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Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral.

Liew YJ, Zoccola D, Li Y, Tambutté E, Venn AA, Michell CT, Cui G, Deutekom ES, Kaandorp JA, Voolstra CR, Forêt S, Allemand D, Tambutté S, Aranda M.

Sci Adv. 2018 Jun 6;4(6):eaar8028. doi: 10.1126/sciadv.aar8028. eCollection 2018 Jun.


Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing.

Urbarova I, Patel H, Forêt S, Karlsen BO, Jørgensen TE, Hall-Spencer JM, Johansen SD.

Genome Biol Evol. 2018 Feb 1;10(2):410-426. doi: 10.1093/gbe/evy003.


Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems.

Quattrini AM, Faircloth BC, Dueñas LF, Bridge TCL, Brugler MR, Calixto-Botía IF, DeLeo DM, Forêt S, Herrera S, Lee SMY, Miller DJ, Prada C, Rádis-Baptista G, Ramírez-Portilla C, Sánchez JA, Rodríguez E, McFadden CS.

Mol Ecol Resour. 2018 Mar;18(2):281-295. doi: 10.1111/1755-0998.12736. Epub 2017 Dec 6.


Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome.

Welsh L, Maleszka R, Foret S.

R Soc Open Sci. 2017 Sep 6;4(9):170248. doi: 10.1098/rsos.170248. eCollection 2017 Sep.


Host modification of a bacterial quorum-sensing signal induces a phenotypic switch in bacterial symbionts.

Pietschke C, Treitz C, Forêt S, Schultze A, Künzel S, Tholey A, Bosch TCG, Fraune S.

Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):E8488-E8497. doi: 10.1073/pnas.1706879114. Epub 2017 Sep 18.


A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei.

Jones DB, Jerry DR, Khatkar MS, Raadsma HW, Steen HV, Prochaska J, Forêt S, Zenger KR.

Sci Rep. 2017 Sep 4;7(1):10360. doi: 10.1038/s41598-017-10515-7.


Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals.

Aguilar C, Raina JB, Motti CA, Fôret S, Hayward DC, Lapeyre B, Bourne DG, Miller DJ.

BMC Genomics. 2017 Aug 14;18(1):612. doi: 10.1186/s12864-017-3959-0.


Contrasting Sex-and Caste-Dependent piRNA Profiles in the Transposon Depleted Haplodiploid Honeybee Apis mellifera.

Wang W, Ashby R, Ying H, Maleszka R, Forêt S.

Genome Biol Evol. 2017 May 1;9(5):1341-1356. doi: 10.1093/gbe/evx087.


Subcellular tracking reveals the location of dimethylsulfoniopropionate in microalgae and visualises its uptake by marine bacteria.

Raina JB, Clode PL, Cheong S, Bougoure J, Kilburn MR, Reeder A, Forêt S, Stat M, Beltran V, Thomas-Hall P, Tapiolas D, Motti CM, Gong B, Pernice M, Marjo CE, Seymour JR, Willis BL, Bourne DG.

Elife. 2017 Apr 4;6. pii: e23008. doi: 10.7554/eLife.23008.


Developmental and loco-like effects of a swainsonine-induced inhibition of α-mannosidase in the honey bee, Apis mellifera.

Wedd L, Ashby R, Foret S, Maleszka R.

PeerJ. 2017 Mar 16;5:e3109. doi: 10.7717/peerj.3109. eCollection 2017.


Transcriptomic Analysis of Thermally Stressed Symbiodinium Reveals Differential Expression of Stress and Metabolism Genes.

Gierz SL, Forêt S, Leggat W.

Front Plant Sci. 2017 Feb 28;8:271. doi: 10.3389/fpls.2017.00271. eCollection 2017.


Analyses of Corallimorpharian Transcriptomes Provide New Perspectives on the Evolution of Calcification in the Scleractinia (Corals).

Lin MF, Moya A, Ying H, Chen CA, Cooke I, Ball EE, Forêt S, Miller DJ.

Genome Biol Evol. 2017 Jan 1;9(1):150-160. doi: 10.1093/gbe/evw297.


Corallimorpharians are not "naked corals": insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses.

Lin MF, Chou WH, Kitahara MV, Chen CL, Miller DJ, Forêt S.

PeerJ. 2016 Oct 11;4:e2463. eCollection 2016.


Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals.

Raina JB, Tapiolas D, Motti CA, Foret S, Seemann T, Tebben J, Willis BL, Bourne DG.

PeerJ. 2016 Aug 18;4:e2275. doi: 10.7717/peerj.2275. eCollection 2016.


Near-future pH conditions severely impact calcification, metabolism and the nervous system in the pteropod Heliconoides inflatus.

Moya A, Howes EL, Lacoue-Labarthe T, Forêt S, Hanna B, Medina M, Munday PL, Ong JS, Teyssié JL, Torda G, Watson SA, Miller DJ, Bijma J, Gattuso JP.

