Publications 2018

Progress in single-access information systems for wheat and rice crop improvement.

Scheben A, Chan CK, Mansueto L, Mauleon R, Larmande P, Alexandrov N, Wing RA, McNally KL, Quesneville H, Edwards D.
Brief Bioinform. 2018 Apr 5.
DOI: https://doi.org/10.1093/bib/bby016.

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes.

Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y.
Current Biology 28(14):2274-2282.e6.  2018
DOI: https://doi.org/10.1016/j.cub.2018.05.066

Porins and amyloids are coded by similar sequence motifs

Villain E., Nikekhin A.A.,  Kajava A. V.
Proteomics e1800075.  2018
DOI: https://doi.org/10.1002/pmic.201800075

Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification

Bondarev S. A., Antonets K. S., Kajava A. V., Nizhnikov A. A., Zhouravleva G. A.
Int. J. Mol. Sci., 19: E2292-2321.  2018
DOI: https://doi.org/10.3390/ijms19082292

Improving pairwise comparison of protein sequences with domain co-occurrence.

Establishment of constraints on amyloid formation imposed by steric exclusion of globular domains

Azizyan R. A., Garro A., Radkova Z., Anikeenko A., Bakulina A., Dumas C. and Kajava A. V.
Journal of Molecular Biology, 430(20):3835-3846, 2018
DOI: https://doi.org/10.1016/j.jmb.2018.05.038

Identification of the autochaperone domain in the Type Va secretion system (T5aSS): A prevalent feature of autotransporters with a β–helical passenger

Rojas-Lopez M., Amine Zorgani M., Kelley L., Bailly X., Kajava A. V., Henderson I., Polticelli F., Pizza M., Rosini R., Desvaux M.
Frontiers in Microbiology 8:2607.  2018
DOI: https://doi.org/10.3389/fmicb.2017.02607

Editorial (for a special issue “Proteins with Tandem Repeats”)

 Kajava A.V., Tosatto S. C.
Journal of Structural Biology,  201(2):86-87. 2018
DOI: https://doi.org/10.1016/j.jsb.2017.12.011.

BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures

Bondarev S. A., Bondareva O. V., Zhouravleva G. A.,  Kajava A. V.
Bioinformatics, 34(4):599-608.  2018
DOI: https://doi.org/10.1093/bioinformatics/btx629

Classification of beta-hairpin repeat proteins

Roche  D. B., Do Viet P.,  Bakulina A., Hirsh L., Tosatto S. C., Kajava A.V.
Journal of Structural Biology, 201, 130-138.  2018
DOI: https://doi.org/10.1016/j.jsb.2017.10.001.

AutoWIG: automatic generation of python bindings for C++ libraries

Fernique P., Pradal C. (2018).
PeerJ Computer Science, 4, e149.
URL : https://peerj.com/articles/cs-149
PDF : https://peerj.com/articles/cs-149.pdf

Inferring sex-specific demographic history from SNP data

Clemente F., Gautier M., Vitalis R.
PLoS Genetics, Volume 14(1), January 2018, Pages e1007191
DOI: 10.1371/journal.pgen.1007191
URL : https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007191
PDF : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1007191&type=printable

Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races

Nouhaud P., Gautier M., Gouin A., Jaquiéry J., Peccoud J., Legeai F., Mieuzet L. Smadja C. M., Lemaitre C., Vitalis R., Simon J.-C.
Molecular Ecology, Volume 27, August 2018 Pages 3287–3300
DOI: 10.1111/mec.14799
URL : https://onlinelibrary.wiley.com/doi/full/10.1111/mec.14799
PDF : https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.14799

Measuring genetic differentiation from Pool-seq data

Hivert V., Leblois R., Petit E. J., Gautier M., Vitalis R.
Genetics, Volume 210, September 2018, Pages 315–330.
DOI: 10.1534/genetics.118.300900
URL : http://www.genetics.org/content/210/1/315
PDF : http://www.genetics.org/content/210/1/315.full.pdf

RecPhyloXML - a format for reconciled gene trees.

Wandrille Duchemin ..., Celine Scornavacca, ...Vincent Daubin.
Bioinformatics, Volume 34, Issue 21, 1 November 2018, Pages 3646–3652,
URL: https://doi.org/10.1093/bioinformatics/bty389

Exploring the tiers of rooted phylogenetic network space using tail moves.

Remie Janssen, Mark Jones, Peter L. Erdos, Leo van Iersel, Celine Scornavacca.
Bulletin of Mathematical Biology (2018), pp 2177-2208.
URL: https://link.springer.com/article/10.1007/s11538-018-0452-0

Improved maximum parsimony models for phylogenetic networks.

