John M. Archibald, Ph.D. - Publications

Affiliations: 
Dalhousie University, Halifax, Nova Scotia, Canada 
Area:
genome evolution

154 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Gallot-Lavallée L, Jerlström-Hultqvist J, Zegarra-Vidarte P, Salas-Leiva DE, Stairs CW, Čepička I, Roger AJ, Archibald JM. Massive intein content in reveals aspects of intein mobility in eukaryotes. Proceedings of the National Academy of Sciences of the United States of America. 120: e2306381120. PMID 38019867 DOI: 10.1073/pnas.2306381120  0.616
2023 Collier JL, Rest JS, Gallot-Lavallée L, Lavington E, Kuo A, Jenkins J, Plott C, Pangilinan J, Daum C, Grigoriev IV, Filloramo GV, Novák Vanclová AMG, Archibald JM. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Current Biology : Cb. PMID 37913769 DOI: 10.1016/j.cub.2023.10.009  0.823
2023 Rius M, Rest JS, Filloramo GV, Novák Vanclová AMG, Archibald JM, Collier JL. Horizontal gene transfer and fusion spread carotenogenesis among diverse heterotrophic protists. Genome Biology and Evolution. PMID 36805209 DOI: 10.1093/gbe/evad029  0.809
2023 Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, ... ... Archibald JM, et al. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Biorxiv : the Preprint Server For Biology. PMID 36778228 DOI: 10.1101/2023.01.31.526407  0.314
2023 Zhang X, Hu Y, Cheng Z, Archibald JM. HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes. Star Protocols. 4: 102014. PMID 36633953 DOI: 10.1016/j.xpro.2022.102014  0.363
2022 Kim JI, Tanifuji G, Jeong M, Shin W, Archibald JM. Gene loss, pseudogenization, and independent genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics. Bmc Biology. 20: 227. PMID 36209116 DOI: 10.1186/s12915-022-01429-6  0.43
2022 Matthey-Doret C, Colp MJ, Escoll P, Thierry A, Moreau P, Curtis B, Sahr T, Sarrasin M, Gray MW, Lang BF, Archibald JM, Buchrieser C, Koszul R. Chromosome-scale assemblies of genomes provide insights into infection-related chromatin reorganization. Genome Research. PMID 36109147 DOI: 10.1101/gr.276375.121  0.815
2022 Hess S, Williams SK, Busch A, Irisarri I, Delwiche CF, de Vries S, Darienko T, Roger AJ, Archibald JM, Buschmann H, von Schwartzenberg K, de Vries J. A phylogenomically informed five-order system for the closest relatives of land plants. Current Biology : Cb. PMID 36055238 DOI: 10.1016/j.cub.2022.08.022  0.502
2022 Kim JI, Jo BY, Park MG, Yoo YD, Shin W, Archibald JM. Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes. Frontiers in Plant Science. 13: 896138. PMID 35769291 DOI: 10.3389/fpls.2022.896138  0.483
2022 Zhang X, Hu Y, Eme L, Maruyama S, Eveleigh RJM, Curtis BA, Sibbald SJ, Hopkins JF, Filloramo GV, van Wijk KJ, Archibald JM. TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. Star Protocols. 3: 101175. PMID 35243369 DOI: 10.1016/j.xpro.2022.101175  0.768
2022 Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, et al. Why sequence all eukaryotes? Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35042801 DOI: 10.1073/pnas.2115636118  0.39
2021 Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Author Correction: Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nature Communications. 12: 7350. PMID 34916502 DOI: 10.1038/s41467-021-27605-w  0.733
2021 Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nature Communications. 12: 6003. PMID 34650064 DOI: 10.1038/s41467-021-26077-2  0.76
2021 Filloramo GV, Curtis BA, Blanche E, Archibald JM. Re-examination of two diatom reference genomes using long-read sequencing. Bmc Genomics. 22: 379. PMID 34030633 DOI: 10.1186/s12864-021-07666-3  0.823
2021 Sibbald SJ, Lawton M, Archibald JM. Mitochondrial Genome Evolution in Pelagophyte Algae. Genome Biology and Evolution. 13. PMID 33675661 DOI: 10.1093/gbe/evab018  0.845
2020 Kim JI, Jeong M, Archibald JM, Shin W. Comparative Plastid Genomics of Non-Photosynthetic Chrysophytes: Genome Reduction and Compaction. Frontiers in Plant Science. 11: 572703. PMID 33013997 DOI: 10.3389/Fpls.2020.572703  0.562
2020 de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. Fems Microbiology Ecology. PMID 32918444 DOI: 10.1093/Femsec/Fiaa184  0.722
