Saw Microbial Diversity Lab

[* denotes equal contribution]

Published

  1. Kumar RS, Galvis F, Wasson BJ, Saw JH, Oline DK, Barja JL, Ushijima B, Koyack MJ, Prado S, Videau P. Draft genome sequence of Vibrio ostreicida strain pp-203, the type strain of a pathogen that infects bivalve larvae. Microbiol Resour Announc. 2020;9(35).
  2. Loughran RM, Mitchell EA, Vining OB, Gallegos DA, Deadmond MC, Wasson BJ, Pfannmuller KM, Paddock BE, Koyack MJ, Oline DK, Ushijima B, Saw JH, McPhail KL, Videau P. Draft genome sequence of Streptomyces sp. Strain ventii, isolated from a microbial mat near hydrothermal vents within the axial seamount in the pacific ocean, and resequencing of the type strains Streptomyces lonarensis ncl 716 and Streptomyces bohaiensis 11A07. Microbiol Resour Announc. 2020;9(32).
  3. Loughran RM, Esquivel AR, Deadmond MC, Koyack MJ, Paddock BE, O’Hanlon SM, Ushijima B, Saw JH, Videau P. Draft genome sequence of Vibrio sp. Strain OCN044, isolated from Palmyra Atoll, northern line islands. Microbiol Resour Announc. 2020;9(12).
  4. Saw JHW, Nunoura T, Hirai M, Takaki Y, Parsons R, Michelsen M, Longnecker K, Kujawinski EB, Stepanauskas R, Landry Z, Carlson CA, Giovannoni SJ. Pangenomics analysis reveals diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria. mBio. 2020;11(1).
  5. Giovannoni SJ, Halsey KH, Saw J, Muslin O, Suffridge CP, Sun J, Lee CP, Moore ER, Temperton B, Noell SE. A parasitic arsenic cycle that shuttles energy from phytoplankton to heterotrophic bacterioplankton. mBio. 2019;10(2).
  6. Spang A, Eme L, Saw JH, Caceres EF, Zaremba-Niedzwiedzka K, Lombard J, Guy L, Ettema TJG. Asgard archaea are the closest prokaryotic relatives of eukaryotes. PLoS Genet. 2018;14(3):e1007080.
  7. Zaremba-Niedzwiedzka K*, Caceres EF*, Saw JH*, Backstrom D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. 2017;541(7637):353–8.
  8. Baker BJ, Saw JH, Lind AE, Lazar CS, Hinrichs KU, Teske AP, Ettema TJ. Genomic inference of the metabolism of cosmopolitan subsurface archaea, Hadesarchaea. Nat Microbiol. 2016;1:16002.
  9. Saw JH, Spang A, Zaremba-Niedzwiedzka K, Juzokaite L, Dodsworth JA, Murugapiran SK, Colman DR, Takacs-Vesbach C, Hedlund BP, Guy L, Ettema TJ. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. Philos Trans R Soc Lond B Biol Sci. 2015;370(1678):20140328.
  10. Zepeda VK, Busse HJ, Golke J, Saw JHW, Alam M, Donachie SP. Terasakiispira papahanaumokuakeensis gen. nov., sp. nov., a gammaproteobacterium from Pearl and Hermes Atoll, Northwestern Hawaiian Islands. Int J Syst Evol Microbiol. 2015;65(10):3609–17.
  11. Spang A*, Saw JH*, Jorgensen SL*, Zaremba-Niedzwiedzka K*, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. 2015;521(7551):173–9.
  12. Guy L, Saw JH, Ettema TJ. The archaeal legacy of eukaryotes: A phylogenomic perspective. Cold Spring Harb Perspect Biol. 2014;6(10):a016022.
  13. Guy L, Spang A, Saw JH, Ettema TJ. ’Geoarchaeote NAG1’ is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum. ISME J. 2014;8(7):1353–7.
  14. Spang A, Martijn J, Saw JH, Lind AE, Guy L, Ettema TJ. Close encounters of the third domain: The emerging genomic view of archaeal diversity and evolution. Archaea. 2013;2013:202358.
  15. Saw JH, Schatz M, Brown MV, Kunkel DD, Foster JS, Shick H, Christensen S, Hou S, Wan X, Donachie SP. Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. Nov., from a lava cave in Kilauea Caldera, Hawai’i. PLoS One. 2013;8(10):e76376.
  16. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY, Donachie SP. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai’i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol. 2013;63(Pt 9):3280–6.
  17. Saw JH, Yuryev A, Kanbe M, Hou S, Young AG, Aizawa S, Alam M. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium. Stand Genomic Sci. 2012;6(1):84–93.
  18. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. Assembling the marine metagenome, one cell at a time. PLoS One. 2009;4(4):e5299.
  19. Saw JH, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G, Wu J, Galperin MY, Koonin EV, Makarova KS, Wolf YI, Rigden DJ, Dunfield PF, Wang L, Alam M. Encapsulated in silica: Genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol. 2008;9(11):R161.
  20. Suzuki JY, Tripathi S, Fermín GA, Jan F-J, Hou S, Saw JH, Ackerman CM, Yu Q, Schatz MC, Pitz KY, Yépes M, Fitch MMM, Manshardt RM, Slightom JL, Ferreira SA, Salzberg SL, Alam M, Ming R, Moore PH, Gonsalves D. Characterization of insertion sites in rainbow papaya, the first commercialized transgenic fruit crop. Tropical Plant Biology. 2008 Dec 1;1(3):293–309.
  21. Hou S*, Makarova KS*, Saw JH*, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M. Complete genome sequence of the extremely acidophilic methanotroph isolate v4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct. 2008;3:26.
  22. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Perez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452(7190):991–6.
  23. Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y, Wang J, Mountain BW, Crowe MA, Weatherby TM, Bodelier PL, Liesack W, Feng L, Wang L, Alam M. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature. 2007;450(7171):879–82.
  24. Yu Q, Hou S, Feltus FA, Jones MR, Murray JE, Veatch O, Lemke C, Saw JH, Moore RC, Thimmapuram J, Liu L, Moore PH, Alam M, Jiang J, Paterson AH, Ming R. Low x/y divergence in four pairs of papaya sex-linked genes. Plant J. 2008;53(1):124–32.
  25. Chen C, Yu Q, Hou S, Li Y, Eustice M, Skelton RL, Veatch O, Herdes RE, Diebold L, Saw J, Feng Y, Qian W, Bynum L, Wang L, Moore PH, Paull RE, Alam M, Ming R. Construction of a sequence-tagged high-density genetic map of papaya for comparative structural and evolutionary genomics in brassicales. Genetics. 2007;177(4):2481–91.
  26. Yu Q, Hou S, Hobza R, Feltus FA, Wang X, Jin W, Skelton RL, Blas A, Lemke C, Saw JH, Moore PH, Alam M, Jiang J, Paterson AH, Vyskot B, Ming R. Chromosomal location and gene paucity of the male specific region on papaya y chromosome. Mol Genet Genomics. 2007;278(2):177–85.
  27. Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Pikina A, Galperin MY, Koonin EV, Makarova KS, Omelchenko MV, Sorokin A, Wolf YI, Li QX, Keum YS, Campbell S, Denery J, Aizawa S, Shibata S, Malahoff A, Alam M. Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A. 2004;101(52):18036–41.
  28. Yu HS, Saw JH, Hou S, Larsen RW, Watts KJ, Johnson MS, Zimmer MA, Ordal GW, Taylor BL, Alam M. Aerotactic responses in bacteria to photoreleased oxygen. FEMS Microbiol Lett. 2002;217(2):237–42.

Home