Glob Chang Biol. 2016 Dec;22(12):3888-3900. doi: 10.1111/gcb.13350. Epub 2016 Jun 18.


Comparative genomics explains the evolutionary success of reef-forming corals.

Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutté S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, Falkowski PG.

Elife. 2016 May 24;5. pii: e13288. doi: 10.7554/eLife.13288.


Hologenome analysis of two marine sponges with different microbiomes.

Ryu T, Seridi L, Moitinho-Silva L, Oates M, Liew YJ, Mavromatis C, Wang X, Haywood A, Lafi FF, Kupresanin M, Sougrat R, Alzahrani MA, Giles E, Ghosheh Y, Schunter C, Baumgarten S, Berumen ML, Gao X, Aranda M, Foret S, Gough J, Voolstra CR, Hentschel U, Ravasi T.

BMC Genomics. 2016 Feb 29;17:158. doi: 10.1186/s12864-016-2501-0.


Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora.

Moya A, Sakamaki K, Mason BM, Huisman L, Forêt S, Weiss Y, Bull TE, Tomii K, Imai K, Hayward DC, Ball EE, Miller DJ.

BMC Genomics. 2016 Jan 16;17:62. doi: 10.1186/s12864-015-2355-x.


MicroRNAs in Honey Bee Caste Determination.

Ashby R, Forêt S, Searle I, Maleszka R.

Sci Rep. 2016 Jan 7;6:18794. doi: 10.1038/srep18794.


EGFR gene methylation is not involved in Royalactin controlled phenotypic polymorphism in honey bees.

Kucharski R, Foret S, Maleszka R.

Sci Rep. 2015 Sep 11;5:14070. doi: 10.1038/srep14070.


Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals.

Bertucci A, Forêt S, Ball EE, Miller DJ.

Mol Ecol. 2015 Sep;24(17):4489-504. doi: 10.1111/mec.13328. Epub 2015 Aug 24.


Estimation of the methylation pattern distribution from deep sequencing data.

Lin P, Forêt S, Wilson SR, Burden CJ.

BMC Bioinformatics. 2015 May 6;16:145. doi: 10.1186/s12859-015-0600-6.


Rapid acclimation of juvenile corals to CO2 -mediated acidification by upregulation of heat shock protein and Bcl-2 genes.

Moya A, Huisman L, Forêt S, Gattuso JP, Hayward DC, Ball EE, Miller DJ.

Mol Ecol. 2015 Jan;24(2):438-52. doi: 10.1111/mec.13021. Epub 2015 Jan 9.


How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans.

Bosch TC, Adamska M, Augustin R, Domazet-Loso T, Foret S, Fraune S, Funayama N, Grasis J, Hamada M, Hatta M, Hobmayer B, Kawai K, Klimovich A, Manuel M, Shinzato C, Technau U, Yum S, Miller DJ.

Bioessays. 2014 Dec;36(12):1185-94. doi: 10.1002/bies.201400065. Epub 2014 Sep 10.


Development of phylogenetic markers for Sebacina (Sebacinaceae) mycorrhizal fungi associated with Australian orchids.

Ruibal MP, Peakall R, Foret S, Linde CC.

Appl Plant Sci. 2014 Jun 4;2(6). pii: apps.1400015. doi: 10.3732/apps.1400015. eCollection 2014 Jun.


The "naked coral" hypothesis revisited--evidence for and against scleractinian monophyly.

Kitahara MV, Lin MF, Forêt S, Huttley G, Miller DJ, Chen CA.

PLoS One. 2014 Apr 16;9(4):e94774. doi: 10.1371/journal.pone.0094774. eCollection 2014.


The distribution of word matches between Markovian sequences with periodic boundary conditions.

Burden CJ, Leopardi P, Forêt S.

J Comput Biol. 2014 Jan;21(1):41-63. doi: 10.1089/cmb.2012.0277. Epub 2013 Oct 26.


DMSP biosynthesis by an animal and its role in coral thermal stress response.

Raina JB, Tapiolas DM, Forêt S, Lutz A, Abrego D, Ceh J, Seneca FO, Clode PL, Bourne DG, Willis BL, Motti CA.

Nature. 2013 Oct 31;502(7473):677-80. doi: 10.1038/nature12677. Epub 2013 Oct 23.


Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima.

Jones DB, Jerry DR, Forêt S, Konovalov DA, Zenger KR.

Mar Biotechnol (NY). 2013 Dec;15(6):647-58. doi: 10.1007/s10126-013-9514-3. Epub 2013 May 30.


Unique features of odorant-binding proteins of the parasitoid wasp Nasonia vitripennis revealed by genome annotation and comparative analyses.

Vieira FG, Forêt S, He X, Rozas J, Field LM, Zhou JJ.

PLoS One. 2012;7(8):e43034. doi: 10.1371/journal.pone.0043034. Epub 2012 Aug 27.


Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO₂-driven acidification during the initiation of calcification.