2020 Sibbald SJ, Eme L, Archibald JM, Roger AJ. Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes. Trends in Parasitology. PMID 32828660 DOI: 10.1016/J.Pt.2020.07.014  0.839
2020 Sibbald SJ, Archibald JM. Genomic insights into plastid evolution. Genome Biology and Evolution. PMID 32402068 DOI: 10.1093/Gbe/Evaa096  0.84
2020 Gallot-Lavallée L, Archibald JM. Phagocytosis in a Shape-shifting Bacterium. Trends in Microbiology. 28: 428-430. PMID 32396823 DOI: 10.1016/J.Tim.2020.02.017  0.306
2020 de Vries J, de Vries S, Curtis BA, Zhou H, Penny S, Feussner K, Pinto DM, Steinert M, Cohen A, von Schwartzenberg K, Archibald JM. Heat stress response in the closest algal relatives of land plants reveals conserved stress signaling circuits. The Plant Journal : For Cell and Molecular Biology. PMID 32333477 DOI: 10.1111/Tpj.14782  0.334
2020 Tanifuji G, Kamikawa R, Moore CE, Mills T, Onodera NT, Kashiyama Y, Archibald JM, Inagaki Y, Hashimoto T. Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis. Genome Biology and Evolution. PMID 31922581 DOI: 10.1093/Gbe/Evaa001  0.521
2019 Colp MJ, Archibald JM. Evolution: New Protist Predators under the Sun. Current Biology : Cb. 29: R936-R938. PMID 31593671 DOI: 10.1016/J.Cub.2019.08.029  0.789
2019 Archibald JM. Genomics reveals alga-associated cyanobacteria hiding in plain sight. Proceedings of the National Academy of Sciences of the United States of America. 116: 15757-15759. PMID 31341089 DOI: 10.1073/Pnas.1909788116  0.465
2019 Åsman AKM, Curtis BA, Archibald JM. Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae. Genome Biology and Evolution. PMID 30949682 DOI: 10.1093/Gbe/Evz064  0.337
2019 Grisdale CJ, Smith DR, Archibald JM. Relative mutation rates in nucleomorph-bearing algae. Genome Biology and Evolution. PMID 30859201 DOI: 10.1093/Gbe/Evz056  0.528
2019 Sibbald SJ, Hopkins JF, Filloramo GV, Archibald JM. Ubiquitin fusion proteins in algae: implications for cell biology and the spread of photosynthesis. Bmc Genomics. 20: 38. PMID 30642248 DOI: 10.1186/S12864-018-5412-4  0.8
2019 Kim JI, Shin H, Škaloud P, Jung J, Yoon HS, Archibald JM, Shin W. Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation. Bmc Evolutionary Biology. 19: 20. PMID 30634905 DOI: 10.1186/S12862-018-1316-9  0.485
2018 Cenci U, Sibbald SJ, Curtis BA, Kamikawa R, Eme L, Moog D, Henrissat B, Maréchal E, Chabi M, Djemiel C, Roger AJ, Kim E, Archibald JM. Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids. Bmc Biology. 16: 137. PMID 30482201 DOI: 10.1186/S12915-018-0593-5  0.82
2018 Lukeš J, Wheeler R, Jirsová D, David V, Archibald JM. Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. Iubmb Life. PMID 30291814 DOI: 10.1002/Iub.1894  0.308
2018 de Vries S, de Vries J, von Dahlen JK, Gould SB, Archibald JM, Rose LE, Slamovits CH. On plant defense signaling networks and early land plant evolution. Communicative & Integrative Biology. 11: 1-14. PMID 30214675 DOI: 10.1080/19420889.2018.1486168  0.665
2018 de Vries J, Archibald JM. Plastid genomes. Current Biology : Cb. 28: R336-R337. PMID 29689202 DOI: 10.1016/j.cub.2018.01.027  0.363
2018 Kim JI, Yoon HS, Yi G, Shin W, Archibald JM. Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements. Bmc Genomics. 19: 275. PMID 29678149 DOI: 10.1186/S12864-018-4626-9  0.522
2018 Cheng S, Melkonian M, Smith SA, Brockington S, Archibald JM, Delaux PM, Li FW, Melkonian B, Mavrodiev EV, Sun W, Fu Y, Yang H, Soltis DE, Graham SW, Soltis PS, et al. 10KP: A phylodiverse genome sequencing plan. Gigascience. 7: 1-9. PMID 29618049 DOI: 10.1093/Gigascience/Giy013  0.475
2018 de Vries J, Curtis BA, Gould SB, Archibald JM. Embryophyte stress signaling evolved in the algal progenitors of land plants. Proceedings of the National Academy of Sciences of the United States of America. PMID 29581286 DOI: 10.1073/Pnas.1719230115  0.358
2018 Raina JB, Eme L, Pollock FJ, Spang A, Archibald JM, Williams TA. Symbiosis in the microbial world: from ecology to genome evolution. Biology Open. 7. PMID 29472284 DOI: 10.1242/Bio.032524  0.443
