Wagele H, Deusch O, Handeler K, Martin R, Schmitt V, Christa G, Pinzger B, Gould SB, Dagan T, Klussmann-Kolb A, Martin W: Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plackobranchus ocellatus does not entail lateral transfer of algal nuclear genes. Mol Biol Evol 28:699-706 (2011).

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Kloesges T, Popa O, Martin W, Dagan T: Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28:1057-74 (2011).

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NS Shijulal, List JM, Geisler H, Fangerau H, Gray RD, Martin W, Dagan T: Networks uncover hidden lexical borrowing in Indo-European language evolution. Proc Biol Sci 278:1794-803 (2011).

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Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T: Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599-609 (2011).

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Dagan T: Phylogenomic networks. Trends Microbiol 19:483-91 (2011).

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Popa O, Dagan T: Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol in press (2011).

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Woehle C, Dagan T, Martin W, Gould SB: Red and Problematic Green Phylogenetic Signals among Thousands of Nuclear Genes from the Photosynthetic and Apicomplexa-Related Chromera velia. Genome Biol Evol 3:1220-30 (2011).

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Burstein D, Gould SB, Zimorski V, Kloesges T, Kiosse F, Major P, Martin W, Pupko T, Dagan T: A machine-learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis. Eukaryot Cell in press (2011).

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Ahmadinejad N, Dagan T, Gruenheit N, Martin W, Gabaldon T: Evolution of spliceosomal introns following endosymbiotic gene transfer. BMC Evol Biol 10:57 (2010).

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Dagan T, Roettger M, Bryant D, Martin W: Genome networks root the tree of life between prokaryotic domains. Genome Biol Evol 2:379-92 (2010).

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Bogumil D, Dagan T: Chaperonin-dependent accelerated substitution rates in prokaryotes. Genome Biol Evol 2:602-8 (2010).

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Atteia A, Adrait A, Brugiere S, Tardif M, van Lis R, Deusch O, Dagan T, Kuhn L, Gontero B, Martin W, Garin J, Joyard J, Rolland N: A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the alpha-proteobacterial mitochondrial ancestor. Mol Biol Evol 26:1533-48 (2009).

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Roettger M, Martin W, Dagan T: A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies. Mol Biol Evol 26:1931-9 (2009).

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Dagan T, Martin W: Microbiology. Seeing green and red in diatom genomes. Science 324:1651-2 (2009).

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Dagan T, Martin W: Getting a better picture of microbial evolution en route to a network of genomes. Philos Trans R Soc Lond B Biol Sci 364:2187-96 (2009).

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Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupre J, Dagan T, Boucher Y, Martin W: Prokaryotic evolution and the tree of life are two different things. Biol Direct 4:34 (2009).

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Basu MK, Rogozin IB, Deusch O, Dagan T, Martin W, Koonin EV: Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues. Mol Biol Evol 25:111-9 (2008).

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Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, Allen JF, Martin W, Dagan T: Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol Biol Evol 25:748-61 (2008).

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Dagan T, Artzy-Randrup Y, Martin W: Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A 105:10039-44 (2008).

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Dagan T, Martin W: Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A 104:870-5 (2007).

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Eßer C, Martin W, Dagan T: The origin of mitochondria in light of a fluid prokaryotic chromosome model. Biol Lett 3:180-4 (2007).

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Dagan T, Martin W: Testing hypotheses without considering predictions. Bioessays 29:500-3 (2007).

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Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA: The evolution of eukaryotes. Science 316:542-3; author reply 542-3 (2007).

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Ahmadinejad N, Dagan T, Martin W: Genome history in the symbiotic hybrid Euglena gracilis. Gene 402:35-9 (2007).

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Kilian B, Ozkan H, Walther A, Kohl J, Dagan T, Salamini F, Martin W: Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (Einkorn) domestication: implications for the origin of agriculture. Mol Biol Evol 24:2657-68 (2007).

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Dagan T, Blekhman R, Graur D: The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens. Mol Biol Evol 23:310-6 (2006).

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Dagan T, Martin W: The tree of one percent. Genome Biol 7:118 (2006).

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Dagan T, Graur D: The comparative method rules! Codon volatility cannot detect positive Darwinian selection using a single genome sequence. Mol Biol Evol 22:496-500 (2005).

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Cohen N, Dagan T, Stone L, Graur D: GC composition of the human genome: in search of isochores. Mol Biol Evol 22:1260-72 (2005).

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Dagan T, Sorek R, Sharon E, Ast G, Graur D: AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res 32:D489-92 (2004).

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Sorek R, Lev-Maor G, Reznik M, Dagan T, Belinky F, Graur D, Ast G: Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. Mol Cell 14:221-31 (2004).

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