University of Hawai`i ASGPB

Prescott, R.D., Chan, Y.L., Tong, E.J., Bunn, F., Onouye, C.T., Handel, C., Lo, C.C., Davenport, K., Johnson, S., Flynn, M., Saito, J.A., Lee Jr, H., Wong, K., Lawson, B.N., Hiura, K., Sager, K., Sadones, M., Hill, E.C., Esibill, D., Cockell, C.S., Santomartino, R., Chain, P.S.G., Decho, A.W., Donachie, S.P. 2023. Bridging place-based astrobiology education with genomics, including descriptions of three novel bacterial species isolated from Mars analog sites of cultural relevance. Astrobiology. 23(12):1348-1367.
Wan, X., Saito, J.A., Hou, S., Geib, S.M., Yuryev, A., Higa, L.M., Womersley, C.Z., & Alam, M. 2021. The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation. Commun Biol. 4(1):1232.
Zhang, M., Lv, Y., Hou, S., Liu, Y., Wang, Y., & Wan, X. 2021. Differential mucosal microbiome profiles across stages of human colorectal cancer. Life. 11(8):831.
Wang, Y., Wan, X., Wu, X., Zhang, C., Liu, J., & Hou, S. 2021. Eubacterium rectale contributes to colorectal cancer initiation via promoting colitis. Gut Pathog. 13(1):2.
Uz Zaman, K.A., Wu, X., Hu, Z., Yoshida, W., Hou, S., Saito, J., Avad, K.A., Hevener, K.E., Alumasa, J.N., & Cao, S. 2021. Antibacterial kaneoheoic acids A-F from a Hawaiian fungus Fusarium sp. FM701. Phytochemistry. 181:112545.
Wang, Y., Zhang, C., Hou, S., Wu, X., Liu, J., & Wan, X. 2020. Analyses of potential driver and passenger bacteria in human colorectal cancer. Cancer Manag Res. 12:11553-11561.
Wang, C., Wu, X., Bai, H., Zaman, K.A.U., Hou, S., Saito, J., Wongwiwatthananukit, S., Kim, K.S., & Cao, S. 2020. Antibacterial and NF-κB inhibitory lumazine peptides, aspochalasin, γ-butyrolactone derivatives, and cyclic peptides from a Hawaiian Aspergillus flavipes. J Nat Prod. 83(7):2233-2240.
Zaman, K.A.U., Hu, Z., Wu, X., Hou, S., Saito, J., Kondratyuk, T.P., Pezzuto, J.M., & Cao, S. 2020. NF-κB inhibitory and antibacterial helvolic and fumagillin derivatives from Aspergillus terreus. J Nat Prod. 83(3):730-737.
Koster, K.J., Largen, A., Foster, J.T., Drees, K.P., Qian, L., Desmond, E., Wan, X., Hou, S., & Douglas, J.T. 2018. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infect Dis. 18(1):608.
Koster, K., Largen, A., Foster, J.T., Drees, K.P., Qian, L., Desmond, E.P., Wan, X., Hou, S., & Douglas, J.T. 2018. Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii. PLoS One. 13(7):e0201146.
Hayashi, K., Busse, H.J., Golke, J., Anderson, J., Wan, X., Hou, S., Chain, P.S.G., Prescott, R.D., & Donachie, S.P. 2018. Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera. Int J Syst Evol Microbiol. 68(1):35-41.
Wan, X., Darris, M., Hou, S., & Donachie, S.P. 2017. Draft genome sequence of a novel Chitinophaga sp. strain, MD30, isolated from a biofilm in an air conditioner condensate pipe. Genome Announc. 5(42):e01161-17.
Wan, X., Saito, J.A., Newhouse, J.S., Hou, S., & Alam, M. 2017. The importance of conserved amino acids in heme-based globin-coupled diguanylate cyclases. PLoS One. 12(8):e0182782.
Wan, X., Koster, K., Qian, L., Desmond, E., Brostrom, R., Hou, S., & Douglas, J. 2017. Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis. PLoS One. 12(4):e0175330.