2018 Nowak BF, Archibald JM. Opportunistic but Lethal: The Mystery of Paramoebae. Trends in Parasitology. PMID 29422444 DOI: 10.1016/J.Pt.2018.01.004  0.428
2018 de Vries J, Archibald JM. Plant evolution: landmarks on the path to terrestrial life. The New Phytologist. PMID 29318635 DOI: 10.1111/Nph.14975  0.342
2017 Archibald JM. Evolution: Protein Import in a Nascent Photosynthetic Organelle. Current Biology : Cb. 27: R1004-R1006. PMID 28950079 DOI: 10.1016/J.Cub.2017.08.013  0.393
2017 Tanifuji G, Cenci U, Moog D, Dean S, Nakayama T, David V, Fiala I, Curtis BA, Sibbald SJ, Onodera NT, Colp M, Flegontov P, Johnson-MacKinnon J, McPhee M, Inagaki Y, ... ... Archibald JM, et al. Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Scientific Reports. 7: 11688. PMID 28916813 DOI: 10.1038/S41598-017-11866-X  0.81
2017 Gentekaki E, Curtis BA, Stairs CW, Klimeš V, Eliáš M, Salas-Leiva DE, Herman EK, Eme L, Arias MC, Henrissat B, Hilliou F, Klute MJ, Suga H, Malik SB, Pightling AW, ... ... Archibald JM, et al. Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. Plos Biology. 15: e2003769. PMID 28892507 DOI: 10.1371/Journal.Pbio.2003769  0.837
2017 Kim JI, Moore CE, Archibald JM, Bhattacharya D, Yi G, Yoon HS, Shin W. Evolutionary Dynamics of Cryptophyte Plastid Genomes. Genome Biology and Evolution. 9: 1859-1872. PMID 28854597 DOI: 10.1093/Gbe/Evx123  0.583
2017 Sibbald SJ, Archibald JM. More protist genomes needed. Nature Ecology & Evolution. 1: 145. PMID 28812681 DOI: 10.1038/S41559-017-0145  0.829
2017 Kamikawa R, Moog D, Zauner S, Tanifuji G, Ishida KI, Miyashita H, Mayama S, Hashimoto T, Maier UG, Archibald JM, Inagaki Y. A non-photosynthetic diatom reveals early steps of reductive evolution in plastids. Molecular Biology and Evolution. PMID 28549159 DOI: 10.1093/Molbev/Msx172  0.777
2017 Muñoz-Gómez SA, Mejía-Franco FG, Durnin K, Colp M, Grisdale CJ, Archibald JM, Slamovits CH. The New Red Algal Subphylum Proteorhodophytina Comprises the Largest and Most Divergent Plastid Genomes Known. Current Biology : Cb. PMID 28528908 DOI: 10.1016/J.Cub.2017.04.054  0.827
2017 de Vries J, de Vries S, Slamovits CH, Rose LE, Archibald JM. How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae? Plant & Cell Physiology. PMID 28340089 DOI: 10.1093/Pcp/Pcx037  0.687
2017 Eme L, Gentekaki E, Curtis B, Archibald JM, Roger AJ. Lateral Gene Transfer in the Adaptation of the Anaerobic Parasite Blastocystis to the Gut. Current Biology : Cb. PMID 28262486 DOI: 10.1016/J.Cub.2017.02.003  0.631
2017 de Vries J, Archibald JM. Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium? Current Biology : Cb. 27: R103-R105. PMID 28171752 DOI: 10.1016/J.Cub.2016.12.006  0.391
2017 de Vries J, Archibald JM, Gould SB. The carboxy terminus of YCF1 contains a motif conserved throughout >500 million years of streptophyte evolution. Genome Biology and Evolution. PMID 28164224 DOI: 10.1093/Gbe/Evx013  0.55
2017 Sibbald SJ, Cenci U, Colp M, Eglit Y, O'Kelly CJ, Archibald JM. Diversity and Evolution of Paramoeba spp. and their Kinetoplastid Endosymbionts. The Journal of Eukaryotic Microbiology. PMID 28150358 DOI: 10.1111/Jeu.12394  0.776
2016 David V, Archibald JM. Evolution: Plumbing the Depths of Diplonemid Diversity. Current Biology : Cb. 26: R1290-R1292. PMID 27997843 DOI: 10.1016/J.Cub.2016.10.050  0.492
2016 Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nature Reviews. Microbiology. PMID 27867198 DOI: 10.1038/Nrmicro.2016.160  0.492
2016 Cenci U, Moog D, Curtis BA, Tanifuji G, Eme L, Lukeš J, Archibald JM. Heme pathway evolution in kinetoplastid protists. Bmc Evolutionary Biology. 16: 109. PMID 27193376 DOI: 10.1186/S12862-016-0664-6  0.79
2016 de Vries J, Stanton A, Archibald JM, Gould SB. Streptophyte Terrestrialization in Light of Plastid Evolution. Trends in Plant Science. PMID 26895731 DOI: 10.1016/J.Tplants.2016.01.021  0.41
2016 Tanifuji G, Archibald JM, Hashimoto T. Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics. Scientific Reports. 6: 21016. PMID 26888293 DOI: 10.1038/Srep21016  0.49
