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Items: 1 to 50 of 76

1.

Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot.

Reiss D, Mialdea G, Miele V, de Vienne DM, Peccoud J, Gilbert C, Duret L, Charlat S.

PLoS Genet. 2019 Feb 1;15(2):e1007965. doi: 10.1371/journal.pgen.1007965. eCollection 2019 Feb.

2.

The genome of Armadillidium vulgare (Crustacea, Isopoda) provides insights into sex chromosome evolution in the context of cytoplasmic sex determination.

Chebbi MA, Becking T, Moumen B, Giraud I, Gilbert C, Peccoud J, Cordaux R.

Mol Biol Evol. 2019 Jan 22. doi: 10.1093/molbev/msz010. [Epub ahead of print]

PMID:
30668787
3.

Yeast genetic interaction screens in the age of CRISPR/Cas.

Adames NR, Gallegos JE, Peccoud J.

Curr Genet. 2019 Apr;65(2):307-327. doi: 10.1007/s00294-018-0887-8. Epub 2018 Sep 25. Review.

PMID:
30255296
4.

The Open Insulin Project: A Case Study for 'Biohacked' Medicines.

Gallegos JE, Boyer C, Pauwels E, Kaplan WA, Peccoud J.

Trends Biotechnol. 2018 Dec;36(12):1211-1218. doi: 10.1016/j.tibtech.2018.07.009. Epub 2018 Sep 13. Review.

5.

A framework for estimating the effects of sequential reproductive barriers: Implementation using Bayesian models with field data from cryptic species.

Peccoud J, Pleydell DRJ, Sauvion N.

Evolution. 2018 Nov;72(11):2503-2512. doi: 10.1111/evo.13595. Epub 2018 Sep 27.

PMID:
30194777
6.

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 CM, Lemaitre C, Vitalis R, Simon JC.

Mol Ecol. 2018 Jul 16. doi: 10.1111/mec.14799. [Epub ahead of print]

PMID:
30010213
7.

Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants.

Boulain H, Legeai F, Guy E, Morlière S, Douglas NE, Oh J, Murugan M, Smith M, Jaquiéry J, Peccoud J, White FF, Carolan JC, Simon JC, Sugio A.

Genome Biol Evol. 2018 Jun 1;10(6):1554-1572. doi: 10.1093/gbe/evy097.

8.

Rapid evolution of aphid pests in agricultural environments.

Simon JC, Peccoud J.

Curr Opin Insect Sci. 2018 Apr;26:17-24. doi: 10.1016/j.cois.2017.12.009. Epub 2018 Jan 8. Review.

PMID:
29764656
9.

Cyberbiosecurity: An Emerging New Discipline to Help Safeguard the Bioeconomy.

Murch RS, So WK, Buchholz WG, Raman S, Peccoud J.

Front Bioeng Biotechnol. 2018 Apr 5;6:39. doi: 10.3389/fbioe.2018.00039. eCollection 2018.

10.

A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation.

Peccoud J, Lequime S, Moltini-Conclois I, Giraud I, Lambrechts L, Gilbert C.

G3 (Bethesda). 2018 Mar 28;8(4):1129-1138. doi: 10.1534/g3.117.300468.

11.

CrossPlan: systematic planning of genetic crosses to validate mathematical models.

Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM.

Bioinformatics. 2018 Jul 1;34(13):2237-2244. doi: 10.1093/bioinformatics/bty072.

PMID:
29432533
12.

Disentangling the Causes for Faster-X Evolution in Aphids.

Jaquiéry J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A, Nouhaud P, Brisson JA, Bickel R, Purandare S, Poulain J, Battail C, Lemaitre C, Mieuzet L, Le Trionnaire G, Simon JC, Rispe C.

Genome Biol Evol. 2018 Feb 1;10(2):507-520. doi: 10.1093/gbe/evy015.

13.

Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects.

Peccoud J, Cordaux R, Gilbert C.

Bioessays. 2018 Feb;40(2). doi: 10.1002/bies.201700177. Epub 2017 Dec 28. Review.

PMID:
29283188
14.

Cyberbiosecurity: From Naive Trust to Risk Awareness.

Peccoud J, Gallegos JE, Murch R, Buchholz WG, Raman S.

Trends Biotechnol. 2018 Jan;36(1):4-7. doi: 10.1016/j.tibtech.2017.10.012. Epub 2017 Dec 7. Review.

PMID:
29224719
15.

GraphSpace: stimulating interdisciplinary collaborations in network biology.

