Oleg Simakov

ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 65

Top Topics

Dna Methylation

Top Venues

Genome research

bioRxiv : the preprint server for biology

Scientific data

This page only lists publications with an associated author ORCID identifier.

Publications

Kevin Nzumbi Mutemi, Oleg Simakov, Leslie Pan, Luca Santangeli, Ryan W Null, Mette Handberg-Thorsager, Bruno Cossermelli Vellutini, Tomas Larsson, Emily L Savage, Mireia Osuna Lopez, Rajna Hercog, Jan Provaznik, Diana Ordoñez-Rueda, Nayara Azevedo, Eve Gazave, Michel Vervoort, Pavel Tomancak, Wenhua Tan, Sylke Winkler, Vladimir Benes, Jerome Ho-Lam Hui, Conrad Helm, B Duygu Özpolat, Detlev Arendt
A genome resource for the marine annelid Platynereis dumerilii . bioRxiv : the preprint server for biology (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Kevin Nzumbi Mutemi, Oleg Simakov, Leslie Pan, Luca Santangeli, Ryan W Null, Mette Handberg-Thorsager, Bruno Cossermelli Vellutini, Tomas Larsson, Emily L Savage, Mireia Osuna Lopez, Rajna Hercog, Jan Provaznik, Diana Ordoñez-Rueda, Nayara Azevedo, Eve Gazave, Michel Vervoort, Pavel Tomancak, Wenhua Tan, Sylke Winkler, Vladimir Benes, Jerome Ho-Lam Hui, Conrad Helm, B Duygu Özpolat, Detlev Arendt
A genome resource for the marine annelid Platynereis dumerilii . bioRxiv : the preprint server for biology (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Darrin T Schultz, Elizabeth A C Heath-Heckman, Christopher J Winchell, Dian-Han Kuo, Yun-Sang Yu, Fabian Oberauer, Kevin M Kocot, Sung-Jin Cho, Oleg Simakov, David A Weisblat
Acceleration of genome rearrangement in clitellate annelids. bioRxiv : the preprint server for biology (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
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)
Paul A Saunders, Carles Ferre-Ortega, Peta L Hill, Oleg Simakov, Tariq Ezaz, Christopher P Burridge, Erik Wapstra
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 16 (4) (2024)
Thea F Rogers, Gözde Yalçın, John Briseno, Nidhi Vijayan, Spencer V Nyholm, Oleg Simakov
Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes. Scientific data 11 (1) (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature (2024)
Darrin T Schultz, Elizabeth A C Heath-Heckman, Christopher J Winchell, Dian-Han Kuo, Yun-Sang Yu, Fabian Oberauer, Kevin M Kocot, Sung-Jin Cho, Oleg Simakov, David A Weisblat
Acceleration of genome rearrangement in clitellate annelids. bioRxiv : the preprint server for biology (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. Genome research (2024)
Manfred Schartl, Joost M Woltering, Iker Irisarri, Kang Du, Susanne Kneitz, Martin Pippel, Thomas Brown, Paolo Franchini, Jing Li, Ming Li, Mateus Adolfi, Sylke Winkler, Josane de Freitas Sousa, Zhuoxin Chen, Sandra Jacinto, Evgeny Z Kvon, Luis Rogério Correa de Oliveira, Erika Monteiro, Danielson Baia Amaral, Thorsten Burmester, Domitille Chalopin, Alexander Suh, Eugene W Myers, Oleg Simakov, Igor Schneider, Axel Meyer
The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature (2024)
Thea F Rogers, Gözde Yalçın, John Briseno, Nidhi Vijayan, Spencer V Nyholm, Oleg Simakov
Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes. Scientific data 11 (1) (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Kevin Nzumbi Mutemi, Oleg Simakov, Leslie Pan, Luca Santangeli, Ryan W Null, Mette Handberg-Thorsager, Bruno Cossermelli Vellutini, Tomas Larsson, Emily L Savage, Mireia Osuna Lopez, Rajna Hercog, Jan Provaznik, Diana Ordoñez-Rueda, Nayara Azevedo, Eve Gazave, Michel Vervoort, Pavel Tomancak, Wenhua Tan, Sylke Winkler, Vladimir Benes, Jerome Ho-Lam Hui, Conrad Helm, B Duygu Özpolat, Detlev Arendt
A genome resource for the marine annelid Platynereis dumerilii . bioRxiv : the preprint server for biology (2024)