2015 David V, Flegontov P, Gerasimov E, Tanifuji G, Hashimi H, Logacheva MD, Maruyama S, Onodera NT, Gray MW, Archibald JM, Lukeš J. Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid. Mbio. 6. PMID 26628723 DOI: 10.1128/Mbio.01498-15  0.394
2015 Moog D, Rensing SA, Archibald JM, Maier UG, Ullrich KK. Localization and evolution of putative triose phosphate translocators in the diatom Phaeodactylum tricornutum. Genome Biology and Evolution. PMID 26454011 DOI: 10.1093/Gbe/Evv190  0.728
2015 Archibald JM. Endosymbiosis and Eukaryotic Cell Evolution. Current Biology : Cb. 25: R911-21. PMID 26439354 DOI: 10.1016/J.Cub.2015.07.055  0.463
2015 Archibald JM. Evolution: Gene transfer in complex cells. Nature. 524: 423-4. PMID 26287464 DOI: 10.1038/Nature15205  0.532
2015 Gile GH, Moog D, Slamovits CH, Maier UG, Archibald JM. Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes. Genome Biology and Evolution. 7: 1728-42. PMID 25994931 DOI: 10.1093/Gbe/Evv095  0.789
2015 Archibald JM. Genomic perspectives on the birth and spread of plastids. Proceedings of the National Academy of Sciences of the United States of America. 112: 10147-53. PMID 25902528 DOI: 10.1073/Pnas.1421374112  0.466
2014 McRose D, Guo J, Monier A, Sudek S, Wilken S, Yan S, Mock T, Archibald JM, Begley TP, Reyes-Prieto A, Worden AZ. Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages. The Isme Journal. 8: 2517-29. PMID 25171333 DOI: 10.1038/Ismej.2014.146  0.441
2014 Nakayama T, Kamikawa R, Tanifuji G, Kashiyama Y, Ohkouchi N, Archibald JM, Inagaki Y. 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. 111: 11407-12. PMID 25049384 DOI: 10.1073/Pnas.1405222111  0.53
2014 Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. Plos Biology. 12: e1001889. PMID 24959919 DOI: 10.1371/Journal.Pbio.1001889  0.828
2014 Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu Wong G, Melkonian M, Archibald JM. Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. Bmc Genomics. 15: 374. PMID 24885563 DOI: 10.1186/1471-2164-15-374  0.68
2014 Hirakawa Y, Suzuki S, Archibald JM, Keeling PJ, Ishida K. Overexpression of molecular chaperone genes in nucleomorph genomes. Molecular Biology and Evolution. 31: 1437-43. PMID 24603278 DOI: 10.1093/Molbev/Msu092  0.764
2014 Tanifuji G, Onodera NT, Moore CE, Archibald JM. Reduced nuclear genomes maintain high gene transcription levels. Molecular Biology and Evolution. 31: 625-35. PMID 24336878 DOI: 10.1093/Molbev/Mst254  0.52
2013 Eveleigh RJ, Meehan CJ, Archibald JM, Beiko RG. Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. Genome Biology and Evolution. 5: 2478-97. PMID 24281050 DOI: 10.1093/Gbe/Evt195  0.542
2013 Flegontov P, Votýpka J, Skalický T, Logacheva MD, Penin AA, Tanifuji G, Onodera NT, Kondrashov AS, Volf P, Archibald JM, Lukeš J. Paratrypanosoma is a novel early-branching trypanosomatid. Current Biology : Cb. 23: 1787-93. PMID 24012313 DOI: 10.1016/J.Cub.2013.07.045  0.501
2013 Smith DR, Hua J, Archibald JM, Lee RW. Palindromic genes in the linear mitochondrial genome of the nonphotosynthetic green alga Polytomella magna. Genome Biology and Evolution. 5: 1661-7. PMID 23940100 DOI: 10.1093/Gbe/Evt122  0.532
2013 Maruyama S, Eveleigh RJ, Archibald JM. Treetrimmer: a method for phylogenetic dataset size reduction. Bmc Research Notes. 6: 145. PMID 23587045 DOI: 10.1186/1756-0500-6-145  0.428
2013 Kim E, Archibald JM. Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov. Protist. 164: 160-82. PMID 23127606 DOI: 10.1016/J.Protis.2012.10.002  0.555
2013 Tanifuji G, Archibald JM. Nucleomorph comparative genomics Endosymbiosis. 197-213. DOI: 10.1007/978-3-7091-1303-5_11  0.339
2012 Nakayama T, Ishida K, Archibald JM. Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolytic reactions in the mitochondrion? Plos One. 7: e52340. PMID 23284996 DOI: 10.1371/Journal.Pone.0052340  0.582
2012 Hopkins JF, Spencer DF, Laboissiere S, Neilson JA, Eveleigh RJ, Durnford DG, Gray MW, Archibald JM. Proteomics reveals plastid- and periplastid-targeted proteins in the chlorarachniophyte alga Bigelowiella natans. Genome Biology and Evolution. 4: 1391-406. PMID 23221610 DOI: 10.1093/Gbe/Evs115  0.373
