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Kirilenko, Bogdan M. [Author] ; Hiller, Michael Thomas [Degree supervisor]; Zerial, Marino [Degree supervisor] Max-Planck-Institut für Molekulare Zellbiologie und Genetik, Max-Planck-Institut für Molekulare Zellbiologie und Genetik

A novel approach to infer orthologs and produce gene annotations at scale

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Dresden, 2021
Kirilenko, Bogdan M. [Author] ; Hiller, Michael [Other]; Zerial, Marino [Other]

A novel approach to infer orthologs and produce gene annotations at scale

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Dresden: Technische Universität Dresden, 2022
Kirilenko, Bogdan M. [Author] ; Hiller, Michael [Other]; Zerial, Marino [Other] Technische Universität Dresden, Max-Planck-Institut für Molekulare Zellbiologie und Genetik, Max-Planck-Institut für Molekulare Zellbiologie und Genetik

A novel approach to infer orthologs and produce gene annotations at scale

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... to E-book via Resolving system

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Dresden: Technische Universität Dresden, 2022
Blumer, Moritz [Author]; Brown, Thomas [Author]; Freitas, Mariella Bontempo [Author]; Destro, Ana Luiza [Author]; Oliveira, Juraci A. [Author]; Morales, Ariadna E. [Author]; Schell, Tilman [Author]; Greve, Carola [Author]; Pippel, Martin [Author]; Jebb, David [Author]; Hecker, Nikolai [Author]; Ahmed, Alexis-Walid [Author]; Kirilenko, Bogdan M. [Author]; Foote, Maddy [Author]; Janke, Axel [Author]; Lim, Burton K. [Author]; Hiller, Michael [Author]

Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding

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Frankfurt am Main: Universitätsbibliothek Johann Christian Senckenberg, 2021
Kirilenko, Bogdan M; Hagey, Lee R; Barnes, Stephen; Falany, Charles N; Hiller, Michael

Evolutionary Analysis of Bile Acid-Conjugating Enzymes Reveals a Complex Duplication and Reciprocal Loss History

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Oxford University Press (OUP), 2019

Published in: Genome Biology and Evolution, 11 (2019) 11, Seite 3256-3268
Lee, Jun-Hoe; Lewis, Kevin M.; Moural, Timothy W.; Kirilenko, Bogdan; Borgonovo, Barbara; Prange, Gisa; Koessl, Manfred; Huggenberger, Stefan; Kang, ChulHee; Hiller, Michael

Molecular parallelism in fast-twitch muscle proteins in echolocating mammals

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American Association for the Advancement of Science (AAAS), 2018

Published in: Science Advances, 4 (2018) 9
Doronina, Liliya; Hughes, Graham M.; Moreno-Santillan, Diana; Lawless, Colleen; Lonergan, Tadhg; Ryan, Louise; Jebb, David; Kirilenko, Bogdan M.; Korstian, Jennifer M.; Dávalos, Liliana M.; Vernes, Sonja C.; Myers, Eugene W.; Teeling, Emma C.; Hiller, Michael; Jermiin, Lars S.; Schmitz, Jürgen; Springer, Mark S.; Ray, David A.

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

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MDPI AG, 2022

Published in: Genes, 13 (2022) 5, Seite 766
Clawson, Hiram; Lee, Brian T.; Raney, Brian J.; Barber, Galt P.; Casper, Jonathan; Diekhans, Mark; Fischer, Clay; Gonzalez, Jairo Navarro; Hinrichs, Angie S.; Lee, Christopher M.; Nassar, Luis R.; Perez, Gerardo; Wick, Brittney; Schmelter, Daniel; Speir, Matthew L.; Armstrong, Joel; Zweig, Ann S.; Kuhn, Robert M.; Kirilenko, Bogdan M.; Hiller, Michael; Haussler, David; Kent, W. James; Haeussler, Maximilian

GenArk: towards a million UCSC genome browsers

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Springer Science and Business Media LLC, 2023

