The origin and early evolution of eukaryotes in the light of phylogenomics

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

THE UBIQUITIN SYSTEM

Hershko, A., & Ciechanover, A. (1998) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.67.1.425 · Cited by 8,840

Mitochondrial Evolution

Gray, M. W., Burger, G., & Lang, B. F. (1999) · Science · doi:10.1126/science.283.5407.1476 · Cited by 1,765

The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

Adl, S., Simpson, A., Farmer, M. A., Andersen, R., Anderson, O., Barta, J. R., Bowser, S., Brugerolle, G., Fensome, R., Fredericq, S., et al. (2005) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2005.00053.x · Cited by 1,749

Phylogenomics and the reconstruction of the tree of life

Delsuc, F., Brinkmann, H., & Philippe, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1603 · Cited by 1,264

A kingdom-level phylogeny of eukaryotes based on combined protein data.

Baldauf, S., Roger, A., Wenk-Siefert, I., & Doolittle, W. (2000) · Science · doi:10.1126/science.290.5493.972 · Cited by 1,243

Protein Tyrosine Kinase Structure and Function

Hubbard, S. R., & Till, J. H. (2000) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.69.1.373 · Cited by 1,176

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Koonin, E. V., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Krylov, D. M., Makarova, K. S., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., Rao, B. S., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-2-r7 · Cited by 1,100

The Age of Crosstalk: Phosphorylation, Ubiquitination, and Beyond

Hunter, T. R. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.11.019 · Cited by 970

Ubiquitin-binding domains — from structures to functions

Đikić, I., Wakatsuki, S., & Walters, K. J. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2767 · Cited by 903

Eukaryotic evolution, changes and challenges

Embley, T. M., & Martin, W. (2006) · Nature · doi:10.1038/nature04546 · Cited by 867

Ubiquitin-mediated proteolysis: biological regulation via destruction

Ciechanover, A. J., Orian, A., & Schwartz, A. L. (2000) · BioEssays · doi:10.1002/(sici)1521-1878(200005)22:5 · Cited by 848

Specificity in Signal Transduction

Pawson, T. J. (2004) · Cell · doi:10.1016/s0092-8674(03)01077-8 · Cited by 821

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

Koonin, E. V., & Wolf, Y. I. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn668 · Cited by 817

Origin and function of ubiquitin-like proteins

Hochstrasser, M. (2009) · Nature · doi:10.1038/nature07958 · Cited by 784

The Deep Roots of Eukaryotes

Baldauf, S. L. (2003) · Science · doi:10.1126/science.1085544 · Cited by 782

Specialization and evolution of endogenous small RNA pathways

Chapman, E. J., & Carrington, J. C. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2179 · Cited by 715

Rare genomic changes as a tool for phylogenetics

Rokas, A., & Holland, P. W. H. (2000) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)01967-4 · Cited by 693

The evolution of spliceosomal introns: patterns, puzzles and progress

Roy, S. W., & Gilbert, W. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1807 · Cited by 657

The Eukaryotic Genome as an RNA Machine

Amaral, P., Dinger, M. E., Mercer, T. R., & Mattick, J. S. (2008) · Science · doi:10.1126/science.1155472 · Cited by 633

The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological DiversityPreprint

Galagan, J. E., Nusbaum, C., Roy, A., Endrizzi, M. G., Macdonald, P., FitzHugh, W., Calvo, S., Engels, R., Smirnov, S., Atnoor, D., et al. (2002) · Genome Research · doi:10.1101/gr.223902 · Cited by 625

You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes

Doolittle, W. F. (1998) · Trends in Genetics · doi:10.1016/s0168-9525(98)01494-2 · Cited by 600

The tree of eukaryotes

Keeling, P. J., Burger, G., Durnford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., & Gray, M. W. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.09.005 · Cited by 579

Conserved domains in DNA repair proteins and evolution of repair systems

Aravind, L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.5.1223 · Cited by 571

Origins and evolution of eukaryotic RNA interference

Shabalina, S. A., & Koonin, E. V. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.06.005 · Cited by 559

The ring of life provides evidence for a genome fusion origin of eukaryotes

Rivera, M. C., & Lake, J. A. (2004) · Nature · doi:10.1038/nature02848 · Cited by 546

Comparative genomics and evolution of proteins involved in RNA metabolism

Anantharaman, V. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1427 · Cited by 541

Introns and the origin of nucleus–cytosol compartmentalization

Martin, W. F., & Koonin, E. V. (2006) · Nature · doi:10.1038/nature04531 · Cited by 506

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

Hampl, V., Hug, L. A., Leigh, J., Dacks, J. B., Lang, B. F., Simpson, A. G. B., & Roger, A. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807880106 · Cited by 488

The origin and early evolution of mitochondria.

