Publications Oleg Simakov

(* Co-first or corresponding Author)

2022

Schmidbaur H, Kawaguchi A, Clarence T, Fu X, Hoang OP, Zimmermann B, Ritschard EA, Weissenbacher A, Foster JS, Nyholm SV, Bates PA, Albertin CB, Tanaka E*, Simakov O*. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nat Commun. 2022 Apr 21;13(1):2172. doi: 10.1038/s41467-022-29694-7.

Albertin CB, Medina-Ruiz S, Mitros T, Schmidbaur H, Sanchez G, Wang ZY, Grimwood J, Rosenthal JJC, Ragsdale CW*, Simakov O*, Rokhsar DS*. Genome and transcriptome mechanisms driving cephalopod evolution. Nat Commun. 2022 May 4;13(1):2427. doi: 10.1038/s41467-022-29748-w.

Marino A, Kizenko A, Wong WY, Ghiselli F, Simakov O. Repeat Age Decomposition Informs an Ancient Set of Repeats Associated With Coleoid Cephalopod Divergence. Front Genet. 2022 Mar 14;13:793734. doi: 10.3389/fgene.2022.793734.

Robert NSM, Sarigol F, Zimmermann B, Meyer A, Voolstra CR, Simakov O. Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. BMC Genomics. 2022 Feb17;23(1):143. doi:10.1186/s12864-022-08304-2.

Simakov O, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O'Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci Adv. 2022 Feb 4;8(5):eabi5884. doi: 10.1126/sciadv.abi5884.

2021

Peterson KJ, Beavan A, Chabot PJ, McPeek MA, Pisani D, Fromm B, Simakov O. microRNAs as Indicators into the Causes and Consequences of Whole Genome Duplication Events. Mol Biol Evol. 2021 Dec 3:msab344. doi:10.1093/molbev/msab344.

Waters PD, Patel HR, Ruiz-Herrera A, Álvarez-González L, Lister NC, Simakov O, Ezaz T, Kaur P, Frere C, Grützner F, Georges A, Graves JAM. Microchromosomes are building blocks of bird, reptile, and mammal chromosomes. Proc Natl Acad Sci U S A. 2021 Nov 9;118(45):e2112494118. doi: 10.1073/pnas.2112494118.

Özpolat BD, Randel N, Williams EA, Bezares-Calderón LA, Andreatta G, Balavoine G, Bertucci PY, Ferrier DEK, Gambi MC, Gazave E, Handberg-Thorsager M, Hardege J, Hird C, Hsieh YW, Hui J, Mutemi KN, Schneider SQ, Simakov O, Vergara HM, Vervoort M, Jékely G, Tessmar-Raible K, Raible F, Arendt D. The Nereid on the rise: Platynereis as a model system. Evodevo. 2021 Sep 27;12(1):10. doi:10.1186/s13227-021-00180-3.

Sanchez G, Simakov O*, Rokhsar D. Beyond "living fossils": can comparative genomics finally reveal novelty? Mol Ecol Resour. 2021 Aug 18. doi: 10.1111/1755-0998.13488. Epub ahead of print. PMID: 34407301.

Vergara HM, Pape C, Meechan KI, Zinchenko V, Genoud C, Wanner AA, Mutemi KN, Titze B, Templin RM, Bertucci PY, Simakov O, Dürichen W, Machado P, Savage EL, Schermelleh L, Schwab Y, Friedrich RW, Kreshuk A, Tischer C, Arendt D. Whole-body integration of gene expression and single-cell morphology. Cell. 2021 Aug 7:S0092-8674(21)00876-X. doi: 10.1016/j.cell.2021.07.017. Epub ahead of print. PMID: 34380046.

Sanchez G, Fernández-Álvarez FÁ, Taite M, Sugimoto C, Jolly J, Simakov O, Marlétaz F, Allcock L, Rokhsar DS. Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida). Commun Biol. 2021 Jun 29;4(1):819. doi: 10.1038/s42003-021-02348-y.

Zhang Y, Mao F, Mu H, Huang M, Bao Y, Wang L, Wong NK, Xiao S, Dai H, Xiang Z, Ma M, Xiong Y, Zhang Z, Zhang L, Song X, Wang F, Mu X, Li J, Ma H, Zhang Y, Zheng H, Simakov O, Yu Z. The genome of Nautilus pompilius illuminates eye evolution and biomineralization. Nat Ecol Evol. 2021 May 10. doi:10.1038/s41559-021-01448-6.

Gomes-Dos-Santos A, Lopes-Lima M, Machado AM, Ramos AM, Usié A, Bolotov IN, Vikhrev IV, Breton S, C Castro LF, da Fonseca RR, Geist J, Österling ME, Prié V, Teixeira A, Gan HM, Simakov O, Froufe E. The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). DNA Res. 2021 Mar 23:dsab002. doi: 10.1093/dnares/dsab002. PMID: 33755103.

Meyer A*, Schloissnig S, Franchini P, Du K, Woltering J, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink H, Volff JN, Simakov O*, Burmester T*, Tanaka EM*, Schartl M*. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature. 2021 Jan 18. doi:10.1038/s41586-021-03198-8. Epub ahead of print. PMID: 33461212.

