Publications by authors named "Oleg Simakov"

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Whole-body integration of gene expression and single-cell morphology.
Hernando M Vergara, Constantin Pape, Kimberly I Meechan, Valentyna Zinchenko, Christel Genoud, Adrian A Wanner, Kevin Nzumbi Mutemi, Benjamin Titze, Rachel M Templin, Paola Y Bertucci

Cell· September 2021

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Maintaining microbiota across diverse symbiotic organs in : Insights into shared immune responses.
Nidhi Vijayan, John Briseño, Oleg Simakov, Spencer V Nyholm

Proc Natl Acad Sci U S A· January 2026

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Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes.
Masa-Aki Yoshida, Emese Tóth, Koto Kon-Nanjo, Tetsuo Kon, Kazuki Hirota, Oleg Simakov

iScience· November 2025

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Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods.
Thea F Rogers, Jessica Stock, Natalie Grace Schulz, Gözde Yalçin, Simone Rencken, Oleg Simakov

bioRxiv· October 2025

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Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).
Paul A Saunders, Francisco M C Sassi, Marcelo B Cioffi, Oleg Simakov, Christopher P Burridge

BMC Biol· October 2025

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Characterization of C2H2 superfamily expansions in cephalopods and their contribution to nervous system evolution.
Christina Holzinger, Elena A Ritschard, Pamela Imperadore, Giovanna Ponte, Caroline B Albertin, Oleg Simakov

iScience· October 2025

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The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes.
Koto Kon-Nanjo, Tetsuo Kon, Tracy Chih-Ting Koubkova Yu, Diego Rodriguez-Terrones, Francisco Falcon, Oleg Simakov

Genome Biol· July 2025

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A genome resource for the marine annelid Platynereis spp.
Kevin Nzumbi Mutemi, Oleg Simakov, Leslie Pan, Luca Santangeli, Ryan Wesley Null

BMC Genomics· July 2025

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The application of irreversible genomic states to define and trace ancient cell type homologies.
Oleg Simakov, Günter P Wagner

Evodevo· May 2025

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Chromosome-level genome assembly of the doctor fish (Garra rufa).
Tetsuo Kon, Koto Kon-Nanjo, Kiki Syaputri Handayani, Liqing Zang, Fahrurrozi Fahrurrozi, Oleg Simakov

Sci Data· May 2025

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Subtelomeric repeat expansion in Hydractinia symbiolongicarpus chromosomes.
Tetsuo Kon, Koto Kon-Nanjo, Oleg Simakov

Mob DNA· March 2025

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Potential of Garra rufa as a novel high-temperature resistant model fish: a review on current and future approaches.
Yasuhito Shimada, Baki Aydın, Koto Kon-Nanjo, Kiki Syaputri Handayani, Victor David Nico Gultom, Oleg Simakov

Zoological Lett· February 2025

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A genome resource for the marine annelid .
Kevin Nzumbi Mutemi, Oleg Simakov, Leslie Pan, Luca Santangeli, Ryan Null

bioRxiv· November 2024

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The genomes of all lungfish inform on genome expansion and tetrapod evolution.
Manfred Schartl, Joost M Woltering, Iker Irisarri, Kang Du, Susanne Kneitz, Oleg Simakov

Nature· October 2024

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The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the Tree of Life.
Victoria McKenna, John M Archibald, Roxanne Beinart, Michael N Dawson, Ute Hentschel, Oleg Simakov

Wellcome Open Res· June 2024

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Acceleration of genome rearrangement in clitellate annelids.
Darrin T Schultz, Elizabeth A C Heath-Heckman, Christopher J Winchell, Dian-Han Kuo, Yun-Sang Yu, Oleg Simakov

bioRxiv· May 2024

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The genome of the colonial hydroid reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals.
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Oleg Simakov

Genome Res· April 2024

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Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes.
Paul A Saunders, Carles Ferre-Ortega, Peta L Hill, Oleg Simakov, Tariq Ezaz

Genome Biol Evol· April 2024

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The hagfish genome and the evolution of vertebrates.
Ferdinand Marlétaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov

Nature· March 2024

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Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes.
Thea F Rogers, Gözde Yalçın, John Briseno, Nidhi Vijayan, Spencer V Nyholm, Oleg Simakov

Sci Data· January 2024

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Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology.
Tom Baden, John Briseño, Gabrielle Coffing, Sophie Cohen-Bodénès, Amy Courtney, Oleg Simakov

Integr Comp Biol· December 2023

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A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797).
Dalila Destanović, Darrin T Schultz, Ruth Styfhals, Fernando Cruz, Jèssica Gómez-Garrido, Oleg Simakov

G3 (Bethesda)· December 2023

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Topological structures and syntenic conservation in sea anemone genomes.
Bob Zimmermann, Juan D Montenegro, Sofia M C Robb, Whitney J Fropf, Lukas Weilguny, Oleg Simakov

Nat Commun· December 2023

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Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians.
Thea F Rogers, Oleg Simakov

Brief Funct Genomics· November 2023

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The genome of the colonial hydroid reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals.
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Oleg Simakov

bioRxiv· August 2023

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Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid.
Lisa Rouressol, John Briseno, Nidhi Vijayan, Grischa Y Chen, Elena A Ritschard, Oleg Simakov

iScience· July 2023

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