Selected publications

The noncoding genome as a reservoir of genetic novelty

The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation
C. Papadopoulos, H. Arbes, D. Cornu, N. Chevrollier, S. Blanchet, P. Roginski, C. Rabier, S. Atia, O. Lespinet, O. Namy, A. Lopes.
Genome Biology 2024, 25, 268
doi.org/10.1186/s13059-024-03403-7
De Novo Emerged Gene Search in Eukaryotes with DENSE
P. Roginski, A. Grandchamp, C. Quignot, A. Lopes.
Genome Biology Evolution 2024, 16, 8, evae159
doi.org/10.1093/gbe/evae159
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.
C. Papadopoulos, I. Callebaut, JC. Gelly, I. Hatin, O. Namy, M. Renard, O. Lespinet, A. Lopes.
Genome Research 2021, 2303–2315
doi: 10.1101/gr.275638.121
Exploring the Peptide Potential of Genomes.
Papadopoulos C, Chevrollier N, Lopes A.
Methods Mol. Biol. 2022, 2405:63-82
doi: 10.1007/978-1-0716-1855-4_3

Functional and non-functional protein interactions: a matter of competition

SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features
Schweke H, Mucchielli MH, Chevrollier N, Gosset S, Lopes A.
J. Chem. Inf. Model. 2022, 62, 7, 1595–1601
doi: 10.1021/acs.jcim.1c01269
Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.
H Schweke, MH Mucchielli, S Sacquin-Mora, W Bei & A Lopes.
J Mol Biol., 2020 Feb.
doi: 10.1016/j.jmb.2019.12.047

Remote homology detection

Automated classification of tailed bacteriophages according to their neck organization.
A Lopes, P Tavares, MA Petit, R Guérois, S Zinn-Justin.
BMC Genomics., 2014 Nov.
doi: 10.1186/1471-2164-15-1027
Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs
A Lopes, J Amarir-Bouhram, G Faure, M-A Petit, R Guerois.
Nucleic Acids Research, 2010 Jul.
doi: 10.1093/nar/gkq096

Protein design

Computational protein design: the Proteus software and selected applications.
Simonson T, Gaillard T, Mignon D, Schmidt am Busch M, Lopes A, Amara N, Polydorides S, Sedano A, Druart K, Archontis G.
J Comput Chem., 2010 Apr.
doi: 10.1002/jcc.21414

Teaching

Educating through research immersion.
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 Comp. Biol., 2018 Mar.
doi.org/10.1371/journal.pcbi.1005992