My NCBISign In
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale
Genome Biol. 2004; 5(2): R7. Published online 2004 January 15.
PMCID:
PMC395751
Abstract Full Text PDF–523K

Is Cited by the Following 80 Articles in this Archive:

Phytozome: a comparative platform for green plant genomics
David M. Goodstein, Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, William Dirks, Uffe Hellsten, Nicholas Putnam, Daniel S. Rokhsar
Nucleic Acids Res. 2012 January; 40(D1): D1178–D1186. Published online 2011 November 22. doi: 10.1093/nar/gkr944
PMCID:
PMC3245001
Abstract Full Text PDF–13M
The Genome Portal of the Department of Energy Joint Genome Institute
Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alex Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak
Nucleic Acids Res. 2012 January; 40(D1): D26–D32. Published online 2011 November 22. doi: 10.1093/nar/gkr947
PMCID:
PMC3245080
Abstract Full Text PDF–9.7M
Comparison of embryonic expression within multigene families employing the FlyExpress discovery platform reveals more spatial than temporal divergence
Charlotte E. Konikoff, Timothy L. Karr, Michael McCutchan, Stuart J. Newfeld, Sudhir Kumar
Dev Dyn. Author manuscript; available in PMC 2013 January 1.
Published in final edited form as: Dev Dyn. 2012 January; 241(1): 150–160. Published online 2011 September 29. doi: 10.1002/dvdy.22749
PMCID:
PMC3241901
Free in PMC on 2013/01/01
Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous Fungus Neurospora tetrasperma
Christopher E. Ellison, Jason E. Stajich, David J. Jacobson, Donald O. Natvig, Alla Lapidus, Brian Foster, Andrea Aerts, Robert Riley, Erika A. Lindquist, Igor V. Grigoriev, John W. Taylor
Genetics. 2011 September; 189(1): 55–69. doi: 10.1534/genetics.111.130690
PMCID:
PMC3176108
Abstract Full Text PDF–1.3M
Energetics and genetics across the prokaryote-eukaryote divide
Nick Lane
Biol Direct. 2011; 6: 35. Published online 2011 June 30. doi: 10.1186/1745-6150-6-35
PMCID:
PMC3152533
Abstract Full Text PDF–1.2M
Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
Stephen B. Goodwin, Sarrah Ben M'Barek, Braham Dhillon, Alexander H. J. Wittenberg, Charles F. Crane, James K. Hane, Andrew J. Foster, Theo A. J. Van der Lee, Jane Grimwood, Andrea Aerts, John Antoniw, Andy Bailey, Burt Bluhm, Judith Bowler, Jim Bristow, Ate van der Burgt, Blondy Canto-Canché, Alice C. L. Churchill, Laura Conde-Ferràez, Hans J. Cools, Pedro M. Coutinho, Michael Csukai, Paramvir Dehal, Pierre De Wit, Bruno Donzelli, Henri C. van de Geest, Roeland C. H. J. van Ham, Kim E. Hammond-Kosack, Bernard Henrissat, Andrzej Kilian, Adilson K. Kobayashi, Edda Koopmann, Yiannis Kourmpetis, Arnold Kuzniar, Erika Lindquist, Vincent Lombard, Chris Maliepaard, Natalia Martins, Rahim Mehrabi, Jan P. H. Nap, Alisa Ponomarenko, Jason J. Rudd, Asaf Salamov, Jeremy Schmutz, Henk J. Schouten, Harris Shapiro, Ioannis Stergiopoulos, Stefano F. F. Torriani, Hank Tu, Ronald P. de Vries, Cees Waalwijk, Sarah B. Ware, Ad Wiebenga, Lute-Harm Zwiers, Richard P. Oliver, Igor V. Grigoriev, Gert H. J. Kema
PLoS Genet. 2011 June; 7(6): e1002070. Published online 2011 June 9. doi: 10.1371/journal.pgen.1002070
PMCID:
PMC3111534
Abstract Full Text PDF–1.8M Supplementary Material
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
Mikael R. Andersen, Margarita P. Salazar, Peter J. Schaap, Peter J.I. van de Vondervoort, David Culley, Jette Thykaer, Jens C. Frisvad, Kristian F. Nielsen, Richard Albang, Kaj Albermann, Randy M. Berka, Gerhard H. Braus, Susanna A. Braus-Stromeyer, Luis M. Corrochano, Ziyu Dai, Piet W.M. van Dijck, Gerald Hofmann, Linda L. Lasure, Jon K. Magnuson, Hildegard Menke, Martin Meijer, Susan L. Meijer, Jakob B. Nielsen, Michael L. Nielsen, Albert J.J. van Ooyen, Herman J. Pel, Lars Poulsen, Rob A. Samson, Hein Stam, Adrian Tsang, Johannes M. van den Brink, Alex Atkins, Andrea Aerts, Harris Shapiro, Jasmyn Pangilinan, Asaf Salamov, Yigong Lou, Erika Lindquist, Susan Lucas, Jane Grimwood, Igor V. Grigoriev, Christian P. Kubicek, Diego Martinez, Noël N.M.E. van Peij, Johannes A. Roubos, Jens Nielsen, Scott E. Baker
Genome Res. 2011 June; 21(6): 885–897. doi: 10.1101/gr.112169.110
PMCID:
PMC3106321
Abstract Full Text PDF–894K
A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
