| # | Title | Journal | Year | Citations |
|---|
| 1 | Phylogenetic Classification and the Universal Tree | Science | 1999 | 1,720 |
| 2 | Mitochondrial genomes: anything goes | Trends in Genetics | 2003 | 555 |
| 3 | Evolution of organellar genomes | Current Opinion in Genetics and Development | 1999 | 309 |
| 4 | Mitochondria of Protists | Annual Review of Genetics | 2004 | 295 |
| 5 | The origins of multicellularity: a multi-taxon genome initiative | Trends in Genetics | 2007 | 201 |
| 6 | Origin of H1 linker histones | FASEB Journal | 2001 | 192 |
| 7 | Bacteriophage origins of mitochondrial replication and transcription proteins | Trends in Genetics | 2006 | 180 |
| 8 | The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation | Philosophical Transactions of the Royal Society B: Biological Sciences | 2006 | 159 |
| 9 | Ancient Ciphers: Translation in Archaea | Cell | 1997 | 155 |
| 10 | The Complete Mitochondrial DNA Sequences of Nephroselmis olivacea and Pedinomonas minor: Two Radically Different Evolutionary Patterns within Green Algae | Plant Cell | 1999 | 154 |
| 11 | Mitochondrial genes on the move | Nature | 2000 | 142 |
| 12 | Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function | Proceedings of the National Academy of Sciences of the United States of America | 2007 | 139 |
| 13 | A comparison of three fission yeast mitochondrial genomes | Nucleic Acids Research | 2003 | 136 |
| 14 | Conserved Meiotic Machinery in Glomus spp., a Putatively Ancient Asexual Fungal Lineage | Genome Biology and Evolution | 2011 | 129 |
| 15 | The nature of the universal ancestor and the evolution of the proteome | Current Opinion in Structural Biology | 2000 | 123 |
| 16 | Widespread and Extensive Editing of Mitochondrial mRNAS in Dinoflagellates | Journal of Molecular Biology | 2002 | 123 |
| 17 | Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle | Proceedings of the National Academy of Sciences of the United States of America | 2014 | 121 |
| 18 | Reconstructing/Deconstructing the Earliest Eukaryotes | Cell | 2001 | 115 |
| 19 | Plastid Genome Sequence of the Cryptophyte Alga Rhodomonas salina CCMP1319: Lateral Transfer of Putative DNA Replication Machinery and a Test of Chromist Plastid Phylogeny | Molecular Biology and Evolution | 2007 | 100 |
| 20 | Twinkle, the Mitochondrial Replicative DNA Helicase, Is Widespread in the Eukaryotic Radiation and May Also Be the Mitochondrial DNA Primase in Most Eukaryotes | Journal of Molecular Evolution | 2006 | 94 |
| 21 | Recurrent paralogy in the evolution of archaeal chaperonins | Current Biology | 1999 | 90 |
| 22 | Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: Cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria | Nucleic Acids Research | 2000 | 79 |
| 23 | Planctomycetes and eukaryotes: A case of analogy not homology | BioEssays | 2011 | 79 |
| 24 | GENOMICS: Enhanced: Are There Bugs in Our Genome? | Science | 2001 | 79 |
| 25 | Analyses of RNA Polymerase II Genes from Free-Living Protists: Phylogeny, Long Branch Attraction, and the Eukaryotic Big Bang | Molecular Biology and Evolution | 2002 | 76 |
| 26 | Novel mitochondrion‐related organelles in the anaerobic amoeba Mastigamoeba balamuthi | Molecular Microbiology | 2007 | 73 |
| 27 | Evolution of the Eukaryotic Translation Termination System: Origins of Release Factors | Molecular Biology and Evolution | 2000 | 71 |
| 28 | The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate | Genome Biology and Evolution | 2009 | 70 |
| 29 | Oxymonads Are Closely Related to the Excavate Taxon Trimastix | Molecular Biology and Evolution | 2001 | 67 |
| 30 | Testing for Covarion-like Evolution in Protein Sequences | Molecular Biology and Evolution | 2007 | 65 |
| 31 | Novel syntaxin gene sequences fromGiardia, Trypanosomaand algae: implications for the ancient evolution of the eukaryotic endomembrane system | Journal of Cell Science | 2002 | 64 |
| 32 | Gene Duplication and the Evolution of Group II Chaperonins: Implications for Structure and Function | Journal of Structural Biology | 2001 | 62 |
| 33 | Complete Nucleomorph Genome Sequence of the Nonphotosynthetic Alga Cryptomonas paramecium Reveals a Core Nucleomorph Gene Set | Genome Biology and Evolution | 2011 | 62 |
| 34 | Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity | Nucleic Acids Research | 2002 | 58 |
| 35 | Novel syntaxin gene sequences from Giardia, Trypanosoma and algae: implications for the ancient evolution of the eukaryotic endomembrane system | Journal of Cell Science | 2002 | 57 |
| 36 | Early origin of canonical introns | Nature | 2002 | 55 |
| 37 | Estimation of Rates-Across-Sites Distributions in Phylogenetic Substitution Models | Systematic Biology | 2003 | 55 |
| 38 | Gene duplication and gene conversion shape the evolution of archaeal chaperonins | Journal of Molecular Biology | 2002 | 53 |
| 39 | An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia | BMC Evolutionary Biology | 2005 | 53 |
| 40 | Widespread distribution of a unique marine protistan lineage | Environmental Microbiology | 2008 | 53 |
| 41 | Nucleomorph Genome Sequence of the Cryptophyte Alga Chroomonas mesostigmatica CCMP1168 Reveals Lineage-Specific Gene Loss and Genome Complexity | Genome Biology and Evolution | 2012 | 50 |
| 42 | Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae) | BMC Genomics | 2008 | 49 |
| 43 | Jumping Genes and Shrinking Genomes – Probing the Evolution of Eukaryotic Photosynthesis with Genomics | IUBMB Life | 2005 | 45 |
| 44 | Separate pathways for excision and processing of 16S and 23S rRNA from the primary rRNA operon transcript from the hyperthermophilic archaebacteriumSulfolobus acldocaldarius: similarities to eukaryotic rRNA processing | Molecular Microbiology | 1994 | 43 |
| 45 | Class I release factors in ciliates with variant genetic codes | Nucleic Acids Research | 2001 | 42 |
| 46 | Insight into the Diversity and Evolution of the Cryptomonad Nucleomorph Genome | Molecular Biology and Evolution | 2006 | 42 |
| 47 | Homologs of Mitochondrial Transcription Factor B, Sparsely Distributed Within the Eukaryotic Radiation, Are Likely Derived from the Dimethyladenosine Methyltransferase of the Mitochondrial Endosymbiont | Molecular Biology and Evolution | 2006 | 39 |
| 48 | Nephromyces, a beneficial apicomplexan symbiont in marine animals | Proceedings of the National Academy of Sciences of the United States of America | 2010 | 39 |
| 49 | The Evolution of Algae by Secondary and Tertiary Endosymbiosis | Advances in Botanical Research | 2012 | 39 |
| 50 | In Vitro Characterization of a tRNA Editing Activity in the Mitochondria of Spizellomyces punctatus, a Chytridiomycete Fungus | Journal of Biological Chemistry | 2005 | 38 |
