Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal, Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta R. Beklemisheva, Maria Logacheva, Polina Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Natalya A. Serdyukova, Michael Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla L. Lapidus, DNA Zoo Consortium, Stephen James O'Brien, Alexander S. Graphodatsky, Klaus-Peter Koepfli, Sergey Kliver
Biology Faculty Articles

Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population, Andrey Shevchenko, Daria V. Zhernakova, Sergey Malov, Aleksey Komissarov, Sofia Kolchanova, Gaik Tamazian, Alexey Antonik, Nikolay Cherkasov, Sergey Kliver, Anastasiia Turenko, Mikhail Rotkevich, Igor Evsyukov, David Vlahov, Prisca K. Thami, Simani Gaseitsiwe, Vladimir Novitsky, Myron Essex, Stephen James O'Brien
Biology Faculty Articles

Genome-wide signatures of complex introgression and adaptive evolution in the big cats, Henrique V. Figueiró, Gang Li, Fernanda J. Trindade, Juliana Assis, Fabiano Pais, Gabriel Fernandes, Sarah H.D. Santos, Graham M. Hughes, Aleksey Komissarov, Agostinho Antunes, Cristine S. Trinca, Maíra R. Rodrigues, Tyler Linderoth, Ke Bi, Leandro Silveira, Fernando C.C. Azevedo, Daniel Kantek, Emiliano Ramalho, Ricardo A. Brassaloti, Priscilla M.S. Villela, Adauto L.V. Nunes, Rodrigo H.F. Teixeira, Ronaldo G. Morato, Damian Loska, Patricia Saragüeta, Toni Gabaldón, Emma C. Teeling, Stephen J. O'Brien, Rasmus Nielsen
Stephen O'Brien

Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola, Kirill Grigorev, Sergey Kliver, Pavel Dobrynin, Aleksey Komissarov, Walter Wolfsberger, Ksenia Krasheninnikova, Yashira M. Afanador-Hernández, Adam L. Brandt, Liz A. Paulino, Rosanna Carreras, Luis E. Rodríguez, Adrell Núñez, Jessica R. Brandt, Filipe Silva, J. David Hernández-Martich, Audrey J. Majeske, Agostinho Antunes, Alfred L. Roca, Stephen J. O'Brien, Juan Carlos Martínez-Cruzado, Taras K. Oleksyk
Stephen O'Brien

PGD: a pangolin genome hub for the research community, Tze King Tan, Ka Yun Tan, Ranjeev Hari, Aini Mohamed Yusoff, Guat Jah Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mike Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O'Brien, Siew Woh Choo
Stephen O'Brien

Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations, Klaus Peter Koepfli, Gaik Tamazian, David Wildt, Pavel Dobrynin, Changhoon Kim, Paul B. Frandsen, Raquel Godinho, Andrey A. Yurchenko, Aleksey Komissarov, Ksenia Krasheninnikova, Sergei Kliver, Sofia Kolchanova, Margarida Gonçalves, Miguel Carneiro, Pedro Vaz Pinto, Nuno Ferrand, Jesús E. Maldonado, Gina M. Ferrie, Leona Chemnick, Oliver A. Ryder, Warren E. Johnson, Pierre Comizzoli, Stephen J. O'Brien, Budhan S. Pukazhenthi
Stephen O'Brien

The complete mitochondrial genome of the parthenogenetic Caucasian rock lizard Darevskia unisexualis (Squamata: Lacertidae) contains long tandem repeat formed by 59 bp monomer, Aleksey Komissarov, Vitaly Korchagin, Sergei Kliver, Pavel Dobrynin, Serafima Semyenova, Andrey Vergun, Stephen O’Brien, Alexey Ryskov
Stephen O'Brien

Draft Genome of Bugula neritina, a Colonial Animal Packing Powerful Symbionts and Potential Medicines, Mikhail Rayko, Aleksey Komissarov, Jason C. Kwan, Grace Lim-Fong, Adelaide C. Rhodes, Sergey Kliver, Polina Kuchur, Stephen James O'Brien, Jose Lopez
Jose Lopez

Draft Genome of Bugula neritina, a Colonial Animal Packing Powerful Symbionts and Potential Medicines, Mikhail Rayko, Aleksey Komissarov, Jason C. Kwan, Grace Lim-Fong, Adelaide C. Rhodes, Sergey Kliver, Polina Kuchur, Stephen James O'Brien, Jose Lopez
Stephen O'Brien

Draft Genome of Bugula neritina, a Colonial Animal Packing Powerful Symbionts and Potential Medicines, Mikhail Rayko, Aleksey Komissarov, Jason C. Kwan, Grace Lim-Fong, Adelaide C. Rhodes, Sergey Kliver, Polina Kuchur, Stephen James O'Brien, Jose Lopez
Biology Faculty Articles

Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations, Klaus Peter Koepfli, Gaik Tamazian, David Wildt, Pavel Dobrynin, Changhoon Kim, Paul B. Frandsen, Raquel Godinho, Andrey A. Yurchenko, Aleksey Komissarov, Ksenia Krasheninnikova, Sergei Kliver, Sofia Kolchanova, Margarida Gonçalves, Miguel Carneiro, Pedro Vaz Pinto, Nuno Ferrand, Jesús E. Maldonado, Gina M. Ferrie, Leona Chemnick, Oliver A. Ryder, Warren E. Johnson, Pierre Comizzoli, Stephen J. O'Brien, Budhan S. Pukazhenthi
Biology Faculty Articles

A Moving Landscape for Comparative Genomics in Mammals, Stephen James O'Brien, Gaik Tamazian, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Sergey Kliver, Nikolay Cherkasov, Klaus-Peter Koepfli
Stephen O'Brien

Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola, Kirill Grigorev, Sergey Kliver, Pavel Dobrynin, Aleksey Komissarov, Walter Wolfsberger, Ksenia Krasheninnikova, Yashira M. Afanador-Hernández, Adam L. Brandt, Liz A. Paulino, Rosanna Carreras, Luis E. Rodríguez, Adrell Núñez, Jessica R. Brandt, Filipe Silva, J. David Hernández-Martich, Audrey J. Majeske, Agostinho Antunes, Alfred L. Roca, Stephen J. O'Brien, Juan Carlos Martínez-Cruzado, Taras K. Oleksyk
Biology Faculty Articles

A Moving Landscape for Comparative Genomics in Mammals, Stephen James O'Brien, Gaik Tamazian, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Sergey Kliver, Nikolay Cherkasov, Klaus-Peter Koepfli
Biology Faculty Proceedings, Presentations, Speeches, Lectures

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding, Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O'Brien, Michael C. Schatz, Tamas Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, Laszlo Orban
Stephen O'Brien

Chromosomer: A Reference-Based Genome Arrangement Tool for Producing Draft Chromosome Sequences, Gaik Tamazian, Pavel Dobrynin, Ksenia Krasheninnikova, Aleksey Komissarov, Klaus-Peter Koepfli, Stephen J. O'Brien
Stephen O'Brien

Mitogenomic Sequences Support a North–South Subspecies Subdivision within Solenodon paradoxus, Adam L. Brandt, Kirill Grigorev, Yashira M. Afanador-Hernandez, Liz A. Paulino, William J. Murphy, Adrell Nunez, Aleksey Komissarov, Jessica R. Brandt, Pavel Dobrynin, J. David Hernandez-Martich, Roberta Maria, Stephen J. O'Brien, Luis Rodriguez, Juan C. Martinez-Cruzado, T. K. Oleksyk, Alfred L. Roca
Stephen O'Brien

Genome-wide signatures of complex introgression and adaptive evolution in the big cats, Henrique V. Figueiró, Gang Li, Fernanda J. Trindade, Juliana Assis, Fabiano Pais, Gabriel Fernandes, Sarah H.D. Santos, Graham M. Hughes, Aleksey Komissarov, Agostinho Antunes, Cristine S. Trinca, Maíra R. Rodrigues, Tyler Linderoth, Ke Bi, Leandro Silveira, Fernando C.C. Azevedo, Daniel Kantek, Emiliano Ramalho, Ricardo A. Brassaloti, Priscilla M.S. Villela, Adauto L.V. Nunes, Rodrigo H.F. Teixeira, Ronaldo G. Morato, Damian Loska, Patricia Saragüeta, Toni Gabaldón, Emma C. Teeling, Stephen J. O'Brien, Rasmus Nielsen
Biology Faculty Articles

Mitogenomic Sequences Support a North–South Subspecies Subdivision within Solenodon paradoxus, Adam L. Brandt, Kirill Grigorev, Yashira M. Afanador-Hernandez, Liz A. Paulino, William J. Murphy, Adrell Nunez, Aleksey Komissarov, Jessica R. Brandt, Pavel Dobrynin, J. David Hernandez-Martich, Roberta Maria, Stephen J. O'Brien, Luis Rodriguez, Juan C. Martinez-Cruzado, T. K. Oleksyk, Alfred L. Roca
Biology Faculty Articles