Moya A, Huisman L, Ball EE, Hayward DC, Grasso LC, Chua CM, Woo HN, Gattuso JP, Forêt S, Miller DJ.

Mol Ecol. 2012 May;21(10):2440-54. doi: 10.1111/j.1365-294X.2012.05554.x. Epub 2012 Apr 10.


DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.

Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4968-73. doi: 10.1073/pnas.1202392109. Epub 2012 Mar 13.


Searching for Eve: basal metazoans and the evolution of multicellular complexity.

Manuel M, Forêt S.

Bioessays. 2012 Mar;34(3):247-51. doi: 10.1002/bies.201100183. Epub 2012 Jan 13. No abstract available.


Differential gene expression at coral settlement and metamorphosis--a subtractive hybridization study.

Hayward DC, Hetherington S, Behm CA, Grasso LC, Forêt S, Miller DJ, Ball EE.

PLoS One. 2011;6(10):e26411. doi: 10.1371/journal.pone.0026411. Epub 2011 Oct 31.


Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis.

Iguchi A, Shinzato C, Forêt S, Miller DJ.

PLoS One. 2011;6(6):e20140. doi: 10.1371/journal.pone.0020140. Epub 2011 Jun 20.


The biology of coral metamorphosis: molecular responses of larvae to inducers of settlement and metamorphosis.

Grasso LC, Negri AP, Fôret S, Saint R, Hayward DC, Miller DJ, Ball EE.

Dev Biol. 2011 May 15;353(2):411-9. doi: 10.1016/j.ydbio.2011.02.010. Epub 2011 Feb 19.


The honey bee epigenomes: differential methylation of brain DNA in queens and workers.

Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R.

PLoS Biol. 2010 Nov 2;8(11):e1000506. doi: 10.1371/journal.pbio.1000506. Erratum in: PLoS Biol. 2011;9(1). doi: 10.1371/annotation/2db9ee19-faa4-43f2-af7a-c8aeacca8037.


Phylogenomics reveals an anomalous distribution of USP genes in metazoans.

Forêt S, Seneca F, de Jong D, Bieller A, Hemmrich G, Augustin R, Hayward DC, Ball EE, Bosch TC, Agata K, Hassel M, Miller DJ.

Mol Biol Evol. 2011 Jan;28(1):153-61. doi: 10.1093/molbev/msq183. Epub 2010 Jul 21.


New tricks with old genes: the genetic bases of novel cnidarian traits.

Forêt S, Knack B, Houliston E, Momose T, Manuel M, Quéinnec E, Hayward DC, Ball EE, Miller DJ.

Trends Genet. 2010 Apr;26(4):154-8. doi: 10.1016/j.tig.2010.01.003. Epub 2010 Feb 1.


Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK; Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA.

Science. 2010 Jan 15;327(5963):343-8. doi: 10.1126/science.1178028. Erratum in: Science. 2010 Mar 26;327(5973):1577.


Patterns of gene expression in a scleractinian coral undergoing natural bleaching.

Seneca FO, Forêt S, Ball EE, Smith-Keune C, Miller DJ, van Oppen MJ.

Mar Biotechnol (NY). 2010 Oct;12(5):594-604. doi: 10.1007/s10126-009-9247-5. Epub 2009 Dec 30.


Characterizing the D2 statistic: word matches in biological sequences.

Forêt S, Wilson SR, Burden CJ.

Stat Appl Genet Mol Biol. 2009;8:Article 43. doi: 10.2202/1544-6115.1447. Epub 2009 Oct 8.


Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes.

Foret S, Kucharski R, Pittelkow Y, Lockett GA, Maleszka R.

BMC Genomics. 2009 Oct 14;10:472. doi: 10.1186/1471-2164-10-472.


The genome of the model beetle and pest Tribolium castaneum.

Tribolium Genome Sequencing Consortium, Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G.

Nature. 2008 Apr 24;452(7190):949-55. doi: 10.1038/nature06784. Epub 2008 Mar 23.


Nutritional control of reproductive status in honeybees via DNA methylation.

Kucharski R, Maleszka J, Foret S, Maleszka R.

Science. 2008 Mar 28;319(5871):1827-30. doi: 10.1126/science.1153069. Epub 2008 Mar 13.


Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences.

Forêt S, Kantorovitz MR, Burden CJ.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S21.


RNAi-induced phenotypes suggest a novel role for a chemosensory protein CSP5 in the development of embryonic integument in the honeybee (Apis mellifera).

Maleszka J, Forêt S, Saint R, Maleszka R.

Dev Genes Evol. 2007 Mar;217(3):189-96. Epub 2007 Jan 10.


Chemosensory proteins in the honey bee: Insights from the annotated genome, comparative analyses and expressional profiling.

Forêt S, Wanner KW, Maleszka R.

Insect Biochem Mol Biol. 2007 Jan;37(1):19-28. Epub 2006 Oct 6. Erratum in: Insect Biochem Mol Biol. 2015 Oct;65:107.


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