Diana Chernikova, Sam Motamedi, Miklós Csürös, Eugene V Koonin, Igor B Rogozin
Biol Direct. 2011; 6: 26. Published online 2011 May 19. doi: 10.1186/1745-6150-6-26
PMCID:
PMC3125394
Abstract Full Text PDF–1.2M Supplementary Material
Evolutionary plasticity determination by orthologous groups distribution
Rodrigo JS Dalmolin, Mauro AA Castro, José L Rybarczyk Filho, Luis HT Souza, Rita MC de Almeida, José CF Moreira
Biol Direct. 2011; 6: 22. Published online 2011 May 17. doi: 10.1186/1745-6150-6-22
PMCID:
PMC3117832
Abstract Full Text PDF–1.0M Supplementary Material
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Christian P Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A Martinez, Irina S Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A Horwitz, Prasun K Mukherjee, Mala Mukherjee, László Kredics, Luis D Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan Deshpande, Hans von Döhren, Daniel J Ebbole, Edgardo U Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Y Gómez-Rodríguez, Sabine Gruber, Cliff Han, Bernard Henrissat, Rosa Hermosa, Miguel Hernández-Oñate, Levente Karaffa, Idit Kosti, Stéphane Le Crom, Erika Lindquist, Susan Lucas, Mette Lübeck, Peter S Lübeck, Antoine Margeot, Benjamin Metz, Monica Misra, Helena Nevalainen, Markus Omann, Nicolle Packer, Giancarlo Perrone, Edith E Uresti-Rivera, Asaf Salamov, Monika Schmoll, Bernhard Seiboth, Harris Shapiro, Serenella Sukno, Juan Antonio Tamayo-Ramos, Doris Tisch, Aric Wiest, Heather H Wilkinson, Michael Zhang, Pedro M Coutinho, Charles M Kenerley, Enrique Monte, Scott E Baker, Igor V Grigoriev
Genome Biol. 2011; 12(4): R40. Published online 2011 April 18. doi: 10.1186/gb-2011-12-4-r40
PMCID:
PMC3218866
Abstract Full Text PDF–1.1M Supplementary Material
Comparative analysis of information contents relevant to recognition of introns in many species
Hiroaki Iwata, Osamu Gotoh
BMC Genomics. 2011; 12: 45. Published online 2011 January 19. doi: 10.1186/1471-2164-12-45
PMCID:
PMC3033335
Abstract Full Text PDF–1.3M Supplementary Material
Measuring the Evolutionary Rewiring of Biological Networks
Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein
PLoS Comput Biol. 2011 January; 7(1): e1001050. Published online 2011 January 6. doi: 10.1371/journal.pcbi.1001050
PMCID:
PMC3017101
Abstract Full Text PDF–681K Supplementary Material
The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina
Aminael Sánchez-Rodríguez, Cindy Martens, Kristof Engelen, Yves Van de Peer, Kathleen Marchal
BMC Evol Biol. 2010; 10: 318. Published online 2010 October 21. doi: 10.1186/1471-2148-10-318
PMCID:
PMC3087541
Abstract Full Text PDF–1.7M Supplementary Material
The Nature of Protein Domain Evolution: Shaping the Interaction Network
Christoph P Bagowski, Wouter Bruins, Aartjan J.W te Velthuis
Curr Genomics. 2010 August; 11(5): 368–376. doi: 10.2174/138920210791616725
PMCID:
PMC2945003
Abstract Full Text PDF–429K
The origin and early evolution of eukaryotes in the light of phylogenomics
Eugene V Koonin
Genome Biol. 2010; 11(5): 209. Published online 2010 May 5. doi: 10.1186/gb-2010-11-5-209
PMCID:
PMC2898073
Abstract Full Text PDF–814K
The Incredible Expanding Ancestor of Eukaryotes
Eugene V. Koonin
Cell. Author manuscript; available in PMC 2012 March 5.
Published in final edited form as: Cell. 2010 March 5; 140(5): 606–608. doi: 10.1016/j.cell.2010.02.022
PMCID:
PMC3293451
Abstract Full Text PDF–568K
Systemic factors dominate mammal protein evolution
Alexander E. Vinogradov
Proc Biol Sci. 2010 May 7; 277(1686): 1403–1408. Published online 2010 January 6. doi: 10.1098/rspb.2009.1865
PMCID:
PMC2871935
Abstract Full Text PDF–146K
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human
Krzysztof Kuchta, Lukasz Knizewski, Lucjan S. Wyrwicz, Leszek Rychlewski, Krzysztof Ginalski
Nucleic Acids Res. 2009 December; 37(22): 7701–7714. Published online 2009 December. doi: 10.1093/nar/gkp854
PMCID:
PMC2794190
Abstract Full Text PDF–12M Supplementary Material
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
Valentín Ruano-Rubio, Olivier Poch, Julie D Thompson
BMC Bioinformatics. 2009; 10: 383. Published online 2009 November 24. doi: 10.1186/1471-2105-10-383
PMCID:
PMC2787529
Abstract Full Text PDF–1.9M
Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?
