Publications récentes PDF Print Email

Some lab publications since 2009:

1. Nesbø CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, Doolittle WF (2009). The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol.;191(6):1974-8.

2. Lopez P, Bapteste E (2009) Molecular phylogeny: reconstructing the forest. C R Biol. Feb-Mar; 332(2-3):171-82. PMID: 19281950

3. Boucher Y, Bapteste E (2009) Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. Bioessays. 31(5):526-36.

4. Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W. (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct.;4:34.

5. Bapteste E, Boucher Y (2009) Epistemological impacts of horizontal gene transfer on classification in microbiology Methods Mol Biol.; 532:55-72. PMID: 19271179

6. Halary S, Leigh J, Cheaib B, Lopez P, Bapteste E (2010). Network analyses structure genetic diversity in independent genetic worlds., Proc Natl Acad Sci U S A. 107(1):127-32. (Evaluated by the Faculty of 1000)

7. Lapointe FJ, Lopez P, Boucher Y, Koenig J, Bapteste E (2010). Clanistics: a multi-level perspective for harvesting unrooted gene trees. Trends Microbiol. 18(8):341-347

8. Bapteste E, Burian RM (2010). On the Need for Integrative Phylogenomics, and Some Steps Toward its Creation. Biology and Philosophy. 25(4) :711-736

9. Bittner L, Halary S, Payri C, Cruaud C, de Reviers B, Lopez P, Bapteste E (2010). Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biol Direct. 5:47.

10. Schliep K, Lopez P, Lapointe FJ, Bapteste E (2011). Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees. Mol Biol Evol. (4):1393-405

11. Boucher Y, Cordero OX, Takemura A, Hunt DE, Schliep K, Bapteste E, Lopez P, Tarr CL and Polz MF (2011). Local Mobile Gene Pools Rapidly Cross Species Boundaries to Create Endemicity Within Global Vibrio cholerae Populations. mBio 2(2). pii: e00335-10.

12. Leigh JW, Schliep K, Lopez P, Bapteste E. (2011) Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol. (10):2773-85.

13. Leigh JW, Lapointe FJ, Lopez P, Bapteste E. (2011) Evaluating phylogenetic congruence in the post-genomic era. Genome Biol Evol. (3):571-87.

14. Beauregard-Racine J, Bicep C, Schliep K, Lopez P, Lapointe FJ, Bapteste E. (2011). Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol Direct. (6):39; discussion 39.

15. McInerney JO, Pisani D, Bapteste E, O'Connell MJ. (2011) The Public Goods Hypothesis for the evolution of life on Earth. Biol Direct. (6):41.

16. Bapteste E, Bouchard F, Burian RM. (2012) Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns. Methods Mol Biol. (856):81-110.

17. Bapteste E, Bicep C, Lopez P. (2012). Evolution of genetic diversity using networks: the human gut microbiome as a case study. Clin Microbiol Infect. (Suppl 4):40-3.

18. Bapteste E, Lopez P, Bouchard F, Baquero F, McInerney JO, Burian RM. (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc Natl Acad Sci U S A.109(45):18266-72.

19. Bhattacharya D, Price D.C, Bicep C, Bapteste E, Sarwade M., Rajah V.D, Yoon HW. (2013) Identification of a marine cyanophage in a protist single cell metagenome assembly. Journal of Phycology. Accepted manuscript online: 27 NOV 2012, DOI: 10.1111/jpy.12028

20. Bapteste E, Dupré J (2013). Towards a Processual Microbial Ontology. Biology and Philosophy. Biol Philos. 28(2):379-404.

21. Jachiet PA, Pogorelcnik R, Berry A, Lopez P, Bapteste E.(2013) MosaicFinder: identification of fused gene families in sequence similarity networks. Bioinformatics. 29(7):837-44.

22. Alvarez-Ponce D, Lopez P, Bapteste E, McInerney JO. (2013) Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proc Natl Acad Sci U S A. 2013;110(17):E1594-603.

23. Misner I, Bicep C, Lopez P, Halary S, Bapteste E, Lane CE. (2013) Sequence comparative analysis using networks: software for evaluating de novo transcript assembly from next-generation sequencing. Mol Biol Evol. 30(8):1975-86.

24. Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitfield J. (2013) Networks: expanding evolutionary thinking. Trends Genet. 29(8):439-41.

25. Halary S, McInerney JO, Lopez P, Bapteste E. (2013) EGN: a wizard for construction of gene and genome similarity networks. BMC Evol Biol. 13:146.

26. Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO. (2014) A pluralistic account of homology: adapting the models to the data. A pluralistic account of homology: adapting the models to the data. Mol Biol Evol. 31(3):501-16.

27. Bapteste E. (2014) The origins of microbial adaptations: how introgressive descent, egalitarian evolutionary transitions and expanded kin selection shape the network of life. Front Microbiol. 5:83.

28. Jachiet PA, Colson P, Lopez P, Bapteste E. (2014). Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Genome Biol Evol. 6(9):2195-205.

29. Dagan T, Bapteste E, McInerney JO, Martin WF. (2014) SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report. Genome Biol Evol.;6(9):2206-9.