Gray, M. W., Burger, G., & Lang, B. F. (2001) · Genome biology · doi:10.1186/gb-2001-2-6-reviews1018 · Cited by 483

The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

Fritz‐Laylin, L. K., Prochnik, S. E., Ginger, M. L., Dacks, J. B., Carpenter, M. L., Field, M. C., Kuo, A., Paredez, A. R., Chapman, J., Pham, J. K., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.032 · Cited by 472

The Puzzle of Plastid Evolution

Archibald, J. M. (2009) · Current Biology · doi:10.1016/j.cub.2008.11.067 · Cited by 469

The Closest BLAST Hit Is Often Not the Nearest Neighbor

Koski, L. B., & Golding, G. B. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010184 · Cited by 466

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

Jacquier, A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2683 · Cited by 439

Myosin domain evolution and the primary divergence of eukaryotes

Richards, T. A., & Cavalier‐Smith, T. (2005) · Nature · doi:10.1038/nature03949 · Cited by 432

Kinomics: methods for deciphering the kinome

Johnson, S. A., & Hunter, T. R. (2004) · Nature Methods · doi:10.1038/nmeth731 · Cited by 432

Phylogenomics Reshuffles the Eukaryotic Supergroups

Burki, F., Shalchian‐Tabrizi, K., Minge, M. A., Skjæveland, Å., Nikolaev, S. I., Jakobsen, K. S., & Pawlowski, J. W. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000790 · Cited by 425

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

Dagan, T., Artzy-Randrup, Y., & Martin, W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800679105 · Cited by 409

The archaebacterial origin of eukaryotes

Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R., & Embley, T. M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810647105 · Cited by 395

Animal Evolution and the Molecular Signature of Radiations Compressed in Time

Rokas, A., Krüger, D., & Carroll, S. B. (2005) · Science · doi:10.1126/science.1116759 · Cited by 374

Estimating the size of the bacterial pan-genome

Lapierre, P., & Gogarten, J. P. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.12.004 · Cited by 373

Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts

von Dohlen, C. D., Kohler, S., Alsop, S. T., & McManus, W. R. (2001) · Nature · doi:10.1038/35086563 · Cited by 353

A unique cell division machinery in the Archaea

Lindås, A., Karlsson, E. A., Lindgren, M. T., Ettema, T. J. G., & Bernander, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809467105 · Cited by 345

The origin of the eukaryotic cell: A genomic investigation

Hartman, H., & Fedorov, A. N. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032658599 · Cited by 336

Rooting the Eukaryote Tree by Using a Derived Gene Fusion

Stechmann, A., & Cavalier‐Smith, T. (2002) · Science · doi:10.1126/science.1071196 · Cited by 332

A Genome Phylogeny for Mitochondria Among -Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes

Esser, C. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh160 · Cited by 324

Bushes in the tree of life

Rokas, A., & Carroll, S. B. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040352 · Cited by 315

Ufd2, a Novel Autoantigen in Scleroderma, Regulates Sister Chromatid Separation

Spinette, S., Christoph Lengauer, C., Mahoney, J. A., Jallepalli, P. V., Wang, Z., Casciola-Rosen, L., & Rosen, A. (2004) · Cell Cycle · doi:10.4161/cc.3.12.1345 · Cited by 309

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

Makarova, K. S., Wolf, Y. I., John van der, O. O. S. T., & Koonin, E. V. (2009) · Biology Direct · doi:10.1186/1745-6150-4-29 · Cited by 305

Comparative Genomics, Evolution and Origins of the Nuclear Envelope and Nuclear Pore Complex

Mans, B., Anantharaman, V., Aravind, L., & Koonin, E. V. (2004) · Cell Cycle · doi:10.4161/cc.3.12.1316 · Cited by 304

A korarchaeal genome reveals insights into the evolution of the Archaea

Elkins, J. G., Podar, M., Graham, D. E., Makarova, K. S., Wolf, Y., Randau, L., Hedlund, B. P., Brochier-Armanet, C., Kunin, V., Anderson, I., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801980105 · Cited by 296

The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?

Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-22 · Cited by 289

Reconstructing Early Events in Eukaryotic Evolution

Roger, A. J. (1999) · The American Naturalist · doi:10.1086/303290 · Cited by 283

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

Iyer, L. M., Anantharaman, V., Wolf, M. Y., & Aravind, L. (2007) · International Journal for Parasitology · doi:10.1016/j.ijpara.2007.07.018 · Cited by 277

Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes

Burki, F., Shalchian‐Tabrizi, K., & Pawlowski, J. W. (2008) · Biology Letters · doi:10.1098/rsbl.2008.0224 · Cited by 268

Phosphoesterase domains associated with DNA polymerases of diverse origins

Aravind, L., & Koonin, E. V. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.16.3746 · Cited by 260

Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic ApproachPreprint

Koonin, E. V., Wolf, Y. I., & Aravind, L. (2001) · Genome Research · doi:10.1101/gr.162001 · Cited by 248

The origins of phagocytosis and eukaryogenesis

Yutin, N., Wolf, M. Y., Wolf, Y. I., & Koonin, E. V. (2009) · Biology Direct · doi:10.1186/1745-6150-4-9 · Cited by 247

Evolution of DNA Polymerase Families: Evidences for Multiple Gene Exchange Between Cellular and Viral Proteins

Filée, J., Forterre, P., Sen-Lin, T., & Laurent, J. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0078-x · Cited by 247

Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of Rhizaria with Chromalveolates

Hackett, J. D., Yoon, H. S., Li, S., Reyes‐Prieto, A., Rümmele, S. E., & Bhattacharya, D. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm089 · Cited by 240

Complex Spliceosomal Organization Ancestral to Extant Eukaryotes

Collins, L., & Penny, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi091 · Cited by 240

Genomics and the Irreducible Nature of Eukaryote Cells

Kurland, C. G., Collins, L. J., & Penny, D. (2006) · Science · doi:10.1126/science.1121674 · Cited by 220

Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata

Moreira, D., von der Heyden, S., Bass, D., López‐García, P., Chao, E. E. Y., & Cavalier‐Smith, T. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.11.001 · Cited by 207

Evolutionary origins of metabolic compartmentalization in eukaryotes

Martin, W. F. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0252 · Cited by 207

Molecular Evolution of FtsZ Protein Sequences Encoded Within the Genomes of Archaea, Bacteria, and Eukaryota

Vaughan, S., Wickstead, B., Gull, K., & Addinall, S. G. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2523-5 · Cited by 202

Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii

Humbard, M. A., Miranda, H. V., Lim, J., Krause, D. J., Pritz, J. R., Zhou, G., Chen, S., Wells, L., & Maupin-furlow, J. A. (2010) · Nature · doi:10.1038/nature08659 · Cited by 197

On the origin of intracellular compartmentation and organized metabolic systems

Ovádi, J., & Saks, V. A. (2003) · Molecular and Cellular Biochemistry · doi:10.1023/b:mcbi.0000009855.14648.2c · Cited by 195

Diversity and reductive evolution of mitochondria among microbial eukaryotes

Hjort, K., Goldberg, A. V., Tsaousis, A. D., Hirt, R. P., & Embley, T. M. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0224 · Cited by 194

Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes

Pisani, D., Cotton, J. A., & McInerney, J. O. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm095 · Cited by 187

The Deep Archaeal Roots of Eukaryotes

Yutin, N., Makarova, K. S., Mekhedov, S., Wolf, Y. I., & Koonin, E. V. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn108 · Cited by 184

Three distinct modes of intron dynamics in the evolution of eukaryotesPreprint

Carmel, L., Wolf, Y. I., Rogozin, I. B., & Koonin, E. V. (2007) · Genome Research · doi:10.1101/gr.6438607 · Cited by 182

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

Roger, A. J., & Hug, L. A. (2006) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2006.1845 · Cited by 180

Biochemical Principles of Small RNA Pathways

Liu, Q., & Paroo, Z. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.052208.151733 · Cited by 180

Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell

Makarova, K. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki775 · Cited by 180

Degenerate mitochondria

van der Giezen, M., & Tovar, J. (2005) · EMBO Reports · doi:10.1038/sj.embor.7400440 · Cited by 180