Manfred Schartl, Joost M Woltering, Iker Irisarri, Kang Du, Susanne Kneitz, Martin Pippel, Thomas Brown, Paolo Franchini, Jing Li, Ming Li, Mateus Adolfi, Sylke Winkler, Josane de Freitas Sousa, Zhuoxin Chen, Sandra Jacinto, Evgeny Z Kvon, Luis Rogério Correa de Oliveira, Erika Monteiro, Danielson Baia Amaral, Thorsten Burmester, Domitille Chalopin, Alexander Suh, Eugene W Myers, Oleg Simakov, Igor Schneider, Axel Meyer
The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Paul A Saunders, Carles Ferre-Ortega, Peta L Hill, Oleg Simakov, Tariq Ezaz, Christopher P Burridge, Erik Wapstra
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 16 (4) (2024)
Thea F Rogers, Gözde Yalçın, John Briseno, Nidhi Vijayan, Spencer V Nyholm, Oleg Simakov
Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes. Scientific data 11 (1) (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Paul A Saunders, Carles Ferre-Ortega, Peta L Hill, Oleg Simakov, Tariq Ezaz, Christopher P Burridge, Erik Wapstra
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)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. Genome research (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature 627 (8005) (2024)
Thea F Rogers, Gözde Yalçın, John Briseno, Nidhi Vijayan, Spencer V Nyholm, Oleg Simakov
Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes. Scientific data 11 (1) (2024)
Manfred Schartl, Joost M Woltering, Iker Irisarri, Kang Du, Susanne Kneitz, Martin Pippel, Thomas Brown, Paolo Franchini, Jing Li, Ming Li, Mateus Adolfi, Sylke Winkler, Josane de Freitas Sousa, Zhuoxin Chen, Sandra Jacinto, Evgeny Z Kvon, Luis Rogério Correa de Oliveira, Erika Monteiro, Danielson Baia Amaral, Thorsten Burmester, Domitille Chalopin, Alexander Suh, Eugene W Myers, Oleg Simakov, Igor Schneider, Axel Meyer
The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature (2024)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Elise Parey, Oleg Simakov, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. Nature (2024)
Jack F Cazet, Stefan Siebert, Hannah Morris Little, Philip Bertemes, Abby S Primack, Peter Ladurner, Matthias Achrainer, Mark T Fredriksen, R Travis Moreland, Sumeeta Singh, Suiyuan Zhang, Tyra G Wolfsberg, Christine E Schnitzler, Andreas D Baxevanis, Oleg Simakov, Bert Hobmayer, Celina E Juliano
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome research 33 (2) (2023)
Jack F Cazet, Stefan Siebert, Hannah Morris Little, Philip Bertemes, Abby S Primack, Peter Ladurner, Matthias Achrainer, Mark T Fredriksen, R Travis Moreland, Sumeeta Singh, Suiyuan Zhang, Tyra G Wolfsberg, Christine E Schnitzler, Andreas D Baxevanis, Oleg Simakov, Bert Hobmayer, Celina E Juliano
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome research 33 (2) (2023)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Oleg Simakov, Elise Parey, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. bioRxiv : the preprint server for biology (2023)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. bioRxiv : the preprint server for biology (2023)
Darrin T Schultz, Steven H D Haddock, Jessen V Bredeson, Richard E Green, Oleg Simakov, Daniel S Rokhsar
Ancient gene linkages support ctenophores as sister to other animals. Nature (2023)
Bob Zimmermann, Juan D Montenegro, Sofia M C Robb, Whitney J Fropf, Lukas Weilguny, Shuonan He, Shiyuan Chen, Jessica Lovegrove-Walsh, Eric M Hill, Cheng-Yi Chen, Katerina Ragkousi, Daniela Praher, David Fredman, Darrin T Schultz, Yehu Moran, Oleg Simakov, Grigory Genikhovich, Matthew C Gibson, Ulrich Technau
Topological structures and syntenic conservation in sea anemone genomes. Nature communications 14 (1) (2023)
Ferdinand Marletaz, Nataliya Timoshevskaya, Vladimir A Timoshevskiy, Oleg Simakov, Elise Parey, Daria Gavriouchkina, Masakazu Suzuki, Kaoru Kubokawa, Sydney Brenner, Jeramiah James Smith, Daniel S Rokhsar