Published in: Genome Biology, 24 (2023) 1
Blumer, Moritz; Brown, Tom; Freitas, Mariella Bontempo; Destro, Ana Luiza; Oliveira, Juraci A.; Morales, Ariadna E.; Schell, Tilman; Greve, Carola; Pippel, Martin; Jebb, David; Hecker, Nikolai; Ahmed, Alexis-Walid; Kirilenko, Bogdan M.; Foote, Maddy; Janke, Axel; Lim, Burton K.; Hiller, Michael

Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding

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American Association for the Advancement of Science (AAAS), 2022

Published in: Science Advances, 8 (2022) 12
Jebb, David; Huang, Zixia; Pippel, Martin; Hughes, Graham M.; Lavrichenko, Ksenia; Devanna, Paolo; Winkler, Sylke; Jermiin, Lars S.; Skirmuntt, Emilia C.; Katzourakis, Aris; Burkitt-Gray, Lucy; Ray, David A.; Sullivan, Kevin A. M.; Roscito, Juliana G.; Kirilenko, Bogdan M.; Dávalos, Liliana M.; Corthals, Angelique P.; Power, Megan L.; Jones, Gareth; Ransome, Roger D.; Dechmann, Dina K. N.; Locatelli, Andrea G.; Puechmaille, Sébastien J.; Fedrigo, Olivier; [...]

Six reference-quality genomes reveal evolution of bat adaptations

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Springer Science and Business Media LLC, 2020

Published in: Nature, 583 (2020) 7817, Seite 578-584
Toh, Huishi; Yang, Chentao; Formenti, Giulio; Raja, Kalpana; Yan, Lily; Tracey, Alan; Chow, William; Howe, Kerstin; Bergeron, Lucie A.; Zhang, Guojie; Haase, Bettina; Mountcastle, Jacquelyn; Fedrigo, Olivier; Fogg, John; Kirilenko, Bogdan; Munegowda, Chetan; Hiller, Michael; Jain, Aashish; Kihara, Daisuke; Rhie, Arang; Phillippy, Adam M.; Swanson, Scott A.; Jiang, Peng; Clegg, Dennis O.; [...]

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

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Springer Science and Business Media LLC, 2022

Published in: BMC Biology, 20 (2022) 1
Bukhman, Yury V; Morin, Phillip A; Meyer, Susanne; Chu, Li-Fang; Jacobsen, Jeff K; Antosiewicz-Bourget, Jessica; Mamott, Daniel; Gonzales, Maylie; Argus, Cara; Bolin, Jennifer; Berres, Mark E; Fedrigo, Olivier; Steill, John; Swanson, Scott A; Jiang, Peng; Rhie, Arang; Formenti, Giulio; Phillippy, Adam M; Harris, Robert S; Wood, Jonathan M D; Howe, Kerstin; Kirilenko, Bogdan M; Munegowda, Chetan; Hiller, Michael; [...]

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

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Oxford University Press (OUP), 2024

Published in: Molecular Biology and Evolution, 41 (2024) 3
Kirilenko, Bogdan M.; Munegowda, Chetan; Osipova, Ekaterina; Jebb, David; Sharma, Virag; Blumer, Moritz; Morales, Ariadna E.; Ahmed, Alexis-Walid; Kontopoulos, Dimitrios-Georgios; Hilgers, Leon; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Hiller, Michael; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; Damas, Joana; Di Palma, Federica; Diekhans, Mark; [...]

Integrating gene annotation with orthology inference at scale

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American Association for the Advancement of Science (AAAS), 2023

Published in: Science, 380 (2023) 6643
Osmanski, Austin B.; Paulat, Nicole S.; Korstian, Jenny; Grimshaw, Jenna R.; Halsey, Michaela; Sullivan, Kevin A. M.; Moreno-Santillán, Diana D.; Crookshanks, Claudia; Roberts, Jacquelyn; Garcia, Carlos; Johnson, Matthew G.; Densmore, Llewellyn D.; Stevens, Richard D.; Rosen, Jeb; Storer, Jessica M.; Hubley, Robert; Smit, Arian F. A.; Dávalos, Liliana M.; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Ray, David A.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; [...]