The root of the eukaryote tree pinpointed

Stechmann, A., & Cavalier‐Smith, T. (2003) · Current Biology · doi:10.1016/s0960-9822(03)00602-x · Cited by 174

Hydrogenosomes and Mitosomes: Conservation and Evolution of Functions 1

van der Giezen, M. (2009) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2009.00407.x · Cited by 169

Evaluating Support for the Current Classification of Eukaryotic Diversity

Parfrey, L. W., Barbero, E., Lasser, E. C., Dunthorn, M., Bhattacharya, D., Patterson, D. J., & Katz, L. A. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020220 · Cited by 165

The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism

Aravind, L., Iyer, L. M., & Anantharaman, V. (2003) · Genome biology · doi:10.1186/gb-2003-4-10-r64 · Cited by 164

Broadly sampled multigene trees of eukaryotes

Yoon, H. S., Grant, J. R., Tekle, Y. I., Wu, M., Chaon, B., Cole, J. C., Logsdon, J. M., Jr., Patterson, D. J., Bhattacharya, D., & Katz, L. A. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-14 · Cited by 159

Secondary (γ- Proteobacteria ) Endosymbionts Infect the Primary (β- Proteobacteria ) Endosymbionts of Mealybugs Multiple Times and Coevolve with Their Hosts

Thao, M. L., Gullan, P. J., & Baumann, P. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.7.3190-3197.2002 · Cited by 144

Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure

Korkhin, Y., Ünligil, U. M., Littlefield, O., Nelson, P. J., Stuart, D. I., Sigler, P. B., Bell, S. D., & Abrescia, N. G. A. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000102 · Cited by 134

Evolution of cytomotive filaments: The cytoskeleton from prokaryotes to eukaryotes

Löwe, J., & Amos, L. (2008) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2008.08.010 · Cited by 134

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

Csürös, M., & Miklos, I. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp123 · Cited by 133

Origins of microsporidia

Keeling, P. J., & McFadden, G. I. (1998) · Trends in Microbiology · doi:10.1016/s0966-842x(97)01185-2 · Cited by 127

The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

Foster, P. G., Cox, C. J., & Embley, T. M. (2009) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0034 · Cited by 124

First and last ancestors: reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes

Field, M. C., & Dacks, J. B. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2008.12.004 · Cited by 123

Structure and function of the GINS complex, a key component of the eukaryotic replisome

MacNeill, S. A. (2010) · Biochemical Journal · doi:10.1042/bj20091531 · Cited by 122

The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved

Guigas, G., Kalla, C., & Weiß, M. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.09.054 · Cited by 119

Reconstructing/Deconstructing the Earliest Eukaryotes

Dacks, J. B., & Doolittle, W. F. (2001) · Cell · doi:10.1016/s0092-8674(01)00584-0 · Cited by 119

The new phylogeny of eukaryotes

Philippe, H., Germot, A., & Moreira, D. (2000) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00137-4 · Cited by 116

The Biological Big Bang model for the major transitions in evolution

Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-21 · Cited by 116

Shifting Players and Paradigms in Cell-Specific Transcription

D’Alessio, J. A., Wright, K. J., & Tjian, R. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.12.011 · Cited by 115

Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors

Tahirov, T. H., Makarova, K. S., Rogozin, I. B., Pavlov, Y. I., & Koonin, E. V. (2009) · Biology Direct · doi:10.1186/1745-6150-4-11 · Cited by 110

Critical Analysis of Eukaryotic Phylogeny: A Case Study Based on the HSP70 Family

Germot, A., & Philippe, H. (1999) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.1999.tb04594.x · Cited by 102

Predation between prokaryotes and the origin of eukaryotes

Davidov, Y., & Jurkevitch, É. (2009) · BioEssays · doi:10.1002/bies.200900018 · Cited by 102

Engulfed by speculation

Poole, A. M., & Penny, D. (2007) · Nature · doi:10.1038/447913a · Cited by 95

The origin of mitochondria in light of a fluid prokaryotic chromosome model

Esser, C., Martin, W., & Dagan, T. (2007) · Biology Letters · doi:10.1098/rsbl.2006.0582 · Cited by 92

Evolutionary position of breviate amoebae and the primary eukaryote divergence

Minge, M. A., Silberman, J. D., Orr, R. J. S., Cavalier‐Smith, T., Shalchian‐Tabrizi, K., Burki, F., Skjæveland, Å., & Jakobsen, K. S. (2008) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.1358 · Cited by 91

