Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock

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Items 101–200 of 580

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    Quoc D. Dang, Enrico Di · 1996 · Proceedings of the National Academy of Sciences
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    Milton H. Saier · 1998 · Advances in microbial physiology/Advances in Microbial Physiology
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    Lee, Michael S.Y. · 1999 · Journal of Molecular Evolution
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    Wai Mun Huang · 1996 · Annual Review of Genetics
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    Kevin E. Omland · 1997 · Evolution
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    Donald R. McCarty, Joanne Chory · 2000 · Cell
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    Otto G. Berg, C. G. Kurland · 2000 · Molecular biology and evolution
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    Wei Zhang, Weihong Qi, Thomas J. Albert, Alifiya S. Motiwala, David Alland, Eija K. Hyytia-Trees, Efrain M. Ribot, Patricia I. Fields, Thomas S. Whittam, Bala Swaminathan · 2006 · Genome Research
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    James J. Gilchrist, Calman Alexander MacLennan · 2019 · EcoSal Plus
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    Niklas Wikström, Paul Kenrick · 2001 · Molecular Phylogenetics and Evolution
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    Mauricio R. Papini · 2002 · Psychological Review
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    Andreas J. Bäumler, A J Gilde, Renée M. Tsolis, A W van der Velden, Brian M. M. Ahmer, Fred Heffron · 1997 · Journal of Bacteriology
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    Simon Y. W. Ho · 2014 · Trends in Ecology & Evolution
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    Evgeny N. Gordienko, Marat D. Kazanov, Mikhail Sergeevich Gelfand · 2013 · Journal of Bacteriology
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    Michael E. Baker · 1997 · Molecular and Cellular Endocrinology
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    NIELSEN, CLAUS · 1998 · Biological Reviews of the Cambridge Philosophical Society
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    Daniel A. Starr, Byron C. Williams, ZeXiao Li, Bijan Etemad-Moghadam, R. Kelly Dawe, Michael Lewis Goldberg · 1997 · The Journal of Cell Biology
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    Douglas N.W. Cooper, Robert P. Boulianne, Stacy Charlton, Eleanor M. Farrell, Anatol Sucher, Benjamin C. Lu · 1997 · Journal of Biological Chemistry
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    Steven A. Benner, Matthias Daniel Caraco, J. Michael Thomson, Eric A. Gaucher · 2002 · Science
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    Yumiko Watanabe, Hiroshi Naraoka, David J. Wronkiewicz, Kent C. Condie, Hiroshi Ohmoto · 1997 · Geochimica et Cosmochimica Acta
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    Peter P. Sheridan, Katherine H. Freeman, Jean E. Brenchley · 2003 · Geomicrobiology Journal
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    Jeffrey D. Palmer, C. Delwiche · 1996 · Proceedings of the National Academy of Sciences of the United States of America
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    James A. Irving, Terry W. Spithill, Robert Neil Pike, James C. Whisstock, Peter M. Smooker · 2003 · Journal of Molecular Evolution
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    Begoña Benito, Blanca Garcíadeblas, Alonso Rodríguez‐Navarro · 2002 · Microbiology
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    José Manuel Peregrín-Alvarez, Sophia Tsoka, Christos Ouzounis · 2003 · Genome Research
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    Michael Remmert, A. Biegert, Dirk Linke, Andrei N. Lupas, Johannes Söding · 2010 · Molecular Biology and Evolution
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    Fortey, Richard A., Briggs, Derek E. G., Wills, Matthew A. · 1997 · BioEssays
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    Howard Ochman · 2003 · Molecular Biology and Evolution
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    Xun Gu, David Hewett‐Emmett, Wen‐Hsiung Li · 1998 · PubMed
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    André‐Denis G. Wright, Denis H. Lynn · 1997 · Archiv für Protistenkunde
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    Antony M. Dean, Geoffrey Brian Golding · 1997 · Proceedings of the National Academy of Sciences
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    Robert M. Kent, Gerald F. Fitzgerald, Colin Hill, Catherine Stanton, R. Paul Ross · 2015 · Nutrients
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    Alexey S. Kondrashov · 1997 · Annual Review of Ecology and Systematics
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    Takashi Miyata, Hiroshi Suga · 2001 · BioEssays
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    Michel Kerszberg, Jean‐Pierre Changeux · 1998 · BioEssays
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    Sudhir Kumar, S. Blair Hedges · 2016 · Molecular Biology and Evolution
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    Michael L. Clawson, Aaron Bourret, David R. Benson · 2003 · Molecular Phylogenetics and Evolution
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    Norberto J. Palleroni · 1997 · Antonie van Leeuwenhoek
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    John E. McRory, Nancy M. Sherwood · 1997 · Endocrinology
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    Maria C. Davis, Christopher A. Kesthely, Emily A. Franklin, Shawn R. MacLellan · 2016 · Canadian Journal of Microbiology
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    Mitchell L. Sogin · 1997 · Current Opinion in Genetics & Development
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    Charles E. Bullerwell · 2003 · Nucleic Acids Research
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    Raúl Álvarez-Venegas, Zoya V. AVRAMOVA · 2002 · Gene
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    Natalie Yeager Stassen, John M. Logsdon Jr., Gary J. Vora, Hildo H. Offenberg, Jeffrey D. Palmer, Miriam E. Zolan · 1997 · Current Genetics
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    Nick V. Grishin, Yuri I. Wolf, Eugene V. Koonin · 2000 · Genome Research
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    Gu, Xun · 1998 · Journal of Molecular Evolution
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    J. R. McQuiston, S. Herrera-Leon, BC Wertheim, J. Doyle, P. I. Fields, R. V. Tauxe, John M. Logsdon Jr. · 2008 · Journal of Bacteriology
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    Masato Taoka, Yoshio Yamauchi, Takashi Shinkawa, Hiroyuki Kaji, Wakana Motohashi, Hiroshi Nakayama, Nobuhiro Takahashi, Toshiaki Isobe · 2004 · Molecular & Cellular Proteomics
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    Edward Louis Braun, Edwina K. Fuge, Pamela A. Padilla, Margaret Werner‐Washburne · 1996 · Journal of Bacteriology
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    Nikoh, Naruo, Iwabe, Naoyuki, Kuma, Kei-ichi, Ohno, Mutsuhito, Sugiyama, Tsutomu, Watanabe, Yoko, Yasui, Kinya, Shi-cui, Zhang, Hori, Katsuji, Shimura, Yoshiro et al. · 1997 · Journal of Molecular Evolution
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    Mark D. Yandell, Chris Mungall, Chris Smith, Simon E. Prochnik, Joshua S. Kaminker, George Hartzell, Suzanna Lewis, Gerald M. Rubin · 2006 · PLoS Computational Biology
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    Joseph L. Kirschvink, Timothy D. Raub · 2003 · Comptes Rendus Géoscience
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100. Something for everyone
     C. G. Kurland · 2000 · EMBO Reports