The hagfish genome and the evolution of vertebrates. bioRxiv : the preprint server for biology (2023)
Thea F Rogers, Oleg Simakov
Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Briefings in functional genomics (2023)
Tom Baden, John Briseño, Gabrielle Coffing, Sophie Cohen-Bodénès, Amy Courtney, Dominick Dickerson, Gül Dölen, Graziano Fiorito, Camino Gestal, Taryn Gustafson, Elizabeth A C Heath-Heckman, Qiaz Q H Hua, Pamela Imperadore, Ryosuke Kimbara, Mirela Król, Zdeněk Lajbner, Nicolás Lichilín, Filippo Macchi, Matthew J McCoy, Michele K Nishiguchi, Spencer V Nyholm, Eve Otjacques, Pedro Antonio Pérez-Ferrer, Giovanna Ponte, Judit R Pungor, Thea F Rogers, Joshua J C Rosenthal, Lisa Rouressol, Noelle Rubas, Gustavo Sanchez, Catarina Pereira Santos, Darrin T Schultz, Eve Seuntjens, Jeremea O Songco-Casey, Ian Erik Stewart, Ruth Styfhals, Surangkana Tuanapaya, Nidhi Vijayan, Anton Weissenbacher, Lucia Zifcakova, Grace Schulz, Willem Weertman, Oleg Simakov, Caroline Albertin
Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integrative and comparative biology (2023)
Jack F Cazet, Stefan Siebert, Hannah Morris Little, Philip Bertemes, Abby S Primack, Peter Ladurner, Matthias Achrainer, Mark T Fredriksen, R Travis Moreland, Sumeeta Singh, Suiyuan Zhang, Tyra G Wolfsberg, Christine E Schnitzler, Andreas D Baxevanis, Oleg Simakov, Bert Hobmayer, Celina E Juliano
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome research 33 (2) (2023)
Jack F Cazet, Stefan Siebert, Hannah Morris Little, Philip Bertemes, Abby S Primack, Peter Ladurner, Matthias Achrainer, Mark T Fredriksen, R Travis Moreland, Sumeeta Singh, Suiyuan Zhang, Tyra G Wolfsberg, Christine E Schnitzler, Andreas D Baxevanis, Oleg Simakov, Bert Hobmayer, Celina E Juliano
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome research 33 (2) (2023)
Jack F Cazet, Stefan Siebert, Hannah Morris Little, Philip Bertemes, Abby S Primack, Peter Ladurner, Matthias Achrainer, Mark T Fredriksen, R Travis Moreland, Sumeeta Singh, Suiyuan Zhang, Tyra G Wolfsberg, Christine E Schnitzler, Andreas D Baxevanis, Oleg Simakov, Bert Hobmayer, Celina E Juliano
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome research (2023)
Jack F Cazet, Stefan Siebert, Hannah Morris Little, Philip Bertemes, Abby S Primack, Peter Ladurner, Matthias Achrainer, Mark T Fredriksen, R Travis Moreland, Sumeeta Singh, Suiyuan Zhang, Tyra G Wolfsberg, Christine E Schnitzler, Andreas D Baxevanis, Oleg Simakov, Bert Hobmayer, Celina E Juliano
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome research (2023)
Caroline B Albertin, Sofia Medina-Ruiz, Therese Mitros, Hannah Schmidbaur, Gustavo Sanchez, Z Yan Wang, Jane Grimwood, Joshua J C Rosenthal, Clifton W Ragsdale, Oleg Simakov, Daniel S Rokhsar
Genome and transcriptome mechanisms driving cephalopod evolution. Nature communications 13 (1) (2022)
Hannah Schmidbaur, Akane Kawaguchi, Tereza Clarence, Xiao Fu, Oi Pui Hoang, Bob Zimmermann, Elena A Ritschard, Anton Weissenbacher, Jamie S Foster, Spencer V Nyholm, Paul A Bates, Caroline B Albertin, Elly M Tanaka, Oleg Simakov
Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nature communications 13 (1) (2022)
Nicolas S M Robert, Fatih Sarigol, Bob Zimmermann, Axel Meyer, Christian R Voolstra, Oleg Simakov
Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. BMC genomics 23 (1) (2022)
Oleg Simakov, Jessen V Bredeson, Kodiak C Berkoff, Ferdinand Marletaz, Therese Mitros, Darrin T Schultz, Brendan L O'Connell, Paul Dear, Daniel E Martinez, Robert E Steele, Richard E Green, Charles N David, Daniel S Rokhsar
Deeply conserved synteny and the evolution of metazoan chromosomes. Science advances 8 (5) (2022)
