Donachie Lab

Ph.D. candidate
Department of Microbiology
University of Hawai'i
Honolulu, HI 96822
jimmy@hawaii.edu

• Ph.D. (2004-present), University of Hawaii at Manoa
• M.S. (2004), University of Hawaii at Manoa
• B.S. (2002), University of Hawaii at Manoa

• (2007-2009) Graduate Research Assistant, Los Alamos National Laboratory, Los Alamos, NM, USA

• Lewis and Clark Fund for Exploration and Field Research in Astrobiology (2009)
• AbGradCon travel grant (2009)
• Metagenomics 2008 travel grant (2008)

• Traveled to Hawaii Volcanoes National Park in 2009 to collect biofilm samples from a lava tube cave in Kilauea Crater.
• Traveled twice in 2000 to Kalaupapa, Molokai, Hawaii to collect water samples from Lake Kauhako, a meromictic lake.

1. Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R (2009). Assembling the marine metagenome, one cell at a time. PLoS ONE. 4(4):e5299.
2. 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 (2008). Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop. Tropical Plant Biology. 1: 293-309.
3. 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 (2008). Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol. 9(11):R161.
   
4. 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 (2008). Complete genome sequence of the extremely acidophilic methanotroph isolate V4, "Methylacidiphilum infernorum", a representative of the bacterial phylum Verrucomicrobia. Biol Direct. 3(1):26. * - co-first authors
   
5. 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-Pérez 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 (2008). The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 452(7190):991-6.
6. 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 (2008). Low X/Y divergence in four pairs of papaya sex-linked genes. Plant J. 53(1):124-32.
7. 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 (2007). Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature. 450(7171):879-82.
   
8. Chen C, Yu Q, Hou S, Li Y, Eustice M, Skelton RL, Veatch O, Herdes R, Diebold L, Saw J, Feng Y, Qian W, Bynum L, Wang L, Moore PH, Paull RE, Alam M, Ming R (2007). Construction of a Sequence-Tagged High Density Genetic Map of Papaya. Genetics. 177(4):2481-91.
9. 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 (2007). Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol Genet Genomics. 278(2):177-85.
10. Hou S, Saw JH, Lee KS, Freitas TA, Belisle C, Kawarabayasi Y, Donachie SP, Galperin MY, Koonin EV, Makarova KS, Omelchenko MV, Sorokin A, Wolf Y, Li Q, Keum YS, Campbell S, Denery J, Aizawa S-I, Shibata S, Malahoff A and Alam M (2004). 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. USA. 101 (52): 18036-18041.
11. Yu HS, Saw JH, Hou S, Larsen RW, Watts KJ, Johnson MS, Zimmer MA, Ordal GW, Taylor BL, Alam M (2002). Aerotactic responses in bacteria to photoreleased oxygen. FEMS Microbiol Lett. 217(2):237-42.