John W Stiller, Jinling Huang, Qin Ding, Jing Tian, Carol Goodwillie
BMC Genomics. 2009; 10: 484. Published online 2009 October 20. doi: 10.1186/1471-2164-10-484
PMCID:
PMC2770532
Abstract Full Text PDF–1.0M Supplementary Material
The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion
Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres, Alan Kuo, Catherine C. Wasmann, Jane Grimwood, Jeremy Schmutz, Masatoki Taga, Gerard J. White, Shiguo Zhou, David C. Schwartz, Michael Freitag, Li-jun Ma, Etienne G. J. Danchin, Bernard Henrissat, Pedro M. Coutinho, David R. Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. Barker, Michael Gribskov, Martijn Rep, Scott Kroken, István Molnár, Christopher Rensing, John C. Kennell, Jorge Zamora, Mark L. Farman, Eric U. Selker, Asaf Salamov, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Casey Lamers, Igor V. Grigoriev, David M. Geiser, Sarah F. Covert, Esteban Temporini, Hans D. VanEtten
PLoS Genet. 2009 August; 5(8): e1000618. Published online 2009 August 28. doi: 10.1371/journal.pgen.1000618
PMCID:
PMC2725324
Abstract Full Text PDF–624K Supplementary Material
webPRC: the Profile Comparer for alignment-based searching of public domain databases
Bernd W. Brandt, Jaap Heringa
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W48–W52. Published online 2009 July 1. doi: 10.1093/nar/gkp279
PMCID:
PMC2703954
Abstract Full Text PDF–2.3M
A complex-centric view of protein network evolution
Nir Yosef, Martin Kupiec, Eytan Ruppin, Roded Sharan
Nucleic Acids Res. 2009 July; 37(12): e88. Published online 2009 July. doi: 10.1093/nar/gkp414
PMCID:
PMC2709590
Abstract Full Text PDF–644K Supplementary Material
Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes
Igor B. Rogozin, Malay Kumar Basu, Miklós Csürös, Eugene V. Koonin
Genome Biol Evol. 2009; 1: 99–113. Published online 2009 May 25. doi: 10.1093/gbe/evp011
PMCID:
PMC2817406
Abstract Full Text PDF–674K Supplementary Material
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE
Xin Wang, Yongjun Zhao, Kim Wong, Peter Ehlers, Yuji Kohara, Steven J Jones, Marco A Marra, Robert A Holt, Donald G Moerman, Dave Hansen
BMC Genomics. 2009; 10: 213. Published online 2009 May 9. doi: 10.1186/1471-2164-10-213
PMCID:
PMC2686737
Abstract Full Text PDF–2.4M Supplementary Material
Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa
Takao Kasuga, Gertrud Mannhaupt, N. Louise Glass
PLoS ONE. 2009; 4(4): e5286. Published online 2009 April 21. doi: 10.1371/journal.pone.0005286
PMCID:
PMC2684829
Abstract Full Text PDF–373K Supplementary Material
Evolutionary constraints on structural similarity in orthologs and paralogs
Mark E Peterson, Feng Chen, Jeffery G Saven, David S Roos, Patricia C Babbitt, Andrej Sali
Protein Sci. 2009 June; 18(6): 1306–1315. Published online 2009 April 16. doi: 10.1002/pro.143
PMCID:
PMC2774440
Abstract Full Text PDF–506K
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
Yuri I. Wolf, Pavel S. Novichkov, Georgy P. Karev, Eugene V. Koonin, David J. Lipman
Proc Natl Acad Sci U S A. 2009 May 5; 106(18): 7273–7280. Published online 2009 April 7. doi: 10.1073/pnas.0901808106
PMCID:
PMC2666616
Abstract Full Text PDF–387K Supplementary Material
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
Sabine P Schrimpf, Manuel Weiss, Lukas Reiter, Christian H Ahrens, Marko Jovanovic, Johan Malmström, Erich Brunner, Sonali Mohanty, Martin J Lercher, Peter E Hunziker, Ruedi Aebersold, Christian von Mering, Michael O Hengartner
PLoS Biol. 2009 March; 7(3): e1000048. Published online 2009 March 3. doi: 10.1371/journal.pbio.1000048
PMCID:
PMC2650730
Abstract Full Text PDF–649K Supplementary Material
Darwinian evolution in the light of genomics
Eugene V. Koonin
Nucleic Acids Res. 2009 March; 37(4): 1011–1034. Published online 2009 March. doi: 10.1093/nar/gkp089
PMCID:
PMC2651812
Abstract Full Text PDF–3.8M
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