Publications

Publications 2017

  • Tria FDK, Landan G, Dagan T. 2017. Phylogenetic rooting using minimal ancestor deviation. Nat Ecol Evol 1:193.
  • Woehle C, Dagan T, Landan G, Vardi A, Rosenwasser S. 2017. Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis. Nat Plants 3:17066. Pubmed
  • Hülter N, Ilhan J, Wein T, Kadibalban AS, Hammerschmidt K, Dagan T. 2017. An evolutionary perspective on plasmid lifestyle modes. Curr. Opin. Microbiol. 38:74–80. Pubmed
  • Hülter N, Sørum V, Borch-Pedersen K, Liljegren MM, Utnes ALG, Primicerio R, Harms K, Johnsen PJ. 2017. Costs and benefits of natural transformation in Acinetobacter baylyi. BMC Microbiol. 17:34. Pubmed
  • Weissenbach J, Ilhan J, Bogumil D, Hülter N, Stucken K, Dagan T. 2017. Evolution of Chaperonin Gene Duplication in Stigonematalean Cyanobacteria (Subsection V). Genome Biol Evol. evw287. Pubmed
  • Ribeiro ÂM, Foote AD, Kupczok A, Frazão B, Limborg MT, Piñeiro R, Abalde S, Rocha S, da Fonseca RR. 2017. Marine genomics: News and views. Mar Genomics. 31:1-8. Pubmed

 

Publications 2016

  • Popa O, Landan G, Dagan T. 2016. Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. ISME J. Pubmed
  • Harms K, Lunnan A, Hülter N, Mourier T, Vinner L, Andam CP, Marttinen P, Fridholm H, Hansen AJ, Hanage WP, Nielsen KM, Willerslev E, Johnsen PJ. 2016. Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc. Natl. Acad. Sci. 113(52): 15066-15071. Pubmed
  • McLeman A, Sierocinski P, Hesse E, Buckling A, Perron G, Hülter N, Johnsen PJ, Vos M. 2016. No effect of natural transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system. Sci. Rep. 6:37144. Pubmed
  • Kadibelban AS, Bogumil D, Landan G, Dagan T. 2016 DnaK-dependent accelerated evolutionary rate in prokaryotes, Genome Biol Evol, 8:1590-1599. Pubmed
 

Publications 2015

  • Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF (2015) Endosymbiotic origin and differential loss of eukaryotic genes, Nature, 524(7566):427-32. Pubmed
  • Rauch C, Vries Jd, Rommel S, Rose LE, Woehle C, Christa G, Laetz EM, Wägele H, Tielens AG, Nickelsen J, Schumann T, Jahns P, Gould SB (2015) Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs, Genome Biol Evol, 7(9):2602-7. Pubmed
  • Habicht J, Woehle C, Gould SB (2015) Tetrahymena Expresses More than a Hundred Proteins with Lipid-binding MORN Motifs that can Differ in their Subcellular Localisations, J Eukaryot Microbiol, 62(5):694-700. Pubmed
  • Kupczok A, Landan G, Dagan T (2015) The Contribution of Genetic Recombination to CRISPR Array Evolution, Genome Biol Evol, 7(7):1925-39. Pubmed
  • Thiergart T, Landan G, Martin WF (2015) Concatenated alignments and the case of the disappearing tree, BMC Evol Biol, 14:266. Pubmed
  • Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney JO, Martin WF (2015) Origins of major archaeal clades correspond to gene acquisitions from bacteria, Nature, 517(7532):77-80. Pubmed
  • Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV (2015) No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales, The ISME Journal, 9:2021–2027. Pubmed
 

Publications 2014

  • Dagan T, Bapteste E, McInerney JO, Martin WF (2014) SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report, Genome Biol Evol, 6(9):2206-9. Pubmed
  • Woehle C, Kusdian G, Radine C, Graur D, Landan G, Gould SB (2014) The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes, BMC Genomics, 5:906. Pubmed
  • Stucken K, Koch R, Dagan T (2014) Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering, Biol Res, 46(4):373-82. Pubmed
  • Kupczok A, Bollback JP (2014) Motif depletion in bacteriophages infecting hosts with CRISPR systems, BMC Genomics, 15:663. Pubmed
  • Bogumil D, Alvarez-Ponce D, Landan G, McInerney J, Dagan T (2014) Integration of two ancestral chaperone systems into one: the evolution of molecular chaperones in light of eukaryogenesis, Mol Biol Evol, 31(2):410-418. Pubmed
 