2012 Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, ... ... Archibald JM, et al. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 492: 59-65. PMID 23201678 DOI: 10.1038/Nature11681  0.832
2012 Moore CE, Curtis B, Mills T, Tanifuji G, Archibald JM. Nucleomorph genome sequence of the cryptophyte alga Chroomonas mesostigmatica CCMP1168 reveals lineage-specific gene loss and genome complexity. Genome Biology and Evolution. 4: 1162-75. PMID 23042551 DOI: 10.1093/Gbe/Evs090  0.561
2012 Onodera NT, Ryu J, Durbic T, Nislow C, Archibald JM, Rohde JR. Genome sequence of Shigella flexneri serotype 5a strain M90T Sm. Journal of Bacteriology. 194: 3022. PMID 22582379 DOI: 10.1128/Jb.00393-12  0.402
2012 Nakayama T, Archibald JM. Evolving a photosynthetic organelle. Bmc Biology. 10: 35. PMID 22531210 DOI: 10.1186/1741-7007-10-35  0.428
2012 Archibald JM. Lynn Margulis (1938–2011) Current Biology. 22: R4-R6. DOI: 10.1016/J.Cub.2011.12.003  0.477
2012 Archibald JM. The Evolution of Algae by Secondary and Tertiary Endosymbiosis Advances in Botanical Research. 64: 87-118. DOI: 10.1016/B978-0-12-391499-6.00003-7  0.467
2011 McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM. Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 810-7. PMID 21858844 DOI: 10.1002/Bies.201100045  0.427
2011 Lukeš J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW. How a neutral evolutionary ratchet can build cellular complexity. Iubmb Life. 63: 528-37. PMID 21698757 DOI: 10.1002/Iub.489  0.735
2011 Tanifuji G, Kim E, Onodera NT, Gibeault R, Dlutek M, Cawthorn RJ, Fiala I, Lukes J, Greenwood SJ, Archibald JM. Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiont. Eukaryotic Cell. 10: 1143-6. PMID 21666073 DOI: 10.1128/Ec.05027-11  0.62
2011 Doolittle WF, Lukeš J, Archibald JM, Keeling PJ, Gray MW. Comment on "Does constructive neutral evolution play an important role in the origin of cellular complexity?" DOI 10.1002/bies.201100010. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 427-9. PMID 21538416 DOI: 10.1002/Bies.201100039  0.743
2011 Maruyama S, Suzaki T, Weber AP, Archibald JM, Nozaki H. Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids. Bmc Evolutionary Biology. 11: 105. PMID 21501489 DOI: 10.1186/1471-2148-11-105  0.53
2011 Richards TA, Archibald JM. Cell evolution: gene transfer agents and the origin of mitochondria. Current Biology : Cb. 21: R112-4. PMID 21300273 DOI: 10.1016/J.Cub.2010.12.036  0.488
2011 Kim E, Harrison JW, Sudek S, Jones MD, Wilcox HM, Richards TA, Worden AZ, Archibald JM. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proceedings of the National Academy of Sciences of the United States of America. 108: 1496-500. PMID 21205890 DOI: 10.1073/Pnas.1013337108  0.6
2011 Tanifuji G, Onodera NT, Wheeler TJ, Dlutek M, Donaher N, Archibald JM. Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. Genome Biology and Evolution. 3: 44-54. PMID 21147880 DOI: 10.1093/Gbe/Evq082  0.555
2011 Archibald JM. Origin of eukaryotic cells: 40 years on Symbiosis. 54: 69-86. DOI: 10.1007/S13199-011-0129-Z  0.447
2010 Archibald JM, Richards TA. Gene transfer: anything goes in plant mitochondria. Bmc Biology. 8: 147. PMID 21176244 DOI: 10.1186/1741-7007-8-147  0.405
2010 Gray MW, Lukes J, Archibald JM, Keeling PJ, Doolittle WF. Cell biology. Irremediable complexity? Science (New York, N.Y.). 330: 920-1. PMID 21071654 DOI: 10.1126/Science.1198594  0.722
2010 Curtis BA, Archibald JM. A spliceosomal intron of mitochondrial DNA origin. Current Biology : Cb. 20: R919-20. PMID 21056829 DOI: 10.1016/J.Cub.2010.09.038  0.429
2010 Silver TD, Moore CE, Archibald JM. Nucleomorph ribosomal DNA and telomere dynamics in chlorarachniophyte algae. The Journal of Eukaryotic Microbiology. 57: 453-9. PMID 21040099 DOI: 10.1111/J.1550-7408.2010.00511.X  0.483
2010 Tanifuji G, Archibald JM. Actin gene family dynamics in cryptomonads and red algae. Journal of Molecular Evolution. 71: 169-79. PMID 20700735 DOI: 10.1007/S00239-010-9375-6  0.492
2010 Kim E, Archibald JM. Plastid evolution: gene transfer and the maintenance of 'stolen' organelles. Bmc Biology. 8: 73. PMID 20594287 DOI: 10.1186/1741-7007-8-73  0.619