B Duygu Özpolat, Nadine Randel, Elizabeth A Williams, Luis Alberto Bezares-Calderón, Gabriele Andreatta, Guillaume Balavoine, Paola Y Bertucci, David E K Ferrier, Maria Cristina Gambi, Eve Gazave, Mette Handberg-Thorsager, Jörg Detlef Hardege, Cameron Hird, Yu-Wen Hsieh, Jerome Hui, Kevin Nzumbi Mutemi, Stephan Q Schneider, Oleg Simakov, Hernando M Vergara, Michel Vervoort, Gáspár Jékely, Kristin Tessmar-Raible, Florian Raible, Detlev Arendt
The Nereid on the rise: Platynereis as a model system. EvoDevo 12 (1) (2021)
Axel Meyer, Siegfried Schloissnig, Paolo Franchini, Kang Du, Joost M Woltering, Iker Irisarri, Wai Yee Wong, Sergej Nowoshilow, Susanne Kneitz, Akane Kawaguchi, Andrej Fabrizius, Peiwen Xiong, Corentin Dechaud, Herman P Spaink, Jean-Nicolas Volff, Oleg Simakov, Thorsten Burmester, Elly M Tanaka, Manfred Schartl
Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 590 (7845) (2021)
Peiwen Xiong, Christopher Darrin Hulsey, Carmelo Fruciano, Wai Yee Wong, Alexander Nater, Andreas F Kautt, Oleg Simakov, Martin Pippel, Shigehiro Kuraku, Axel Meyer, Paolo Franchini
The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. Molecular ecology 30 (4) (2021)
Paul D Waters, Hardip R Patel, Aurora Ruiz-Herrera, Lucía Álvarez-González, Nicholas C Lister, Oleg Simakov, Tariq Ezaz, Parwinder Kaur, Celine Frere, Frank Grützner, Arthur Georges, Jennifer Ann Marshall Graves
Microchromosomes are building blocks of bird, reptile, and mammal chromosomes. Proceedings of the National Academy of Sciences of the United States of America 118 (45) (2021)
André Gomes-Dos-Santos, Manuel Lopes-Lima, André M Machado, António Marcos Ramos, Ana Usié, Ivan N Bolotov, Ilya V Vikhrev, Sophie Breton, L Filipe C Castro, Rute R da Fonseca, Juergen P Geist, Martin E Österling, Vincent Prié, Amílcar Teixeira, Han Ming Gan, Oleg Simakov, Elsa Froufe
The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). DNA research : an international journal for rapid publication of reports on genes and genomes 28 (2) (2021)
Yang Zhang, Fan Mao, Huawei Mu, Minwei Huang, Yongbo Bao, Lili Wang, Nai-Kei Wong, Shu Xiao, He Dai, Zhiming Xiang, Mingli Ma, Yuanyan Xiong, Ziwei Zhang, Lvping Zhang, Xiaoyuan Song, Fan Wang, Xiyu Mu, Jun Li, Haitao Ma, Yuehuan Zhang, Hongkun Zheng, Oleg Simakov, Ziniu Yu
The genome of Nautilus pompilius illuminates eye evolution and biomineralization. Nature ecology & evolution 5 (7) (2021)
Gustavo Sanchez, Oleg Simakov, Daniel S Rokhsar
Beyond "living fossils": Can comparative genomics finally reveal novelty? Molecular ecology resources (2021)
Gustavo Sanchez, Fernando Ángel Fernández-Álvarez, Morag Taite, Chikatoshi Sugimoto, Jeffrey Jolly, Oleg Simakov, Ferdinand Marlétaz, A Louise Allcock, Daniel S Rokhsar
Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida). Communications biology 4 (1) (2021)
Ira R Cooke, Hua Ying, Sylvain Forêt, Pim Bongaerts, Jan M Strugnell, Oleg Simakov, Jia Zhang, Matthew A Field, Mauricio Rodriguez-Lanetty, Sara C Bell, David G Bourne, Madeleine J H van Oppen, Mark A Ragan, David J Miller
Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts. Science advances 6 (48) (2020)
Oleg Simakov, Ferdinand Marletaz, Jia-Xing Yue, Brendan L O'Connell, Jerry W Jenkins, Alexander Brandt, Robert Calef, Che-Huang Tung, Tzu-Kai Huang, Jeremy Schmutz, Noriyuki Satoh, Jr-Kai Yu, Nicholas H Putnam, Richard E Green, Daniel S Rokhsar
Deeply conserved synteny resolves early events in vertebrate evolution. Nature ecology & evolution 4 (6) (2020)
Marko Pende, Karim Vadiwala, Hannah Schmidbaur, Alexander W Stockinger, Prayag Murawala, Saiedeh Saghafi, Marcus P S Dekens, Klaus Becker, Roger Revilla-I-Domingo, Sofia-Christina Papadopoulos, Martin Zurl, Pawel Pasierbek, Oleg Simakov, Elly M Tanaka, Florian Raible, Hans-Ulrich Dodt
A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. Science advances 6 (22) (2020)
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