacques, and V. Leclère
Synthetic and Systems Biotechnology (in press)
doi: 10.1016/j.synbio.2015.11.001

[15] Smiles2Monomers: a link between chemical and biological structures for polymers
Y. Dufresne, L. Noé, V. Leclère, and M. Pupin
Journal of Cheminformatics (2015) 7, 1, pp. 1–11
doi: 10.1186/s13321-015-0111-5

[14] Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing
A. Flissi, Y. Dufresne, J. Michalik, L. Tonon, S. Janot, L. Noé, P. Jacques, V. Leclère, and M. Pupin
Nucleic Acids Research (2015) 44, D1, pp. D1113–D1118
doi: 10.1093/nar/gkv1143

[13] Prediction of New Bioactive Molecules using Bayesian Belief Network
A. Abdo, V. Leclère, P. Jacques, N. Salim, and M. Pupin
Journal of Chemical Information and Modeling (2014) 54, 1, pp. 30–36
doi: 10.1021/ci4004909

[12] Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Non-ribosomal Peptide Discovery
T. Caradec, M. Pupin, A. Vanvlassenbroeck, M.-D. Devignes, M. Smaïl-Tabbone, P. Jacques, and V. Leclère
PLoS ONE (2014) 9, 1, e85667
doi: 10.1371/journal.pone.0085667

[11] A new fingerprint to predict nonribosomal peptides activity
A. Abdo, S. Caboche, V. Leclère, P. Jacques, and M. Pupin
Journal of Computer-Aided Molecular Design (2012) 26, 10, pp. 1187–1194
doi: 10.1007/s10822-012-9608-4

[10] Structure, biosynthesis, and properties of kurstakins, nonribosomal lipopeptides from Bacillus spp.
M. Béchet, T. Caradec, W. Hussein, A. Abderrahmani, M. Chollet, V. Leclère, T. Dubois, D. Lereclus, M. Pupin, and P. Jacques
Applied Microbiology and Biotechnology (2012) 95, 3, pp. 593–600
doi: 10.1007/s00253-012-4181-2

[9] Diversity of Monomers in Nonribosomal Peptides: towards the Prediction of Origin and Biological Activity
S. Caboche, V. Leclère, M. Pupin, G. Kucherov, and P. Jacques
Journal of Bacteriology (2010) 192, 19, pp. 5143–5150
doi: 10.1128/JB.00315-10

[8] Structural pattern matching of nonribosomal peptides
S. Caboche, M. Pupin, V. Leclère, P. Jacques, and G. Kucherov
BMC Structural Biology (2009) 9, 1, p. 15
doi: 10.1186/1472-6807-9-15

[7] NORINE: a database of nonribosomal peptides
S. Caboche, M. Pupin, V. Leclère, A. Fontaine, P. Jacques, and G. Kucherov
Nucleic Acids Research (2008) 36, suppl 1, pp. D326–D331
doi: 10.1093/nar/gkm792

[6] Comparing sequences without using alignments: application to HIV/SIV subtyping
G. Didier, L. Debomy, M. Pupin, M. Zhang, A. Grossmann, C. Devauchelle, and I. Laprevotte
BMC Bioinformatics (2007) 8, 1, p. 1
doi: 10.1186/1471-2105-8-1

[5] Local Decoding of Sequences and Alignment-Free Comparison
G. Didier, I. Laprevotte, M. Pupin, and A. Hénaut
Journal of Computational Biology (2006) 13, 8, pp. 1465–1476
doi: 10.1089/cmb.2006.13.1465

[4] A revised annotation and comparative analysis of Helicobacter pylori genomes
I. G. Boneca, H. d. Reuse, J.-C. Epinat, M. Pupin, A. Labigne, and I. Moszer
Nucleic Acids Research (2003) 31, 6, pp. 1704–1714
doi: 10.1093/nar/gkg250

[3] HIV-1 and HIV-2 LTR Nucleotide Sequences: Assessment of the Alignment by N-block Presentation, "Retroviral Signatures" of Overrepeated Oligonucleotides, and a Probable Important Role of Scrambled Stepwise Duplications/Deletions in Molecular Evolution
I. Laprevotte, M. Pupin, E. Coward, G. Didier, C. Terzian, C. Devauchelle, and A. Hénaut
Molecular Biology and Evolution (2001) 18, 7, pp. 1231–1245
doi: 10.1093/oxfordjournals.molbev.a003909