Publications 2013

  • Stucken K, Koch R, Dagan T (2013) Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engeneering, Biol Res 46(4):373-382. Pubmed
  • Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin W (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol, 5:31-44. Pubmed
 

Publications 2012

  • Bogumil D, Dagan T (2012) The cumulative impact of chaperone mediated folding on genome evolution. Biochemistry, 51:9941-9953.Pubmed
  • Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney J, Deppenmeier U, Martin WF (2012) Acquisition of a thousand eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci USA, in press.Pubmed
  • Martin WF, Hazkani-Covo E, Shavit-Greivink L, Schmitt V, Händeler K, Gould SB, Landan G, Graur D, Dagan T (2012) Gene transfers from organelles to the nucleus: How much, what happens, and why none in Elysia? J Endocytobiosis Cell Res 23:16-20.
  • Martin WF, Roettger M, Kloesges T, Thiergart T, Woehle C, Gould S, Dagan T(2012)Modern endosymbiotic theory: Getting lateral gene transfer into the equation. J Endocytobiosis Cell Res 23:1-5.
  • Bogumil D, Landan G, Ilhan J, Dagan T (2012) Chaperones divide yeast proteins intoclasses of evolutionary rate and expression level, Genome Biol Evol, 4:618-625.Pubmed
  • Stucken K, Ilhan J, Dagan T, Martin W (2012) Transformation and conjugal transfer of foreign genes into the filamentous multicellular cyanobacteria (Subsection V) Fischerella and Chlorogloeopsis. Current Microbiology, in press. Pubmed
  • Heinz E, Williams T, Nakjang S, Noël CJ, Swan DC, Goldberg AV, Harris SR, Weinmaier T, Markert S, Becher D, Dagan T, Schweder T, Rattei T, Hall N, Hirt RP, Embley TM (2012) Trachipleistophora hominis prodives novel insights into reductive genome evolution in eukaryotes, in press.
  • Külzer S, Charnaud S, Riedel J, Mandal P, Dagan T, Crabb BS, Gilson PR, Przyborski JM (2012) An exported chaperone system in P. falciparum infected erythrocytes, in press.Pubmed
  • Thiergart T, Landan G, Schenk M, Dagan T, Martin WF: An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol Evol 4:466-85 (2012). Pubmed

Publications 2011

  • 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).Pubmed
  • 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).Pubmed
  • 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). Pubmed
  • 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). Pubmed
  • Dagan T: Phylogenomic networks. Trends Microbiol 19:483-91 (2011). Pubmed
  • Popa O, Dagan T: Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol in press (2011). Pubmed
  • 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).Pubmed
  • 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).Pubmed

Publications 2010

  • Ahmadinejad N, Dagan T, Gruenheit N, Martin W, Gabaldon T: Evolution of spliceosomal introns following endosymbiotic gene transfer. BMC Evol Biol 10:57 (2010). Pubmed
  • 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). Pubmed
  • Bogumil D, Dagan T: Chaperonin-dependent accelerated substitution rates in prokaryotes. Genome Biol Evol 2:602-8 (2010). Pubmed

Publications 2009

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

Publications 2008

  • 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). Pubmed
  • 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). Pubmed
  • 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). Pubmed

Publications 2007

  • 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). Pubmed
  • Eßer C, Martin W, Dagan T: The origin of mitochondria in light of a fluid prokaryotic chromosome model. Biol Lett 3:180-4 (2007).  Pubmed
  • Dagan T, Martin W: Testing hypotheses without considering predictions. Bioessays 29:500-3 (2007). Pubmed
  • 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). Pubmed
  • Ahmadinejad N, Dagan T, Martin W: Genome history in the symbiotic hybrid Euglena gracilis. Gene 402:35-9 (2007). Pubmed
  • 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). Pubmed

Publications 2006

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

Publications 2005

  • 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). Pubmed
  • 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). Pubmed

Publications 2004

  • 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). Pubmed
  • 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). Pubmed

Publications 2003

  • Fleishman SJ, Dagan T, Graur D: pANT: a method for the pairwise assessment of nonfunctionalization times of processed pseudogenes. Mol Biol Evol 20:1876-80 (2003). Pubmed

Publications 2002

  • Dagan T, Talmor Y, Graur D: Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol Biol Evol 19:1022-5 (2002). Pubmed