Transcription and Translation are Coupled in Archaea

French, S. L., Santangelo, T. J., Beyer, A. L., & Reeve, J. N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm007 · Cited by 91

Comparative genomics and structural biology of the molecular innovations of eukaryotes

Aravind, L., Iyer, L. M., & Koonin, E. V. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.04.006 · Cited by 90

Kinome signaling through regulated protein–protein interactions in normal and cancer cells

Pawson, T. J., & Kofler, M. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.02.005 · Cited by 90

Evolution of specificity in the eukaryotic endomembrane system

Dacks, J. B., Peden, A. A., & Field, M. C. (2008) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2008.08.041 · Cited by 89

The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure

Bapteste, E., Charlebois, R. L., MacLeod, D., & Brochier, C. (2005) · Genome Biology · doi:10.1186/gb-2005-6-10-r85 · Cited by 89

Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes

Rogozin, I. B., Basu, M. K., Csürös, M., & Koonin, E. V. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp011 · Cited by 88

Genomes as documents of evolutionary history

Boussau, B., & Daubin, V. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.09.007 · Cited by 85

The Incredible Expanding Ancestor of Eukaryotes

Koonin, E. V. (2010) · Cell · doi:10.1016/j.cell.2010.02.022 · Cited by 83

Organization of Mammalian Cytoplasm

Hudder, A., Nathanson, L., & Deutscher, M. P. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.24.9318-9326.2003 · Cited by 77

Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer

Hoffmeister, M., & Martin, W. F. (2003) · Environmental Microbiology · doi:10.1046/j.1462-2920.2003.00454.x · Cited by 75

The Diversity Of Eukaryotes And The Root Of The Eukaryotic Tree

Brinkmann, H., & Philippe, H. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-74021-8_2 · Cited by 67

Intron-rich ancestors

ROY, S. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.07.002 · Cited by 62

Ancient ESCRTs and the evolution of binary fission

Samson, R. Y., & Bell, S. D. (2009) · Trends in Microbiology · doi:10.1016/j.tim.2009.08.003 · Cited by 61

Cell division and the ESCRT complex

Ettema, T. J. G., & Bernander, R. (2009) · Communicative & Integrative Biology · doi:10.4161/cib.7523 · Cited by 61

Horizontal gene transfer: the path to maturity

Koonin, E. V. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03808.x · Cited by 56

Evolution of transcriptional control in mammals

Wilson, M. D., & Odom, D. T. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.10.003 · Cited by 56

Extremely Intron-Rich Genes in the Alveolate Ancestors Inferred with a Flexible Maximum-Likelihood Approach

Csürös, M., Rogozin, I. B., & Koonin, E. V. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn039 · Cited by 54

Proteasomes in the archaea from structure to function

Maupin-furlow, J. A. (2000) · Frontiers in bioscience · doi:10.2741/furlow · Cited by 54

The oligomerization and ligand‐binding properties of Sm‐like archaeal proteins (SmAPs)

Mura, C., Kozhukhovsky, A., Gingery, M., Phillips, M., & Eisenberg, D. S. (2003) · Protein Science · doi:10.1110/ps.0224703 · Cited by 53

Early evolution comes full circle

Martin, W. F., & Embley, T. M. (2004) · Nature · doi:10.1038/431134a · Cited by 52

Archaeal histones: structures, stability and DNA binding

Reeve, J. N., Bailey, K. A., Li, W.-T., Marc, F., Sandman, K., & Soares, D. J. (2004) · Biochemical Society Transactions · doi:10.1042/bst0320227 · Cited by 52

Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes

Vishwanath, P., Favaretto, P., Hartman, H., Mohr, S. C., & Smith, T. F. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.07.003 · Cited by 49

Sizing up the genomic footprint of endosymbiosis

Eliáš, M., & Archibald, J. M. (2009) · BioEssays · doi:10.1002/bies.200900117 · Cited by 48

A positive definition of prokaryotes

Martin, W. F., & Koonin, E. V. (2006) · Nature · doi:10.1038/442868c · Cited by 48

Ancestral relationships of the major eukaryotic lineages.