[2] Detecting localized repeats in genomic sequences: a new strategy and its application to Bacillus subtilis and Arabidopsis thaliana sequences
M. Klaerr-Blanchard (Pupin), H. Chiapello, and E. Coward
Computers & Chemistry (2000) 24, 1, pp. 57–70
doi: 10.1016/S0097-8485(00)80007-8

[1] The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
F. Kunst et al.
Nature (1997) 390, 6657, pp. 249–256
doi: 10.1038/36786

Book chapters

[2] Bioinformatics tools for the discovery of new nonribosomal peptides.
V. Leclère, T. Weber, P. Jacques, and M. Pupin.
In: Nonribosomal Peptide and Polyketide Biosynthesis.
Ed. by B. S. Evens.
Methods in Molecular Biology. Humana Press, 2016, pp. 209–232.
doi: 10.1007/978-1-4939-3375-4_14

[1] In silico genome analysis.
E. Rocha, I. Moszer, A. Sekowska, M. Klaerr-Blanchard (Pupin), C. Médigue, A. Viari, and A. Danchin.
In: Functional analysis of bacterial genes: A practical manual.
Ed. by S. Ehrlich, W. Schuman, and N. Ogasawara.
John Wiley & Sons, 2000.

Oral presentations in international conferences

[4] Bioinformatics tools to decrypt NonRibosomal Peptide diversity in bacteria.
V. Leclère, M. Pupin, W. Hussein, A. Vanvlassenbroeck, M. Bèchet, J. Deravel, Krier, F., F. Gancel, M. Chollet, C. S., and P. Jacques.
In: AMP, 3rd international symposium on AntiMicrobial Peptides.
Villeneuve d'Ascq, France, 2012
conference site

[3] Bioinformatics tools to decrypt NonRibosomal Peptide diversity in Bacilli.
V. Leclère, M. Pupin, W. Hussein, M. Béchet, F. Gancel, M. Chollet, S. Caboche, and P. Jacques.
In: Bacell, meeting of the European Bacillus community.
Gottingen, Allemagne, 2011
conference site

[2] Novel approaches to isolate antimicrobial peptides using bioinformatics and molecular tools.
P. Jacques, R. Froidevaux, M. Chollet-Imbert, A. Tapi, S. Caboche, M. Pupin, G. Kucherov, P. Dhulster, G. Le Flem, D. Vercaigne-Marko, and V. Leclère.
In: AMP, 2nd international symposium on AntiMicrobial Peptides.
Saint Malo, France, 2009.
conference site

[1] Relationships between producing organisms, activities and monomers incorporated into NRPS peptides.
V. Leclère, S. Caboche, M. Pupin, G. Kucherov, and P. Jacques.
In: FEMS 3rd congress of European microbiologists.
Gothenburg, Suède, 2009.
conference site

Oral presentations in national conferences

[4] Non Ribosomal Peptides: A monomeric puzzle.
Y. Dufresne, V. Leclère, P. Jacques, L. Noé, and M. Pupin.
In: JOBIM, 14ème édition de la conférence nationale de bio-informatique.
Toulouse, France, 2013.
HAL | conference site

[3] NRPS toolbox for the discovery of new nonribosomal peptides and synthetases.
M. Pupin, M. Smail-Tabbone, P. Jacques, M.-D. Devignes, and V. Leclère.
In: JOBIM, 13ème édition de la conférence nationale de bio-informatique.
Rennes, France, 2012.
HAL | conference site

[2] Exploration bioinformatique des génomes : vers la découverte de nouveaux peptides actifs et mise en évidence de nouvelles NRPS.
V. Leclère, M. Pupin, J. D’aes, M. Höfte, A. Abderrahmani, M. Chollet, and P. Jacques.
In: Congrès annuel de la Société Française de Biochimie et de Biologie Moléculaire.
Ax-les-Thermes, France, 2011.
conference site

[1] Database and comparison of non ribosomal peptides.
S. Caboche, V. Leclère, P. Jacques, M. Pupin, and G. Kucherov.
In: JOBIM, 7ème édition de la conférence nationale de bio-informatique.
Bordeaux, France, 2006.
conference schedule