Simakov Publications

2026

Rencken SD, Tushev G, Hain D, Ciirdaeva E, Simakov O, Laurent G. Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis. eLife. 2026 Mai 28;14. doi: 10.7554/eLife.107393

Kramml HM, Herpell JB, Priemer C, Wessely Z, Schindler F, Berger A et al. Clusia genomes shed light on the evolution and diversity of crassulacean acid metabolism physiotypes. Nature Communications. 2026 Mai 5;17(1):3937. doi: 10.1038/s41467-026-71958-z

Sanchez G, Fernández-Álvarez FÁ, Bernal A, Heath-Heckman E, Lami R, McFall-Ngai M et al. Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches. Nature Ecology & Evolution. 2026 Apr.;10(4):662-676. doi: 10.1038/s41559-026-03009-1

Schultz DT, Simakov O. Topological Approaches in Animal Comparative Genomics. Annual Review of Animal Biosciences. 2026 Feb.;14(1):17-48. doi: 10.1146/annurev-animal-030424-084541

Vijayan N, Briseño J, Simakov O, Nyholm SV. Maintaining microbiota across diverse symbiotic organs in Euprymna scolopes: Insights into shared immune responses. Proceedings of the National Academy of Sciences of the United States of America. 2026 Jan. 6;123(1):e2512903122. doi: 10.1073/pnas.2512903122

2025

Simakov O , Wagner GP. The application of irreversible genomic states to define and trace ancient cell type homologies. EvoDevo. 2025 Dez.;16(1):5. 5. doi: 10.1186/s13227-025-00242-w

Kon-Nanjo K, Kon T, Yu TCTK, Rodriguez-Terrones D, Falcon F, Martínez DE et al. The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes. Genome Biology. 2025 Dez.;26(1):186. doi: 10.1186/s13059-025-03653-z

Yoshida MA, Tóth E, Kon-Nanjo K, Kon T, Hirota K, Toyoda A et al. Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes. Iscience. 2025 Nov. 21;28(11):113832. doi: 10.1016/j.isci.2025.113832

Holzinger C, Ritschard EA, Imperadore P, Ponte G, Albertin CB, Fiorito G et al. Characterization of C2H2 superfamily expansions in cephalopods and their contribution to nervous system evolution. Iscience. 2025 Okt. 17;28(10):113561. doi: 10.1016/j.isci.2025.113561

Mutemi KN, Simakov O, Pan L, Santangeli L, Null RW, Handberg-Thorsager M et al. A genome resource for the marine annelid Platynereis spp. BMC Genomics. 2025 Juli 14;26:665. doi: 10.1186/s12864-025-11727-2

Kon T, Kon-Nanjo K, Handayani KS, Zang L, Fahrurrozi F, Simakov O et al. Chromosome-level genome assembly of the doctor fish (Garra rufa). Scientific Data. 2025 Mai 9;12(1):765. 765. doi: 10.1038/s41597-025-05101-w

Kon T, Kon-Nanjo K, Simakov O. Subtelomeric repeat expansion in Hydractinia symbiolongicarpus chromosomes. Mobile DNA. 2025 März 25;16(1):14. 14. doi: 10.1186/s13100-025-00355-y

Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team. The chromosomal genome sequence of the bigfin reef squid, Sepioteuthis lessoniana d'Orbigny, 1826 and its associated microbial metagenome sequences. Wellcome open research. 2025;10:351. doi: 10.12688/wellcomeopenres.24553.1

2024

Schartl M, Woltering JM, Irisarri I, Du K, Kneitz S, Pippel M et al. The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature. 2024 Okt. 3;634(8032):96-103. Epub 2024 Aug. 14. doi: 10.1038/s41586-024-07830-1

McKenna V, Archibald JM, Beinart R, Dawson MN, Hentschel U, Keeling PJ et al. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the Tree of Life. Wellcome open research. 2024 Juni 10;6:254. doi: 10.12688/wellcomeopenres.17222.2

Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D et al. The hagfish genome and the evolution of vertebrates. Nature. 2024 März 28;627(8005):811-820. Epub 2024 Jan. 23. doi: 10.1038/s41586-024-07070-3

Saunders PA, Ferre-Ortega C, Hill PL, Simakov O, Ezaz T, Burridge CP et al. Using a handful of transcriptomes to detect sex-linked markers and develop molecular sexing assays in a species with homomorphic sex chromosomes. Genome Biology and Evolution. 2024 März 25;16(4):evae060. Epub 2024. doi: 10.1093/gbe/evae060

Rogers TF, Yalçın G, Briseno J, Vijayan N, Nyholm SV, Simakov O. Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes. Scientific Data. 2024 Jan. 6;11(1):40. doi: 10.1038/s41597-023-02903-8

Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD et al. The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome Research. 2024;34(3):498-513. Epub 2024. doi: 10.1101/gr.278382.123

2023

Destanović D, Schultz DT, Styfhals R, Cruz F, Gómez-Garrido J, Gut M et al. A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797). G3: Genes, Genomes, Genetics. 2023 Dez. 6;13(12). Epub 2023. doi: 10.1093/g3journal/jkad220