Publications

 

[2019]

Marlétaz F, Peijnenburg KTCA, Goto T, Satoh N, Rokhsar DS. 2019. A new spiralian phylogeny places the enigmatic arrow worms among gnathiferans.  Curr Biol. 29, 1–7,doi:10.1016/j.cub.2018.11.042.

Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai M, Simakov O, Foster JS, Nyholm SV. 2019. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. Proc Natl Acad Sci U S A. 2019 Jan 11. pii: 201817322. doi:10.1073/pnas.1817322116.

[2018]

Marlétaz F*, Firmbas PN*, Maeso I*, Tena J*, Bogdanovic O*, Perry M*, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M. 2018. Amphioxus functional genomics pinpoints the origin of chordate regulatory novelties.  Nature.  564,  64–70. doi:10.1038/s41586-018-0734-6 [*, equal contributions]

Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J,Alonso R, Curk F, Du D, Ollitrault P, Roose ML, Dopazo J, Gmitter FG, Rokhsar DS, Talon M, Curk F, 2018. Genomics of the origin and evolution of Citrus. Nature, 554(7692), p.311.doi:10.1038/nature25447

Sanchez G, Setiamarga DHE, Tuanapaya S, Tongtherm K, Winkelmann IE, Schmidbaur H, Umino T, Albertin C, Allcock L, Perales-Raya C, Gleadall I, Strugnell JM, Simakov O, Nabhitabhata J. 2018. Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas. PeerJ.  Feb 12;6:e4331. doi:10.7717/peerj.4331.

Lukoseviciute M*, Gavriouchkina D*, Williams RM*, Hochgreb-Hagele T, Senanayake U, Chong-Morrison V, Thongjuea S, Repapi E, Mead A and Sauka-Spengler T, 2018. From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape in vivo. Developmental Cell, 47(5), pp.608-628.doi:10.1016/j.devcel.2018.11.009 [*, equal contributions]

[2017]

Suzuki A., Uno Y, Takahashi S, Grimwood J, Schmutz J, Mawaribuchi S, Yoshida H, Takebayashi-Suzuki K, Ito M, Matsuda Y, Rokhsar DS, 2017. Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Developmental biology, 426(2), pp.236-244. doi:10.1016/j.ydbio.2016.04.014

Hargreaves A, Long Z, Christensen J, Marlétaz F, Liu S, Li F, Jansen PG, Spiga E, Hansen MT, Pedersen SVH, Biswas S, Serikawa K, Fox B, Taylor WR, Mulley JF, Zhan G, Heller RS, Holland PWH. 2017. Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster. Proc Nat Acad U S A. 114 (29) 7677-7682. doi:10.1073/pnas.1702930114

Holland PWH, Marlétaz F, Maeso I, Dunwell TL, Paps J. 2017. New genes from old: asymmetric divergence of gene duplicates and the evolution of development. Phil Trans R Soc B. 372: 20150480. doi: 10.1098/rstb.2015.0480 [Review]

Marlétaz F, Le Parco Y, Liu S, Peijnenburg K. 2017. Extreme mitogenomic variation without cryptic speciation in chaetognaths. Genome Biol Evol. 9 (6):1374-1384. doi:10.1093/gbe/evx090

Burridge AK, Hörnlein C, Janssen AW, Hughes M, Bush SL, Marlétaz F, Gasca R, Pierrot-Bults AC, Michel E, Todd JA, Young JR, Osborn KJ, Menken SBJ, Peijnenburg KTCA. 2017. Time-calibrated molecular phylogeny of pteropods. PLoS One. 12 (6):e0177325. doi:10.1371/journal.pone.0177325

Simakov O, Kawashima T, 2017. Independent evolution of genomic characters during major metazoan transitions. Developmental biology, 427(2), pp.179-192.doi:10.1016/j.ydbio.2016.11.012

[2016]

Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SP, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJC, Fujiyama A, Harland RM, Taira M,  Rokhsar DS. 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature, 538(7625), p.336.doi:10.1038/nature19840

Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, Grimwood J,  Schmutz J, Rabbi IY, Egesi C, Nauluvula P, Lebot V, Ndunguru J, Mkamilo G, Bart RS, Setter TS, Gleadow RM, Kulakow PM, Ferguson ME, Rounsley S, Rokhsar DS. 2016. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nature Biotechnology, 34(5), p.562. doi:10.1038/nbt.3535

[2015]

Simakov O*, Kawashima T*, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM , Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su YH, Putnam NH, Schmutz J, Fujiyama A, Yu JK, Tagawa K, Worley KC, Gibbs RA, Kiorschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J 2015. Hemichordate genomes and deuterostome origins. Nature, 527(7579), p.459. [*, equal contributions] doi: 10.1038/nature16150

Albertin CB*, Simakov O*, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, Brenner S, Ragsdale CW, Rokhsar DS. 2015. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature 524(7564):220-4. [*, equal contributions] doi:10.1038/nature14668

Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, Li Y, Hambleton EA, Guse A, Oates ME, Gough J, Weis VM, Aranda M, Pringle JR, Voolstra  CR. The genome of Aiptasia, a sea anemone model for coral symbiosis. Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11893-8. doi:10.1073/pnas.1513318112

Petersen HO, Höger SK, Looso M, Lengfeld T, Kuhn A, Warnken U, Nishimiya-Fujisawa C, Schnölzer M, Krüger M, Özbek S, Simakov O, Holstein TW. A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. Mol Biol Evol. 2015 Aug;32(8):1928-47. doi:10.1093/molbev/msv079