30. Cheng S., Karkar S., Bapteste E., Yee N., Falkowski P., Bhattacharya D. (2014) Sequence similarity network reveals the imprints of major diversification events in the evolution of microbial life. Frontiers in Ecology and Evolution. 2 (72):1-13

31. Forster D., Bittner, L. Karkar S., Dunthorn M., Romac S., Audic S., Lopez P., Stoeck T., Bapteste E. (2015) Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biology 13:16 (24 February 2015)

32. Boon E., Halary S., Bapteste E., Hijri M. (2015). Genome Heterogeneity within the Cytoplasm? The Case of Arbuscular Mycorrhizal Fungi. Genome Biol Evol. 7(2):505-21

33. Méheust R., Lopez P., Bapteste E., (2015). Metabolic bacterial genes and the construction of high-level composite lineages of life. Trends in Ecology and Evolution. 30(3):127-9

34. Lopez P, Halary S, Bapteste E. (2015). Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life. Biol Direct. 2015 Oct 26;10(1):64.

35. Corel E, Lopez P, Méheust R, Bapteste E. (2015) Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends Microbiol. 2016 Mar;24(3):224-37.

36. Méheust R, Zelzion E, Bhattacharya D, Lopez P, Bapteste E. (2016) Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis. Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3579-84.

37. Jaffe AL, Corel E, Pathmanathan JS, Lopez P, Bapteste E. (2016) Bipartite graph analyses reveal interdomain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins. Environ Microbiol. 2016 Aug 3.

38. List JM, Pathmanathan JS, Lopez P, Bapteste E. (2016) Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics. Biol Direct. 2016 Aug 20;11:39.

39. Lord E, Le Cam M, Bapteste É, Méheust R, Makarenkov V, Lapointe FJ. (2016) BRIDES: A  New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts. PloS One. 2016 Aug 31;11(8):e0161474.

40. List, J.-M., P. Lopez, and E. Bapteste (2016): Using sequence similarity networks to identify partial cognates in multilingual wordlists. In: Proceedings of the Association of Computational Linguistics 2016 (Volume 2: Short Papers). Association of Computational Linguistics 599-605. doi: Janvier

41. Richard G Dorrell, Gillian Gile, Giselle McCallum, Raphaël Méheust, Eric P Bapteste,Christen M Klinger, Loraine Brillet-Guéguen, Katalina D Freeman, Daniel J Richter, Chris Bowler (2017): Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife;10.7554/eLife.23717

42. List, J.-M.; Pathmanathan, J. S.; Hill, N. W.; Bapteste, E. & Lopez, P. Vowel purity and rhyme evidence in Old Chinese reconstruction. In: Lingua Sinica, 2017. DOI: 10.1186/s40655-017-0021-8.

43. Eric Bapteste et Liliane Campos (2018) Raconter le virus : Dialogue interdisciplinaire sur la transposition narrative du discours biologique. Epistémocritique. Volume 17. 9 /05/ 2018

44. Pathmanathan JS, Lopez P, Lapointe FJ, Bapteste E. CompositeSearch, a generalized network approach for composite gene families detection. Mol Biol Evol. 2017 Oct 30. doi: 10.1093/molbev/msx283.

45. Eduardo Corel, Raphaël Méheust, Andrew K. Watson, James O. McInerney, Philippe Lopez, Eric Bapteste (accepted December 23rd 2017) Bipartite network analysis of gene sharings in the microbial world. Mol Biol Evol. Apr 1;35(4):899-913. doi: 10.1093/molbev/msy001.

46. Bernard G, Pathmanathan JS, Lannes R, Lopez P, Bapteste E. Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. Genome Biol Evol. 2018 Mar 1;10(3):707-715. doi: 10.1093/gbe/evy031.

47.  Méheust R, Bhattacharya D, Pathmanathan JS, McInerney JO, Lopez P, Bapteste E. Formation of chimeric genes with essential functions at the origin of eukaryotes. BMC Biol. 2018 Mar 13;16(1):30. doi: 10.1186/s12915-018-0500-0.

48. Méheust R., Watson AK, Lapointe FJ, Papke RT, Lopez P, Bapteste E, Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution, Genome Biol. 2018 Jun 7;19(1):75. doi: 10.1186/s13059-018-1454-9.

49. Bapteste E., Huneman P. (2018) Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory. BMC Biol. 2018 May 29;16(1):56. doi: 10.1186/s12915-018-0531-6.

50. Vigliotti C, Bicep C, Bapteste E, Lopez P, Corel E. Tracking the Rules of Transmission and Introgression with Networks. Microbiol Spectr. 2018 Apr;6(2). doi: 10.1128/microbiolspec.MTBP-0008-2016.

51. Corel E, Pathmanathan JS, Watson AK, Karkar S, Lopez P, Bapteste E. MultiTwin: a software suite to analyze evolution at multiple levels of organization using multipartite graphs. Genome Biol Evol. 2018 Sep 22. doi: 10.1093/gbe/evy209. [Epub ahead of print]