Xiong P, Hulsey CD, Fruciano C, Wong WY, Nater A, Kautt AF, Simakov O, Pippel M, Kuraku S, Meyer A, Franchini P. The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. Mol Ecol. 2021 Feb;30(4):955-972. doi:10.1111/mec.15774. Epub 2021 Jan 6. PMID: 33305470.

2020

Xiong P, Hulsey CD, Fruciano C, Wong WY, Nater A, Kautt AF, Simakov O, Pippel M, Kuraku S, Meyer A, Franchini P. The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. Mol Ecol. 2020 Dec 11. doi:10.1111/mec.15774. Epub ahead of print. PMID: 33305470.

Cooke I, Ying H, Forêt S, Bongaerts P, Strugnell JM, Simakov O, Zhang J, Field MA, Rodriguez-Lanetty M, Bell SC, Bourne DG, van Oppen MJ, Ragan MA, Miller DJ. Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts. Sci Adv. 2020 Nov 27;6(48):eabc6318. doi: 10.1126/sciadv.abc6318. PMID: 33246955; PMCID:PMC7695477.

Whitelaw BL, Cooke IR, Finn J, da Fonseca RR, Ritschard EA, Gilbert MTP, Simakov O, Strugnell JM. Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss. Gigascience. 2020 Nov 10;9(11):giaa120. doi: 10.1093/gigascience/giaa120. PMID: 33175168.

M Real F, Haas SA, Franchini P, Xiong P, Simakov O, Kuhl H, Schöpflin R, Heller D, Moeinzadeh MH, Heinrich V, Krannich T, Bressin A, Hartmann MF, Wudy SA, Dechmann DKN, Hurtado A, Barrionuevo FJ, Schindler M, Harabula I, Osterwalder M, Hiller M, Wittler L, Visel A, Timmermann B, Meyer A, Vingron M, Jiménez R, Mundlos S, Lupiáñez DG. The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science. 2020 Oct 9;370(6513):208-214. doi: 10.1126/science.aaz2582. PMID: 33033216.

Pende M, Vadiwala K, Schmidbaur H, Stockinger AW, Murawala P, Saghafi S, Dekens MPS, Becker K, Revilla-I-Domingo R, Papadopoulos SC, Zurl M, Pasierbek P, Simakov O, Tanaka EM, Raible F, Dodt HU. A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. Sci Adv. 2020 May 29;6(22):eaba0365. doi: 10.1126/sciadv.aba0365. PMID: 32523996; PMCID: PMC7259959.

Simakov O*, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS*. Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol. 2020 Jun;4(6):820-830. doi: 10.1038/s41559-020-1156-z. Epub 2020 Apr 20. PMID: 32313176; PMCID: PMC7269912.

da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, et al . A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience. 2020 Jan 1;9(1). pii: giz152. doi:10.1093/gigascience/giz152

Albertin CB, Simakov O. Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties. Annu Rev Anim Biosci. 2020, in press. doi:10.1146/annurev-animal-021419-083609.

2019

Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marletaz F, Simakov O*, Rokhsar DS*, New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis. Commun Bio, 2019 2:465. doi:10.1038/s42003-019-0661-6

Wong WY, Simakov O*, Bridge DM, Cartwright P, Bellantuono AJ, Kuhn A, Holstein TW, David CN, Steele RE, Martínez DE*. Expansion of a single transposable element family is associated with genome-size increase and radiation in the genus Hydra. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):22915-22917. doi:10.1073/pnas.1910106116.

Ritschard E, Whitelaw B, Albertin C, Cooke I, Strugnell J, Simakov O, Coupled genomic evolutionary histories as signatures of organismal innovations in cephalopods, Bioessays. 2019 Oct 30:e1900073. doi: 10.1002/bies.201900073. (inside cover)

Calcino AD, de Oliveira AL, Simakov O, Schwaha T, Zieger E, Wollesen T, Wanninger A, The quagga mussel genome and the evolution of freshwater tolerance, DNA Research, in press 2019, dsz019, doi.org/10.1093/dnares/dsz019

Zimmermann B, Robert NSM, Technau U, Simakov O*. Ancient animal genome architecture reflects cell type identities. Nat Ecol Evol. 2019 Aug 5. doi: 10.1038/s41559-019-0946-7.

Zarrella I, Herten K, Maes GE, Tai S, Yang M, Seuntjens E, Ritschard EA, Zach M, Styfhals R, Sanges R, Simakov O*, Ponte G, Fiorito G*. The survey and reference assisted assembly of the Octopus vulgaris genome. Sci Data. 2019 Apr 1;6(1):13. doi: 10.1038/s41597-019-0017-6.

Ritschard EA*, Fitak RR, Simakov O*, Johnsen S. Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction. Proc Biol Sci. 2019 Feb 27;286(1897):20182929. doi: 10.1098/rspb.2018.2929.

Styfhals R, Seuntjens E, Simakov O, Sanges R, Fiorito G. In silico Identification and Expression of Protocadherin Gene Family in Octopus vulgaris. Front Physiol. 2019 Jan 14;9:1905. doi: 10.3389/fphys.2018.01905.

