Shaobin Hou
Advanced Studies in Genomics, Proteomics and Bioinformatics
University of Hawaii
2538 McCarthy Mall, Snyder Hall 312
Honolulu, HI 96822
(808) 956-8039 (phone)
(808) 956-0925 (fax)
shaobin@hawaii.edu

Education

Ph.D. Microbiology      2000    University of Hawaii at Manoa 

1. Microbial Genome Sequencing

Microbes have evolved for some 3.8 billion years and are found in virtually every environment, surviving and thriving in extremes of heat, cold, radiation, pressure, salt, acidity, and darkness. The diversity and range of their environmental adaptations indicate that microbes “solved” many problems long time ago for which scientists are still actively seeking solutions. Knowledge about the enormous range of microbial capacities has broad and far-reaching implications for environmental, energy, health, and industrial applications.  Researchers now are starting to apply the tools of genomics to studying this enormous untapped natural treasure. It becomes real to sequence more genomes as the next-generation Sequencers become available.

We employ the whole-genome random shotgun approach to produce high-quality draft sequence. Three insert size libraries will be constructed for each genome sequencing project, including 3-Kb, 8-Kb, and 40-Kb DNA libraries. Paired end sequences will be produced by sequencing from both sides of the library insert. Typically, we generate approximately 10-fold coverage. Raw sequences are assembled using various genome assemblers to produce the primary draft assembly, which consists of contigs linked into larger scaffolds by paired-end information.  Finishing work including gap closing, quality improvement, and assembly verification will be performed if necessary. GLIMMER is used for Protein-coding gene prediction, followed by BLASTX searches of intergenic regions between predicted ORFs. Transfer RNAs will be predicted by tRNAscan-SE. Genome annotation will be performed by running BLAST and PSI-BLAST against the NCBI protein database and the COG database with manual verification. Metabolic pathways will be analyzed by comparing COG assignments with the standard sets of COGs involved in each pathway.

2.  ASGPB DNA Sequencing Service

The ASGPB Genomics Laboratory has been in operation as a high-throughput "user friendly" DNA sequencing core lab since May of 2005.  The facility is currently open to any University of Hawaii researcher, as well as researchers outside UH. We are committed to specifically support high-throughput projects such as genome-wide analyses and will assist with the preparation of relevant grant applications. In addition, we will provide assistance with sequence assembly and bioinformatic analysis of sequencing projects.
We also provide genotyping service for researchers conducting studies with fluorescently labeled primers. All genotyping samples are run on an Applied Biosystems 3730XL Genetic Analyzer. We are able to process a number of marker types including microsatellites, AFLPs, SNPs, and tRFLPs, etc.

The ASGPB website (http://asgpb.mhpcc.hawaii.edu) facilitates access to numerous international genomics centers and web-based bioinformatics tools with high computational capacity. More importantly, the link provides up-to-date access to major NCBI databases, including all completed bacterial and eukaryotic genomes, conserved domain and protein structural databases (CDD, COG, SMART, PFAM), and enables rapid batch analysis of large sequence compilations using the BLAST, ClustalW and Pfam algorithms. In addition, a collection of smaller analysis tools (EMBOSS, JEMBOSS, Primer3, etc.) is available. 

Publications

Saito, J.A., Wan, X., Lee, K.S., Hou, S., Alam, M.  2008.  Globin-coupled sensors and protoglobins share a common signaling mechanism.  FEBS Lett.  In press.

Stott, M.B., Crowe, M.A., Mountain, B.W., Smirnova, A.V., Hou, S., Alam, M., Dunfield, P.F.  2008.  Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand.  Environ Microbiol.  In press.

Ming, R., Hou, S., et al.  2008.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).  Nature.  452(7190):991-996.

Eustice, M., Yu, Q., Lai, C.W., Hou, S., Thimmapuram, J., Liu, L., Alam, M., Moore, P.H., Presting, G.G., & Ming, M.  2008.  Development and application of microsatellite markers for genomic analysis of papaya.  Tree Genetics and Genomics.  4:333-341.