Bharadwaj A, Singh DP, Ritz A, Tegge AN, Poirel CL, Kraikivski P, Adames N, Luther K, Kale SD, Peccoud J, Tyson JJ, Murali TM.

Bioinformatics. 2017 Oct 1;33(19):3134-3136. doi: 10.1093/bioinformatics/btx382.

16.

Untangling Heteroplasmy, Structure, and Evolution of an Atypical Mitochondrial Genome by PacBio Sequencing.

Peccoud J, Chebbi MA, Cormier A, Moumen B, Gilbert C, Marcadé I, Chandler C, Cordaux R.

Genetics. 2017 Sep;207(1):269-280. doi: 10.1534/genetics.117.203380. Epub 2017 Jul 5.

17.

Massive horizontal transfer of transposable elements in insects.

Peccoud J, Loiseau V, Cordaux R, Gilbert C.

Proc Natl Acad Sci U S A. 2017 May 2;114(18):4721-4726. doi: 10.1073/pnas.1621178114. Epub 2017 Apr 17.

18.

[Insect mobile elements jump frequently into viral genomes].

Gilbert C, Peccoud J.

Med Sci (Paris). 2016 Nov;32(11):1017-1019. doi: 10.1051/medsci/20163211019. Epub 2016 Dec 23. French. No abstract available.

19.

A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability.

Barik D, Ball DA, Peccoud J, Tyson JJ.

PLoS Comput Biol. 2016 Dec 9;12(12):e1005230. doi: 10.1371/journal.pcbi.1005230. eCollection 2016 Dec. Erratum in: PLoS Comput Biol. 2017 Jan 12;13(1):e1005323.

20.

GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis.

Coll A, Wilson ML, Gruden K, Peccoud J.

Methods Mol Biol. 2016;1482:219-32. doi: 10.1007/978-1-4939-6396-6_14.

PMID:
27557770
21.

Continuous Influx of Genetic Material from Host to Virus Populations.

Gilbert C, Peccoud J, Chateigner A, Moumen B, Cordaux R, Herniou EA.

PLoS Genet. 2016 Feb 1;12(2):e1005838. doi: 10.1371/journal.pgen.1005838. eCollection 2016 Feb.

22.

Experimental testing of a new integrated model of the budding yeast Start transition.

Adames NR, Schuck PL, Chen KC, Murali TM, Tyson JJ, Peccoud J.

Mol Biol Cell. 2015 Nov 5;26(22):3966-84. doi: 10.1091/mbc.E15-06-0358. Epub 2015 Aug 26.

23.

Correction: Rule-Based Design of Plant Expression Vectors Using GenoCAD.

Coll A, Wilson ML, Gruden K, Peccoud J.

PLoS One. 2015 Aug 13;10(8):e0136004. doi: 10.1371/journal.pone.0136004. eCollection 2015. No abstract available.

24.

Rule-Based Design of Plant Expression Vectors Using GenoCAD.

Coll A, Wilson ML, Gruden K, Peccoud J.

PLoS One. 2015 Jul 6;10(7):e0132502. doi: 10.1371/journal.pone.0132502. eCollection 2015. Erratum in: PLoS One. 2015;10(8):e0136004.

25.

GenoLIB: a database of biological parts derived from a library of common plasmid features.

Adames NR, Wilson ML, Fang G, Lux MW, Glick BS, Peccoud J.

Nucleic Acids Res. 2015 May 26;43(10):4823-32. doi: 10.1093/nar/gkv272. Epub 2015 Apr 29.

26.

Genomics of adaptation to host-plants in herbivorous insects.

Simon JC, d'Alençon E, Guy E, Jacquin-Joly E, Jaquiéry J, Nouhaud P, Peccoud J, Sugio A, Streiff R.

Brief Funct Genomics. 2015 Nov;14(6):413-23. doi: 10.1093/bfgp/elv015. Epub 2015 Apr 6. Review.

PMID:
25846754
27.

Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology.

Ball DA, Lux MW, Adames NR, Peccoud J.

PLoS One. 2014 Sep 11;9(9):e107087. doi: 10.1371/journal.pone.0107087. eCollection 2014.

28.

Widespread host-dependent hybrid unfitness in the pea aphid species complex.

Peccoud J, de la Huerta M, Bonhomme J, Laurence C, Outreman Y, Smadja CM, Simon JC.

Evolution. 2014 Oct;68(10):2983-95. doi: 10.1111/evo.12478. Epub 2014 Jul 25.

PMID:
24957707
29.

Genomic regions repeatedly involved in divergence among plant-specialized pea aphid biotypes.