Sogin, M. L., Morrison, H. G., Hinkle, G., & Silberman, J. D. (1996) · PubMed · Cited by 48

Origin of Eukaryotic Endomembranes: A Critical Evaluation of Different Model Scenarios

Jékely, G. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-74021-8_3 · Cited by 47

The archaebacterial origin of eukaryotes

Embley, T. M. (2009) · Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology · doi:10.1016/j.cbpa.2009.04.498 · Cited by 47

Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota"

Koonin, E. V., Makarova, K. S., & Elkins, J. G. (2007) · Biology Direct · doi:10.1186/1745-6150-2-38 · Cited by 41

Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea

Blombach, F., Makarova, K. S., Marrero, J., Siebers, B., Koonin, E. V., & John van der, O. O. S. T. (2009) · Biology Direct · doi:10.1186/1745-6150-4-39 · Cited by 36

Deep Questions in the Tree of Life

Keeling, P. J. (2007) · Science · doi:10.1126/science.1149593 · Cited by 33

Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions

Venâncio, T. M., Balaji, S., Iyer, L. M., & Aravind, L. (2009) · Genome biology · doi:10.1186/gb-2009-10-3-r33 · Cited by 33

The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system

Podar, M., Wall, M. A., Makarova, K. S., & Koonin, E. V. (2008) · Biology Direct · doi:10.1186/1745-6150-3-2 · Cited by 28

The Evolution of Eukaryotes

Martin, W. F., Dagan, T., Koonin, E. V., DiPippo, J. L., Gogarten, J. P., & Lake, J. A. (2007) · Science · doi:10.1126/science.316.5824.542c · Cited by 26

Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea

Daniels, J., Kelly, S. L., Wickstead, B., & Keith Gull, B. (2009) · Biology Direct · doi:10.1186/1745-6150-4-24 · Cited by 23

Lessons from structural and biochemical studies on the archaeal exosome

Hartung, S., & Hopfner, K. (2009) · Biochemical Society Transactions · doi:10.1042/bst0370083 · Cited by 22

Evaluating Support for the Current Classification of Eukaryotic Diversity

Parfrey, L. W., Barbero, E., Lasser, E. C., Dunthorn, M. S., Bhattacharya, D., Patterson, D. J., & Katz, L. A. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0020220.eor · Cited by 19

Comprehensive analysis of the origin of eukaryotic genomes

Saruhashi, S., Hamada, K., Miyata, D., Horiike, T., & Shinozawa, T. (2008) · Genes & Genetic Systems · doi:10.1266/ggs.83.285 · Cited by 18

Approaches to defining the ancestral eukaryotic protein complexome

Ceulemans, H., Beke, L., & Bollen, M. (2006) · BioEssays · doi:10.1002/bies.20373 · Cited by 10

Complex archaea that bridge the gap between prokaryotes and eukaryotes

Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., van Eijk, R., Schleper, C., Guy, L., & Ettema, T. J. G. (2015) · Nature · doi:10.1038/nature14447 · Cited by 1,324

Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes

Müller, M., Mentel, M., van Hellemond, J. J., Henze, K., Woehle, C., Gould, S. B., Yu, R.-Y., van der Giezen, M., Tielens, A. G. M., & Martin, W. F. (2012) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.05024-11 · Cited by 838

Endosymbiosis and Eukaryotic Cell Evolution

Archibald, J. M. (2015) · Current Biology · doi:10.1016/j.cub.2015.07.055 · Cited by 654

Mitochondrial Evolution

Gray, M. W. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a011403 · Cited by 639

Archaea and the origin of eukaryotes

Eme, L., Spang, A., Lombard, J., Stairs, C. W., & Ettema, T. J. G. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.133 · Cited by 575

Origin and Early Evolution of the Eukaryotic Cell

Gabaldón, T. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090817-062213 · Cited by 121

The unlikely cell: origins and diversification of eukaryotes

Ligrone, R. (2022) · Università degli Studi di Napoli Federico II · doi:10.6093/2724-4393/9380 · Cited by 1

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

Koonin, E. V. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0333 · Cited by 145

Evolution: A gene-rich mitochondrial genome sheds light on the last eukaryotic common ancestor

Leger, M. M., & Gawryluk, R. M. R. (2024) · Current Biology · doi:10.1016/j.cub.2024.06.067 · Cited by 2

Open Questions on the Origin of Eukaryotes

López-García, P., & Moreira, D. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2015.09.005 · Cited by 135