Yu, Q., Hou, S., Feltus, F.A., Jones, M.R., Murray, J.E., Veatch, O., Lemke, C., Saw, J.H., Moore, R.C., Thimmapuram, J., Liu, L., Moore, P.H., Alam, M., Jiang, J., Paterson, A.H., & Ming, R.  2008. Low X/Y divergence in four pairs of papaya sex-linked genes.  Plant J.  53(1):124-132.

Dunfield, P.F., Yuryev, A., Senin, P., Smirnova, A.V., Stott, M.B., Hou, S., Ly, B., Saw, J.H., Zhou, Z., Ren, Y., Wang, J., Mountain, B.W., Crowe, M.A., Weatherby, T.M., Bodelier, P.L., Liesack, W., Feng, L., Wang, L. & Alam, M.  2007.  Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia.  Nature. 450(7171):879-882.

Freitas, T.A.K., Saito, J.A., Wan, X., Hou, S., & Alam, M.  2007.  Protoglobin and globin-coupled sensors.  In Ghosh, A. (Ed.)  The smallest biomolecules: diatomics and their interactions with heme proteins.  pp. 175-202.

Chen, C., Yu, Q., Hou, S., Li, Y., Eustice, M., Skelton, R.L., Veatch, O., Herdes, R., Diebold, L., Saw, J., Feng, Y., Qian, W., Bynum, L., Wang, L., Moore, P.H., Paull, R.E., Alam, M. & Ming, R.  2007.  Construction of a Sequence-Tagged High Density Genetic Map of Papaya for Comparative Structural and Evolutionary Genomics in Brassicales.  Genetics.  177(4):2481-2491.

Yu, Q., Hou, S., Hobza, R., Feltus, F.A., Wang, X., Jin, W., Skelton, R.L., Blas, A., Lemke, C., Saw, J.H., Moore, P.H., Alam, M., Jiang, J., Paterson, A.H., Vyskot, B. & Ming, R.  2007.  Chromosomal location and gene paucity of the male specific region on papaya Y chromosome.  Mol Genet Genomics.  278(2):177-185.

Lai, C.W., Yu, Q., Hou, S., Skelton, R.L., Jones, M.R., Lewis, K.L., Murray, J., Eustice, M., Guan, P., Agbayani, R., Moore, P.H., Ming, R., & Presting, G.G.  2006.  Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome.  Mol Genet Genomics.  276(1):1-12.

Freitas, T.A., Saito, J.A., Hou, S., & Alam, M.  2005.  Globin-coupled sensors, protoglobins, and the last universal common ancestor.  J Inorg Biochem. 99(1):23-33.

Hou, S., Saw, J.H., Lee, K.S., Freitas, T.A., Belisle, C., Kawarabayasi, Y., Donachie, S.P., Galperin, M.Y., Koonin, E.V., Makarova, K.S., Omelchenko, M.V., Sorokin, A., Wolf, Y.I., Li, Q., Keum, Y.S., Campbell, S., Denery, J., Aizawa, S.-I., Shibata, S., Malahoff, A., & Alam, M.  2004.  Genome Sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy.  Pro Natl Acad Sci USA.  101(52):18036-18041.

Donachie, S.P., Hou, S., Lee, K.S., Riley, C.W., Pikina, A., Belisle, C., Kempe, S., Gregory, T.S., Bossuyt, A., Boerema, J., Liu, J., Freitas, T.A., Malahoff, A., & Alam, M.  2004.  The Hawaiian Archipelago: a microbial diversity hotspot.  Microb Ecol.  48(4):509-520.

Freitas, T.A.K., Hou, S., Dioum, E.M., Saito, J.A., Newhouse, J., Gonzalez, G., Gilles-Gonzalez, M., & Alam, M.  2004.  Ancestral Hemoglobins in Archaea.  Proc Natl Acad Sci USA.  101(17):6675-6680.