Nouhaud P, Peccoud J, Mahéo F, Mieuzet L, Jaquiéry J, Simon JC.

J Evol Biol. 2014 Sep;27(9):2013-20. doi: 10.1111/jeb.12441. Epub 2014 Jun 23.

30.

Rule-based design of synthetic transcription factors in eukaryotes.

Purcell O, Peccoud J, Lu TK.

ACS Synth Biol. 2014 Oct 17;3(10):737-44. doi: 10.1021/sb400134k. Epub 2014 Jan 3.

31.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM.

Nat Biotechnol. 2014 Jun;32(6):545-50. doi: 10.1038/nbt.2891. Epub 2014 Jun 6.

PMID:
24911500
32.

If you can't measure it, you can't manage it.

Peccoud J.

PLoS Comput Biol. 2014 Mar 20;10(3):e1003462. doi: 10.1371/journal.pcbi.1003462. eCollection 2014 Mar. No abstract available.

33.

Inheritance patterns of secondary symbionts during sexual reproduction of pea aphid biotypes.

Peccoud J, Bonhomme J, Mahéo F, de la Huerta M, Cosson O, Simon JC.

Insect Sci. 2014 Jun;21(3):291-300. doi: 10.1111/1744-7917.12083. Epub 2013 Dec 31.

PMID:
24382700
34.

Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors.

Wilson ML, Okumoto S, Adam L, Peccoud J.

Bioinformatics. 2014 Jan 15;30(2):251-7. doi: 10.1093/bioinformatics/btt646. Epub 2013 Nov 8.

PMID:
24215020
35.

Measurement and modeling of transcriptional noise in the cell cycle regulatory network.

Ball DA, Adames NR, Reischmann N, Barik D, Franck CT, Tyson JJ, Peccoud J.

Cell Cycle. 2013 Oct 1;12(19):3203-18. doi: 10.4161/cc.26257. Epub 2013 Sep 4.

36.

Horizontally transmitted symbionts and host colonization of ecological niches.

Henry LM, Peccoud J, Simon JC, Hadfield JD, Maiden MJ, Ferrari J, Godfray HC.

Curr Biol. 2013 Sep 9;23(17):1713-7. doi: 10.1016/j.cub.2013.07.029. Epub 2013 Aug 29.

37.

Molecular test to assign individuals within the Cacopsylla pruni complex.

Peccoud J, Labonne G, Sauvion N.

PLoS One. 2013 Aug 19;8(8):e72454. doi: 10.1371/journal.pone.0072454. eCollection 2013.

38.

Multi-locus phylogenies of the genus Barteria (Passifloraceae) portray complex patterns in the evolution of myrmecophytism.

Peccoud J, Piatscheck F, Yockteng R, Garcia M, Sauve M, Djiéto-Lordon C, Harris DJ, Wieringa JJ, Breteler FJ, Born C, McKey D, Blatrix R.

Mol Phylogenet Evol. 2013 Mar;66(3):824-32. doi: 10.1016/j.ympev.2012.11.006. Epub 2012 Nov 21.

PMID:
23178742
39.

Sequence verification of synthetic DNA by assembly of sequencing reads.

Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, Setubal JC, Tyler BM, Peccoud J.

Nucleic Acids Res. 2013 Jan 7;41(1):e25. doi: 10.1093/nar/gks908. Epub 2012 Oct 4.

40.

The PLOS ONE synthetic biology collection: six years and counting.

Peccoud J, Isalan M.

PLoS One. 2012;7(8):e43231. doi: 10.1371/journal.pone.0043231. Epub 2012 Aug 15. Review.

41.

The synthetic futures of vesicular stomatitis virus.

Overend C, Yuan L, Peccoud J.

Trends Biotechnol. 2012 Oct;30(10):497-8. doi: 10.1016/j.tibtech.2012.06.002. Epub 2012 Jul 11. No abstract available.

PMID:
22789133
42.

Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012.

Molecular Ecology Resources Primer Development Consortium,, Arias MC, Arnoux E, Bell JJ, Bernadou A, Bino G, Blatrix R, Bourguet D, Carrea C, Clamens AL, Cunha HA, d'Alençon E, Ding Y, Djieto-Lordon C, Dubois MP, Dumas P, Eraud C, Faivre B, Francisco FO, Françoso E, Garcia M, Gardner JP, Garnier S, Gimenez S, Gold JR, Harris DJ, He G, Hellemans B, Hollenbeck CM, Jing S, Kergoat GJ, Liu B, McDowell JR, McKey D, Miller TL, Newton E, Pagenkopp Lohan KM, Papetti C, Paterson I, Peccoud J, Peng X, Piatscheck F, Ponsard S, Reece KS, Reisser CM, Renshaw MA, Ruzzante DE, Sauve M, Shields JD, Solé-Cava A, Souche EL, Van Houdt JK, Vasconcellos A, Volckaert FA, Wang S, Xiao J, Yu H, Zane L, Zannato B, Zemlak TS, Zhang C, Zhao Y, Zhou X, Zhu L.