2010 Kim E, Park JS, Simpson AG, Matsunaga S, Watanabe M, Murakami A, Sommerfeld K, Onodera NT, Archibald JM. Complex array of endobionts in Petalomonas sphagnophila, a large heterotrophic euglenid protist from Sphagnum-dominated peatlands. The Isme Journal. 4: 1108-20. PMID 20376101 DOI: 10.1038/Ismej.2010.40  0.589
2009 Donaher N, Tanifuji G, Onodera NT, Malfatti SA, Chain PS, Hara Y, Archibald JM. The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biology and Evolution. 1: 439-48. PMID 20333213 DOI: 10.1093/Gbe/Evp047  0.509
2009 Burki F, Inagaki Y, Bråte J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-Tabrizi K. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biology and Evolution. 1: 231-8. PMID 20333193 DOI: 10.1093/Gbe/Evp022  0.732
2009 Elias M, Archibald JM. Sizing up the genomic footprint of endosymbiosis. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 31: 1273-9. PMID 19921698 DOI: 10.1002/Bies.200900117  0.544
2009 Moore CE, Archibald JM. Nucleomorph genomes. Annual Review of Genetics. 43: 251-64. PMID 19686079 DOI: 10.1146/annurev-genet-102108-134809  0.423
2009 Archibald JM, Lane CE. Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. The Journal of Heredity. 100: 582-90. PMID 19617523 DOI: 10.1093/Jhered/Esp055  0.518
2009 Elias M, Archibald JM. The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus. Gene. 442: 63-72. PMID 19393304 DOI: 10.1016/J.Gene.2009.04.011  0.413
2009 Archibald JM. Genomics. Green evolution, green revolution. Science (New York, N.Y.). 324: 191-2. PMID 19359572 DOI: 10.1126/Science.1172972  0.471
2009 Archibald JM. The puzzle of plastid evolution. Current Biology : Cb. 19: R81-8. PMID 19174147 DOI: 10.1016/J.Cub.2008.11.067  0.421
2009 Ota S, Silver TD, Archibald JM, Ishida KI. Lotharella oceanica sp. nov. - A new planktonic chlorarachniophyte studied by light and electron microscopy Phycologia. 48: 315-323. DOI: 10.2216/09-02.1  0.537
2009 Archibald JM. The origin and spread of eukaryotic photosynthesis: Evolving views in light of genomics Botanica Marina. 52: 95-103. DOI: 10.1515/Bot.2008.060  0.443
2009 Lane CE, Archibald JM. Reply to Bodył, Stiller and Mackiewicz: "Chromalveolate plastids: direct descent or multiple endosymbioses?" Trends in Ecology and Evolution. 24: 121-122. DOI: 10.1016/J.Tree.2008.11.002  0.504
2009 Kim E, Archibald JM. Diversity and evolution of plastids and their genomes Plant Cell Monographs. 13: 1-40. DOI: 10.1007/978-3-540-68696-5_1  0.405
2008 Lane CE, Archibald JM. NEW MARINE MEMBERS OF THE GENUS HEMISELMIS (CRYPTOMONADALES, CRYPTOPHYCEAE)(1). Journal of Phycology. 44: 439-50. PMID 27041199 DOI: 10.1111/J.1529-8817.2008.00486.X  0.326
2008 Phipps KD, Donaher NA, Lane CE, Archibald JM. NUCLEOMORPH KARYOTYPE DIVERSITY IN THE FRESHWATER CRYPTOPHYTE GENUS CRYPTOMONAS(1). Journal of Phycology. 44: 11-4. PMID 27041033 DOI: 10.1111/J.1529-8817.2007.00434.X  0.505
2008 Archibald JM. The eocyte hypothesis and the origin of eukaryotic cells. Proceedings of the National Academy of Sciences of the United States of America. 105: 20049-50. PMID 19091952 DOI: 10.1073/Pnas.0811118106  0.414
2008 Archibald JM. Plastid evolution: remnant algal genes in ciliates. Current Biology : Cb. 18: R663-R665. PMID 18682209 DOI: 10.1016/J.Cub.2008.06.031  0.476
2008 Kim E, Lane CE, Curtis BA, Kozera C, Bowman S, Archibald JM. Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). Bmc Genomics. 9: 215. PMID 18474103 DOI: 10.1186/1471-2164-9-215  0.636
2008 Keeling PJ, Archibald JM. Organelle evolution: what's in a name? Current Biology : Cb. 18: R345-7. PMID 18430636 DOI: 10.1016/J.Cub.2008.02.065  0.704
2008 Khan H, Archibald JM. Lateral transfer of introns in the cryptophyte plastid genome. Nucleic Acids Research. 36: 3043-53. PMID 18397952 DOI: 10.1093/Nar/Gkn095  0.478
2008 Lane CE, Archibald JM. The eukaryotic tree of life: endosymbiosis takes its TOL. Trends in Ecology & Evolution. 23: 268-75. PMID 18378040 DOI: 10.1016/J.Tree.2008.02.004  0.539