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*. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. Proc Natl Acad Sci USA. 2019 Feb 19;116(8):3030-3035. doi: 10.1073/pnas.1817322116. (cover)

2018

Wong WY, Simakov O*. RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation. Bioinformatics. 2018 Aug 25. doi: 10.1093/bioinformatics/bty745.

Revilla-I-Domingo R, Simakov O*. The Diversification of Early Emerging Metazoans: A Window into the Evolution of Animal Multicellularity. Bioessays.2018 May;40(5):e1800029. doi:10.1002/bies.201800029.

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*. Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas. PeerJ. 2018 Feb 12;6:e4331. doi: 10.7717/peerj.4331.

2017

Simakov O*, Kawashima T. Independent evolution of genomic characters during major metazoan transitions. Dev Biol. 2017 Jul 15;427(2):179-192. doi: 10.1016/j.ydbio.2016.11.012.

2016

Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, Piel J, Ashoor H, Bougouffa S, Bajic VB, Ryu T, Ravasi T, Bayer T, Micklem G, Kim H, Bhak J, LaJeunesse TC, Voolstra CR. Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci Rep. 2016 Dec 22;6:39734. doi: 10.1038/srep39734.

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, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016 Oct 20;538(7625):336-343. doi:10.1038/nature19840.

Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu SY, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, et al. The mid-developmental transition and the evolution of animal body plans. Nature. 2016 Mar 31;531(7596):637-641. doi: 10.1038/nature16994.

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 Jr, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, et al. Hemichordate genomes and deuterostome origins. Nature. 2015 Nov 26;527(7579):459-65. doi: 10.1038/nature16150.

Ramanathan N*, Simakov O*, Merten CA, Arendt D. Quantifying Preferences and Responsiveness of Marine Zooplankton to Changing Environmental Conditions using Microfluidics. PLoS One. 2015 Oct 30;10(10):e0140553. doi:10.1371/journal.pone.0140553.

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 USA. 2015 Sep 22;112(38):11893-8. doi: 10.1073/pnas.1513318112.

Albertin CB*, Simakov O*, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, Brenner S, Ragsdale CW, Rokhsar DS. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 2015 Aug 13;524(7564):220-4. doi: 10.1038/nature14668. (cover)

Wäge J, Hardege JD, Larsson TA, Simakov O, Chapman EC, Arendt D, Rotchell JM. Effects of low seawater pH on the marine polychaete Platynereis dumerilii. Mar Pollut Bull. 2015 Jun 15;95(1):166-72. doi: 10.1016/j.marpolbul.2015.04.027.

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.

2014

Lauri A, Brunet T, Handberg-Thorsager M, Fischer AH, Simakov O, Steinmetz PR, Tomer R, Keller PJ, Arendt D. Development of the annelid axochord: insights into notochord evolution. Science. 2014 Sep 12;345(6202):1365-8. doi: 10.1126/science.1253396.

Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, et al. Nature. 2014 Sep 18;513(7518):375-381. doi:10.1038/nature13726.

Chalopin D, Fan S, Simakov O, Meyer A, Schartl M, Volff JN. Evolutionary active transposable elements in the genome of the coelacanth. J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):322-33. doi: 10.1002/jez.b.22521.

2013

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D,et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 18;496(7445):311-6. doi:10.1038/nature12027. (cover)

Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, et al. Insights into bilaterian evolution from three spiralian genomes. Nature. 2013 Jan 24;493(7433):526-31. doi: 10.1038/nature11696.

Simakov O, Larsson TA, Arendt D. Linking micro- and macro-evolution at the cell type level: a view from the lophotrochozoan Platynereis dumerilii. Brief Funct Genomics. 2013 Sep;12(5):430-9. doi: 10.1093/bfgp/els049.

2010

Gurley KA, Elliott SA, Simakov O, Schmidt HA, Holstein TW, Sánchez Alvarado A. Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response. Dev Biol. 2010 Nov 1;347(1):24-39. doi: 10.1016/j.ydbio.2010.08.007.

Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201.

Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, et al. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science. 2010 Jul 9;329(5988):223-6. doi: 10.1126/science.1188800.

Chapman JA*, Kirkness EF*, Simakov O*, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, et al. The dynamic genome of Hydra. Nature. 2010 Mar 25;464(7288):592-6. doi:10.1038/nature08830.

Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D. Ancient animal microRNAs and the evolution of tissue identity. Nature. 2010 Feb 25;463(7284):1084-8. doi: 10.1038/nature08744.

2009

Lengfeld T, Watanabe H, Simakov O, Lindgens D, Gee L, Law L, Schmidt HA, Ozbek S, Bode H, Holstein TW. Multiple Wnts are involved in Hydra organizer formation and regeneration. Dev Biol. 2009 Jun 1;330(1):186-99. doi:10.1016/j.ydbio.2009.02.004.

2006

Melcher C, Bader R, Walther S, Simakov O, Pankratz MJ. Neuromedin U and its putative Drosophila homolog hugin. PLoS Biol. 2006 Mar;4(3):e68. PubMed PMID: 16524341; PubMed Central PMCID: PMC1397894.