Mol Ecol Resour. 2012 May;12(3):570-2. doi: 10.1111/j.1755-0998.2012.03133.x. Epub 2012 Mar 26.

PMID:
22448966
43.

Building block synthesis using the polymerase chain assembly method.

Marchand JA, Peccoud J.

Methods Mol Biol. 2012;852:3-10. doi: 10.1007/978-1-61779-564-0_1.

PMID:
22328421
44.

Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2011-30 September 2011.

Molecular Ecology Resources Primer Development Consortium, A'Hara SW, Amouroux P, Argo EE, Avand-Faghih A, Barat A, Barbieri L, Bert TM, Blatrix R, Blin A, Bouktila D, Broome A, Burban C, Capdevielle-Dulac C, Casse N, Chandra S, Cho KJ, Cottrell JE, Crawford CR, Davis MC, Delatte H, Desneux N, Djieto-Lordon C, Dubois MP, El-Mergawy RA, Gallardo-Escárate C, Garcia M, Gardiner MM, Guillemaud T, Haye PA, Hellemans B, Hinrichsen P, Jeon JH, Kerdelhué C, Kharrat I, Kim KH, Kim YY, Kwan YS, Labbe EM, LaHood E, Lee KM, Lee WO, Lee YH, Legoff I, Li H, Lin CP, Liu SS, Liu YG, Long D, Maes GE, Magnoux E, Mahanta PC, Makni H, Makni M, Malausa T, Matura R, McKey D, McMillen-Jackson AL, Méndez MA, Mezghani-Khemakhem M, Michel AP, Paul M, Muriel-Cunha J, Nibouche S, Normand F, Palkovacs EP, Pande V, Parmentier K, Peccoud J, Piatscheck F, Puchulutegui C, Ramos R, Ravest G, Richner H, Robbens J, Rochat D, Rousselet J, Saladin V, Sauve M, Schlei O, Schultz TF, Scobie AR, Segovia NI, Seyoum S, Silvain JF, Tabone E, Van Houdt JK, Vandamme SG, Volckaert FA, Wenburg J, Willis TV, Won YJ, Ye NH, Zhang W, Zhang YX.

Mol Ecol Resour. 2012 Jan;12(1):185-9. doi: 10.1111/j.1755-0998.2011.03088.x. Epub 2011 Dec 4.

PMID:
22136175
45.

Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry.

Ball DA, Marchand J, Poulet M, Baumann WT, Chen KC, Tyson JJ, Peccoud J.

PLoS One. 2011;6(10):e26272. doi: 10.1371/journal.pone.0026272. Epub 2011 Oct 26.

46.

Genetic design automation: engineering fantasy or scientific renewal?

Lux MW, Bramlett BW, Ball DA, Peccoud J.

Trends Biotechnol. 2012 Feb;30(2):120-6. doi: 10.1016/j.tibtech.2011.09.001. Epub 2011 Oct 14. Review.

47.

A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD.

Wilson ML, Hertzberg R, Adam L, Peccoud J.

Methods Enzymol. 2011;498:173-88. doi: 10.1016/B978-0-12-385120-8.00008-5.

PMID:
21601678
48.

Strengths and limitations of the federal guidance on synthetic DNA.

Adam L, Kozar M, Letort G, Mirat O, Srivastava A, Stewart T, Wilson ML, Peccoud J.

Nat Biotechnol. 2011 Mar;29(3):208-10. doi: 10.1038/nbt.1802. No abstract available.

PMID:
21390018
49.

Stochastic exit from mitosis in budding yeast: model predictions and experimental observations.

Ball DA, Ahn TH, Wang P, Chen KC, Cao Y, Tyson JJ, Peccoud J, Baumann WT.

Cell Cycle. 2011 Mar 15;10(6):999-1009. Epub 2011 Mar 15.

50.

Essential information for synthetic DNA sequences.

Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Stan GB, Sauro HM.

Nat Biotechnol. 2011 Jan;29(1):22; discussion 22-3. doi: 10.1038/nbt.1753. No abstract available.

PMID:
21221092

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