Donachie, S.P., Hou, S., Gregory, T.S., Malahoff, A., & Alam, M.  2003.  Idiomarina loihiensis, sp. nov., a novel, halophilic γ-proteobacterium from the Loihi submarine volcano, Hawai'i.  Int J Syst Evol Microbiol. 53: 1873-1879.

Freitas, T.A., Hou, S., & Alam, M.  2003.  The Diversity of Globin-Coupled Sensors. FEBS Lett.  552(2-3):99-104.

Boudko, D., Yu, H.S., Ruiz, M., Hou, S., & Alam, M.  2003.  A time-lapse capillary assay to study aerotaxis in the archaeon Halobacterium salinarum.  J Microbiol Methods.  53(1):123-126.

Yu, H.S., Saw, J.H., Hou, S., Larsen, R.W., Watts, K.J., Johnson, M.S., Zimmer, M.A., Ordal, G.W., Taylor, B.L., & Alam, M.  2002.  Aerotactic responses in bacteria to photoreleased oxygen.  FEMS Microbiol Lett.  217(2):237-242.

Hou, S., Belisle, C., Lam, S., Piatibratov, M., Sivozhelezov, V., Takami, H., & Alam, M.  2001.  A globin-coupled oxygen sensor from the facultatively alkaliphilic Bacillus halodurans C-125.  Extremophiles.  5(5):351-354.

Hou, S., Freitas, T., Larsen, R.W., Piatibratov, M., Sivozhelezov, V., Yamamoto, A., Meleshkevitch, E.A., Zimmer, M., Ordal, G.W., & Alam, M.  2001.  Globin-coupled sensors: a class of heme-containing sensors in Archaea and Bacteria.  Proc Natl Acad Sci USA.  98(16):9353-9358.

Piatibratov, M., Hou, S., Brooun, A., Yang, J., Chen, H., & Alam, M.  2000.  Expression and fast-flow purification of a polyhistidine-tagged myoglobin-like aerotaxis transducer.  Biochim Biophys Acta.  1524(2-3):149-154.

Ng, W.V., Kennedy, S.P., Mahairas, G.G., Berquist, B., Pan, M., Shukla, H.D., Lasky, S.R., Baliga, N.S., Thorsson, V., Sbrogna, J., Swartzell, S., Weir, D., Hall, J., Dahl, T.A., Welti, R., Goo, Y.A., Leithauser, B., Keller, K., Cruz, R., Danson, M.J., Hough, D.W., Maddocks, D.G., Jablonski, P.E., Krebs, M.P., Angevine, C.M., Dale, H., Isenbarger, T.A., Peck, R.F., Pohlschroder, M., Spudich, J.L., Jung, K.W., Alam, M., Freitas, T., Hou, S., Daniels, C.J., Dennis, P.P., Omer, A.D., Ebhardt, H., Lowe, T.M., Liang, P., Riley, M., Hood, L., & DasSarma, S.  2000.  Genome sequence of Halobacterium species NRC-1.  Proc Natl Acad Sci USA.  24;97(22):12176-12181.

Hou, S., Larsen, R.W., Boudko, D., Riley, C.W., Karatan, E., Zimmer, M., Ordal, G.W., & Alam, M.  2000.  Myoglobin-like aerotaxis transducers in Archaea and Bacteria.  Nature.  403(6769):540-544.

Larsen, R.W., Yang, J., Hou, S., Helms, M.K., Jameson, D.M., & Alam, M.  1999.  Spectroscopic characterization of two soluble transducers from the Archaeon Halobacterium salinarum.  J Protein Chem.  18(3):269-275.

Hou, S., Brooun, A., Yu, H.S., Freitas, T., & Alam, M.  1998.  Sensory rhodopsin II transducer HtrII is also responsible for serine chemotaxis in the archaeon Halobacterium salinarum.  J Bacteriol.  180(6):1600-1602.