Pangolin genomes and the evolution of mammalian scales and immunity, Siew Who Choo, Mike Rayko, Tze King Tan, Ranjeev Hari, Aleksey Komissarov, Wei Yee Wee, Andrey A. Yurchenko, Sergey Kliver, Gaik Tamazian, Agostinho Antunes, Richard K. Wilson, Wesley C. Warren, Klaus Peter Koepfli, Patrick Minx, Ksenia Krasheninnikova, Antoinette Kotze, Desire L. Dalton, Elaine Vermaak, Ian C. Paterson, Pavel Dobrynin, Frankie Thomas Sitam, Jeffrine J. Rovie-Ryan, Warren E. Johnson, Aini Mohamed Yusoff, Shu Jin Luo, Kayal Vizi Karuppannan, Gang Fang, Deyou Zheng, Mark B. Gerstein
Biology Faculty Articles

Annotated Features of Domestic Cat – Felis catus Genome, Gaik Tamazian, Serguei Simonov, Pavel Dobrynin, Alexey Makunin, Anton Logachev, Aleksey Komissarov, Andrey Shevchenko, Vladimir Brukhin, Nikolay Cherkasov, Anton Svitin, Klaus-Peter Koepfli, Joan Pontius, Carlos A. Driscoll, Kevin Blackistone, Cristina Barr, David Goldman, Agostinho Antunes, Javier Quilez, Belen Lorente-Galdos, Can Alkan, Tomas Marques-Bonet, Marilyn Menotti-Raymond, Victor A. David, Kristina Narfstrom, Stephen J. O'Brien
Stephen O'Brien

Genomic Legacy of the African Cheetah, Acinonyx jubatus, Pavel Dobrynin, Shiping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergey Kliver, A. Schmidt-Kunzel, Klaus-Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel Garcia-Perez, Marc de Manuel, Ricardo Godinez, Aleksey Komissarov, Alexey Makunin, Vladimir Brukhin, Weilin Qiu, Long Zhou, Fang Li, Jian Yi, Carlos A. Driscoll, Agostinho Antunes, T. K. Oleksyk, Eduardo Eizirik, Polina Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O'Brien
Stephen O'Brien

Chromosomer: A Reference-Based Genome Arrangement Tool for Producing Draft Chromosome Sequences, Gaik Tamazian, Pavel Dobrynin, Ksenia Krasheninnikova, Aleksey Komissarov, Klaus-Peter Koepfli, Stephen J. O'Brien
Biology Faculty Articles

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding, Shubha Vij, Heiner Kuhl, Inna S. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O'Brien, Michael C. Schatz, Tamas Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, Laszlo Orban
Biology Faculty Articles

The complete mitochondrial genome of the parthenogenetic Caucasian rock lizard Darevskia unisexualis (Squamata: Lacertidae) contains long tandem repeat formed by 59 bp monomer, Aleksey Komissarov, Vitaly Korchagin, Sergei Kliver, Pavel Dobrynin, Serafima Semyenova, Andrey Vergun, Stephen O’Brien, Alexey Ryskov
Biology Faculty Articles

PGD: a pangolin genome hub for the research community, Tze King Tan, Ka Yun Tan, Ranjeev Hari, Aini Mohamed Yusoff, Guat Jah Wong, Cheuk Chuen Siow, Naresh V.R. Mutha, Mike Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C. Paterson, Wesley C. Warren, Warren E. Johnson, Stephen J. O'Brien, Siew Woh Choo
Biology Faculty Articles

Genomic Legacy of the African Cheetah, Acinonyx jubatus, Pavel Dobrynin, Shiping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergey Kliver, A. Schmidt-Kunzel, Klaus-Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel Garcia-Perez, Marc de Manuel, Ricardo Godinez, Aleksey Komissarov, Alexey Makunin, Vladimir Brukhin, Weilin Qiu, Long Zhou, Fang Li, Jian Yi, Carlos A. Driscoll, Agostinho Antunes, T. K. Oleksyk, Eduardo Eizirik, Polina Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O'Brien
Biology Faculty Articles

Cookiecutter: A Tool for Kmer-Based Read Filtering and Extraction, Ekaterina Starostina, Gaik Tamazian, Pavel Dobrynin, Stephen J. O'Brien, Aleksey Komissarov
Biology Faculty Articles

Annotated Features of Domestic Cat – Felis catus Genome, Gaik Tamazian, Serguei Simonov, Pavel Dobrynin, Alexey Makunin, Anton Logachev, Aleksey Komissarov, Andrey Shevchenko, Vladimir Brukhin, Nikolay Cherkasov, Anton Svitin, Klaus-Peter Koepfli, Joan Pontius, Carlos A. Driscoll, Kevin Blackistone, Cristina Barr, David Goldman, Agostinho Antunes, Javier Quilez, Belen Lorente-Galdos, Can Alkan, Tomas Marques-Bonet, Marilyn Menotti-Raymond, Victor A. David, Kristina Narfstrom, Stephen J. O'Brien
Biology Faculty Articles