Insights into mammalian TE diversity through the curation of 248 genome assemblies

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American Association for the Advancement of Science (AAAS), 2023

Published in: Science, 380 (2023) 6643
Foley, Nicole M.; Mason, Victor C.; Harris, Andrew J.; Bredemeyer, Kevin R.; Damas, Joana; Lewin, Harris A.; Eizirik, Eduardo; Gatesy, John; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Springer, Mark S.; Murphy, William J.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; Damas, Joana; Di Palma, Federica; Diekhans, Mark; Dong, Michael X.; [...]

A genomic timescale for placental mammal evolution

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American Association for the Advancement of Science (AAAS), 2023

Published in: Science, 380 (2023) 6643
Kaplow, Irene M.; Lawler, Alyssa J.; Schäffer, Daniel E.; Srinivasan, Chaitanya; Sestili, Heather H.; Wirthlin, Morgan E.; Phan, BaDoi N.; Prasad, Kavya; Brown, Ashley R.; Zhang, Xiaomeng; Foley, Kathleen; Genereux, Diane P.; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Meyer, Wynn K.; Pfenning, Andreas R.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; [...]

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

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American Association for the Advancement of Science (AAAS), 2023

Published in: Science, 380 (2023) 6643
Damas, Joana; Corbo, Marco; Kim, Jaebum; Turner-Maier, Jason; Farré, Marta; Larkin, Denis M.; Ryder, Oliver A.; Steiner, Cynthia; Houck, Marlys L.; Hall, Shaune; Shiue, Lily; Thomas, Stephen; Swale, Thomas; Daly, Mark; Korlach, Jonas; Uliano-Silva, Marcela; Mazzoni, Camila J.; Birren, Bruce W.; Genereux, Diane P.; Johnson, Jeremy; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Nweeia, Martin T.; Johnson, Rebecca N.; [...]

Evolution of the ancestral mammalian karyotype and syntenic regions

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Proceedings of the National Academy of Sciences, 2022

Published in: Proceedings of the National Academy of Sciences, 119 (2022) 40
Wilder, Aryn P.; Supple, Megan A.; Subramanian, Ayshwarya; Mudide, Anish; Swofford, Ross; Serres-Armero, Aitor; Steiner, Cynthia; Koepfli, Klaus-Peter; Genereux, Diane P.; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Marques-Bonet, Tomas; Munoz Fuentes, Violeta; Foley, Kathleen; Meyer, Wynn K.; Ryder, Oliver A.; Shapiro, Beth; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; [...]

The contribution of historical processes to contemporary extinction risk in placental mammals

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American Association for the Advancement of Science (AAAS), 2023

Published in: Science, 380 (2023) 6643
Xue, James R.; Mackay-Smith, Ava; Mouri, Kousuke; Garcia, Meilin Fernandez; Dong, Michael X.; Akers, Jared F.; Noble, Mark; Li, Xue; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Noonan, James P.; Capellini, Terence D.; Brennand, Kristen J.; Tewhey, Ryan; Sabeti, Pardis C.; Reilly, Steven K.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; [...]

The functional and evolutionary impacts of human-specific deletions in conserved elements

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American Association for the Advancement of Science (AAAS), 2023

Published in: Science, 380 (2023) 6643
Andrews, Gregory; Fan, Kaili; Pratt, Henry E.; Phalke, Nishigandha; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Gazal, Steven; Moore, Jill E.; Weng, Zhiping; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; Damas, Joana; Di Palma, Federica; Diekhans, Mark; Dong, Michael X.; Eizirik, Eduardo; Fan, Kaili; Fanter, Cornelia; [...]

Mammalian evolution of human cis-regulatory elements and transcription factor binding sites

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American Association for the Advancement of Science (AAAS), 2023

Published in: Science, 380 (2023) 6643

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