Leo van Iersel, Mark Jones, Celine Scornavacca.
Systematic Biology, 67(2018), no. 3, pp 518-542.
URL https://doi.org/10.1093/sysbio/syx094

Practical lower and upper bounds for the Shortest Linear Superstring

B. Cazaux, S. Juhel, E. Rivals
17th International Symposium on Experimental Algorithms (SEA 2018)
LIPICs series, vol. 103(18), 2018. doi: http://dx.doi.org/10.4230/LIPIcs.SEA.2018.18

Superstrings with multiplicities

B. Cazaux, E. Rivals
29th International Conference Combinatorial Pattern Matching (CPM), July 2--4, 2018, Qingdao, China;
LIPICs series, vol. 105(21), 2018
DOI: http://dx.doi.org/10.4230/LIPIcs.CPM.2018.21

Relationship between superstring and compression measures: new insights on the greedy conjecture

B. Cazaux, E. Rivals
Discrete Applied Mathematics, Volume 245, Pages 59-64 (online 2017), 20 August 2018,
DOI:  http://dx.doi.org/10.1016/j.dam.2017.04.017
HAL: https://hal-lirmm.ccsd.cnrs.fr/lirmm-01617213

Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish.

Coleman RA, Gauffre B, Pavlova A, Beheregaray LB, Kearns J, Lyon J, Sasaki M, Leblois R, Sgro C, Sunnucks P. Heredity (Edinb). 2018 Jan 12. doi: 10.1038/s41437-017-0008-3.
URL: https://www.nature.com/articles/s41437-017-0008-3

Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa.

Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa.
Leblois R, Gautier M, Rohfritsch A, Foucaud J, Burban C, Galan M, Loiseau A, Sauné L, Branco M, Gharbi K, Vitalis R, Kerdelhué C.

Mol Ecol. 2018 Jan;27(1):264-278. doi: 10.1111/mec.14411.
URL: http://onlinelibrary.wiley.com/doi/10.1111/mec.14411/abstract
PDF: http://onlinelibrary.wiley.com/doi/10.1111/mec.14411/pdf

Differential long non-coding RNA expression profiles in human oocytes and cumulus cells

Bouckenheimer J, Fauque P, Lecellier CH, Bruno C, Commes T, Lemaître JM, De Vos J, Assou S. Sci Rep. 2018 Feb 2;8(1):2202. doi: 10.1038/s41598-018-20727-0.
URL: https://www.nature.com/articles/s41598-018-20727-0
PDF: https://www.nature.com/articles/s41598-018-20727-0.pdf

AgroPortal: A vocabulary and ontology repository for agronomy

Clement Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzale Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce and Pierre Larmande. Computers and Electronics in Agriculture, Elsevier, 2018, 144, pp.126-143. Doi:10.1016/j.compag.2017.10.012.

Computational pan-genomics: status, promises and challenges

Marschall T., Marz M., Abeel T., Dijkstra L., Dutilh B. E., Ghaffaari A., Kersey P., Kloosterman W. P., Makinen V., Novak A. M., Paten B., Porubsky D., Rivals E., Alkan C., Baaijens J. A., De Bakker P. I. W., Boeva V., Bonnal R. J. P., Chiaromonte F., Chikhi R., Ciccarelli F. D., Cijvat R., Datema E., Van Duijn C. M., Eichler E. E., Ernst C., Eskin E., Garrison E.,El-Kebir M., Klau G. W., Korbel J. O., Lameijer E-W., Langmead B., Martin M., Medvedev P, Mu J. C., Neerincx P., Ouwens K., Peterlongo P., Pisanti N., Rahmann S., Raphael B., Reinert K., De Ridder D., De Ridder J., Schlesner M., Schulz-Trieglaff O., Sanders A. D., Sheikhizadeh S., Shneider C., Smit S., Valenzuela D., Wang J., Wessels L., Zhang Y., Guryev V., Vandin F., Ye K., Schönhuth A.
Briefings in Bioinformatics, Vol 19(1), p. 118-135, doi: 10.1093/bib/bbw089 2018.
URL : http://dx.doi.org/10.1093/bib/bbw089
PDF : https://academic.oup.com/bib/article-pdf/19/1/118/25406834/bbw089.pdf

Probing instructions for expression regulation in gene nucleotide compositions

Bessière C, Taha M, Petitprez F, Vandel J, Marin, J-M, Bréhélin L, Lèbre S, Lecellier C-H
PLOS Computational Biology, January 2, 2018
URL: https://doi.org/10.1371/journal.pcbi.1005921