2008 Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, Archibald JM, Worden AZ. Widespread distribution of a unique marine protistan lineage. Environmental Microbiology. 10: 1621-34. PMID 18341584 DOI: 10.1111/J.1462-2920.2008.01580.X  0.566
2008 Fong A, Archibald JM. Evolutionary dynamics of light-independent protochlorophyllide oxidoreductase genes in the secondary plastids of cryptophyte algae. Eukaryotic Cell. 7: 550-3. PMID 18178774 DOI: 10.1128/Ec.00396-07  0.396
2007 Lane CE, van den Heuvel K, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM. 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. 104: 19908-13. PMID 18077423 DOI: 10.1073/Pnas.0707419104  0.52
2007 Bhattacharya D, Archibald JM, Weber AP, Reyes-Prieto A. How do endosymbionts become organelles? Understanding early events in plastid evolution. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 29: 1239-46. PMID 18027391 DOI: 10.1002/Bies.20671  0.438
2007 Silver TD, Koike S, Yabuki A, Kofuji R, Archibald JM, Ishida K. Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algae. The Journal of Eukaryotic Microbiology. 54: 403-10. PMID 17910684 DOI: 10.1111/J.1550-7408.2007.00279.X  0.659
2007 Adl SM, Leander BS, Simpson AG, Archibald JM, Anderson OR, Bass D, Bowser SS, Brugerolle G, Farmer MA, Karpov S, Kolisko M, Lane CE, Lodge DJ, Mann DG, Meisterfeld R, et al. Diversity, nomenclature, and taxonomy of protists. Systematic Biology. 56: 684-9. PMID 17661235 DOI: 10.1080/10635150701494127  0.768
2007 Khan H, Parks N, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM. 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. 24: 1832-42. PMID 17522086 DOI: 10.1093/Molbev/Msm101  0.561
2007 Archibald JM. Nucleomorph genomes: structure, function, origin and evolution. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 29: 392-402. PMID 17373660 DOI: 10.1002/Bies.20551  0.537
2007 Khan H, Kozera C, Curtis BA, Bussey JT, Theophilou S, Bowman S, Archibald JM. Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae. Journal of Molecular Evolution. 64: 223-36. PMID 17211547 DOI: 10.1007/S00239-006-0088-9  0.525
2007 Archibald J. Genomics and Evolution of Microbial Eukaryotes. Edited by Laura A Katz and , Debashish Bhattacharya. Oxford and New York: Oxford University Press. $110.00. xi + 243 p; ill.; index. ISBN: 0‐19‐856974‐2. 2006. The Quarterly Review of Biology. 82: 275-276. DOI: 10.1086/523144  0.308
2006 Archibald JM. Algal genomics: exploring the imprint of endosymbiosis. Current Biology : Cb. 16: R1033-5. PMID 17174910 DOI: 10.1016/J.Cub.2006.11.008  0.534
2006 Lane CE, Archibald JM. Novel nucleomorph genome architecture in the cryptomonad genus hemiselmis. The Journal of Eukaryotic Microbiology. 53: 515-21. PMID 17123416 DOI: 10.1111/J.1550-7408.2006.00135.X  0.477
2006 Ruiz-Trillo I, Lane CE, Archibald JM, Roger AJ. Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. The Journal of Eukaryotic Microbiology. 53: 379-84. PMID 16968456 DOI: 10.1111/J.1550-7408.2006.00118.X  0.657
2006 Archibald JM. Endosymbiosis: double-take on plastid origins. Current Biology : Cb. 16: R690-2. PMID 16950094 DOI: 10.1016/J.Cub.2006.08.006  0.362
2006 Archibald JM. Genome complexity in a lean, mean photosynthetic machine. Proceedings of the National Academy of Sciences of the United States of America. 103: 11433-4. PMID 16868076 DOI: 10.1073/Pnas.0605255103  0.464
2006 Lane CE, Khan H, MacKinnon M, Fong A, Theophilou S, Archibald JM. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Insight into the diversity and evolution of the cryptomonad nucleomorph genome. Molecular Biology and Evolution. 23: 856-65. PMID 16306383 DOI: 10.1093/Molbev/Msj066  0.54
2006 Bhattacharya D, Archibald JM. Response to Theissen and Martin Current Biology. 16: R1017-R1018. DOI: 10.1016/J.Cub.2006.11.021  0.433
2005 Archibald JM. Jumping genes and shrinking genomes--probing the evolution of eukaryotic photosynthesis with genomics. Iubmb Life. 57: 539-47. PMID 16118111 DOI: 10.1080/15216540500167732  0.538
2005 Patron NJ, Waller RF, Archibald JM, Keeling PJ. Complex protein targeting to dinoflagellate plastids. Journal of Molecular Biology. 348: 1015-24. PMID 15843030 DOI: 10.1016/J.Jmb.2005.03.030  0.775
2005 Kim JC, Ou YY, Badano JL, Esmail MA, Leitch CC, Fiedrich E, Beales PL, Archibald JM, Katsanis N, Rattner JB, Leroux MR. MKKS/BBS6, a divergent chaperonin-like protein linked to the obesity disorder Bardet-Biedl syndrome, is a novel centrosomal component required for cytokinesis. Journal of Cell Science. 118: 1007-20. PMID 15731008 DOI: 10.1242/Jcs.01676  0.32
2005 ARCHIBALD JM. Phagotrophy in chlorarachniophyte algae: implications for eukaryotic genome evolution The Journal of Eukaryotic Microbiology. 52: 7S-27S. DOI: 10.1111/J.1550-7408.2005.05202003_1_5.X  0.503
2004 Keeling PJ, Archibald JM, Fast NM, Palmer JD. Comment on "The evolution of modern eukaryotic phytoplankton". Science (New York, N.Y.). 306: 2191; author reply 2. PMID 15618503 DOI: 10.1126/Science.1103879  0.684
2004 Rogers MB, Archibald JM, Field MA, Li C, Striepen B, Keeling PJ. Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natans. The Journal of Eukaryotic Microbiology. 51: 529-35. PMID 15537087 DOI: 10.1111/J.1550-7408.2004.Tb00288.X  0.744
2004 Archibald JM, Keeling PJ. Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens. The Journal of Eukaryotic Microbiology. 51: 113-8. PMID 15068273 DOI: 10.1111/J.1550-7408.2004.Tb00172.X  0.709
2003 Longet D, Archibald JM, Keeling PJ, Pawlowski J. Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. International Journal of Systematic and Evolutionary Microbiology. 53: 1735-9. PMID 14657101 DOI: 10.1099/Ijs.0.02597-0  0.671
2003 Archibald JM, Rogers MB, Toop M, Ishida K, Keeling PJ. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proceedings of the National Academy of Sciences of the United States of America. 100: 7678-83. PMID 12777624 DOI: 10.1073/Pnas.1230951100  0.808
2003 Archibald JM, Teh EM, Keeling PJ. Novel ubiquitin fusion proteins: ribosomal protein P1 and actin. Journal of Molecular Biology. 328: 771-8. PMID 12729753 DOI: 10.1016/S0022-2836(03)00374-7  0.639
2003 Archibald JM, Keeling PJ. Comparative genomics. Plant genomes: cyanobacterial genes revealed. Heredity. 90: 2-3. PMID 12522415 DOI: 10.1038/Sj.Hdy.6800204  0.712
2003 Archibald JM, Longet D, Pawlowski J, Keeling PJ. A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Molecular Biology and Evolution. 20: 62-6. PMID 12519907 DOI: 10.1093/Molbev/Msg006  0.684
2002 Archibald JM, Keeling PJ. Recycled plastids: a 'green movement' in eukaryotic evolution. Trends in Genetics : Tig. 18: 577-84. PMID 12414188 DOI: 10.1016/S0168-9525(02)02777-4  0.692
2002 Archibald JM, Roger AJ. Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals. Journal of Molecular Evolution. 55: 232-45. PMID 12107599 DOI: 10.1007/S00239-002-2321-5  0.589
2002 Archibald JM, O'Kelly CJ, Doolittle WF. The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution. Molecular Biology and Evolution. 19: 422-31. PMID 11919283 DOI: 10.1093/Oxfordjournals.Molbev.A004097  0.736
2002 Archibald JM, Roger AJ. Gene duplication and gene conversion shape the evolution of archaeal chaperonins. Journal of Molecular Biology. 316: 1041-50. PMID 11884142 DOI: 10.1006/Jmbi.2002.5409  0.597
2001 Archibald JM, Blouin C, Doolittle WF. Gene duplication and the evolution of group II chaperonins: implications for structure and function. Journal of Structural Biology. 135: 157-69. PMID 11580265 DOI: 10.1006/Jsbi.2001.4353  0.724
2001 Archibald JM, Cavalier-Smith T, Maier U, Douglas S. Molecular chaperones encoded by a reduced nucleus: the cryptomonad nucleomorph. Journal of Molecular Evolution. 52: 490-501. PMID 11443352 DOI: 10.1007/S002390010179  0.386
2000 Archibald JM, Logsdon JM, Doolittle WF. Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes. Molecular Biology and Evolution. 17: 1456-66. PMID 11018153 DOI: 10.1093/Oxfordjournals.Molbev.A026246  0.728
1999 Archibald JM, Logsdon JM, Doolittle WF. Recurrent paralogy in the evolution of archaeal chaperonins. Current Biology : Cb. 9: 1053-6. PMID 10508614 DOI: 10.1016/S0960-9822(99)80457-6  0.733
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