Wang, Y., Zhang, C., Zhang, S., Zhao, Z., Wang, J., Song, J., Wang, Y., Liu, J., & Hou, S. 2017. Kanglaite sensitizes colorectal cancer cells to Taxol via NF-κB inhibition and connexin 43 upregulation. Sci Rep. 7:1280.
Islam, M.S., Saito, J.A., Emdad, E.M., Ahmed, B., Islam, M.M., Halim, A., Hossen, Q.M.M., Hossain, M.Z., Ahmed, R., Hossain, M.S., Kabir, S.M.T., Khan, M.S.A., Khan, M.M., Hasan, R., Aktar, N., Honi, U., Islam, R., Rashid, M.M., Wan, X., Hou, S., Haque, T., Azam, M.S., Moosa, M.M., Elias, S.M., Hasan, A.M.M., Mahmood, N, Shafiuddin, M., Shahid, S., Shommu, N.S., Jahan, S., Roy, S., Chowdhury, A., Akhand, A.I., Nisho, G.M., Uddin, K.S., Rabeya, T., Hoque, S.M.E., Snigdha, A.R., Mortoza, S., Matin, S.A., Islam, M.K., Lashkar, M.Z.H., Zaman, M., Yuryev, A., Uddin, M.K., Rahman, M.S., Haque, M.S., Alam, M.M., Khan, H., & Alam, M. 2017. Comparative genomics of two jute species and insight into fibre biogenesis. Nat Plants. 3:16223.
Wan, X., Hou, S., Hayashi, K., Anderson, J., & Donachie, S.P. 2016. Genome sequence of Rheinheimera salexigens sp. nov. isolated from a fishing hook off O’ahu, Hawai’i. Genome Announc. 4(6):e01390-16.
Wan, X., Hou, S., Burns, S.L., Saito, J.A., & Donachie, S.P. 2016. Draft genome sequence of a novel Marinobacter sp. strain from Honolulu Harbor, Hawai’i. Genome Announc. 4(6):e01354-16.
Wan, X., Lee, A.J., Hou, S., Ushijima, B., Nguyen, Y.P., Thawley, J.A., & Donachie, S.P. 2016. Draft genome sequence of Piscirickettsia litoralis, isolated from seawater. Genome Announc. 4(6):e01252-16.
Wan, X., Miller, J.M., Rowley, S.J., Hou, S., & Donachie, S.P. 2016. Draft genome sequence of a novel Luteimonas sp. strain from coral mucus, Hawai’i. Genome Announc. 4(6):e01228-16.
Wan, X., Dasilveira, L., Hou, S., Saito, J.A., & Donachie, S.P. 2016. Draft genome sequence of Terasakiispira papahanaumokuakeensis PH27AT, a spiral bacterium from the Northwestern Hawaiian Islands. Genome Announc. 4(5):e01166-16.
Wan, X., Hou, S., Saito, J.A., Kaneshiro, K.Y., & Donachie, S.P. 2015. Genome sequence of Flavobacterium akiainvivens IK-1T, isolated from decaying Wikstroemia oahuensis, an endemic Hawaiian shrub. Genome Announc. 3(5):e01222-15.
Teh, B.S., Lau, N.S., Ng, F.L., Abdul Rahman, A.Y., Wan, X., Saito, J.A., Hou, S., Teh, A.H., Najimudin, N., & Alam, M. 2015. Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. Stand Genomic Sci. 10:76.
Teh, A. H., Saito, J.A., Najimudin, N., & Alam, M. 2015. Open and Lys-His hexacoordinated closed structures of a globin with swapped proximal and distal sites. Sci Rep. 5:11407.
Wan, X., Hou, S., Phan, N., Malone Moss, J.S., Donachie, S.P., & Alam, M. 2015. Draft genome sequence of Pantoea anthophila strain 11-2 from hypersaline Lake Laysan, Hawaii. Genome Announc. 3(3):e00321-15.
Wan, X., Qian, L., Hou, S., Drees, K.P., Foster, J.T., & Douglas, J.T. 2014. Complete genome sequences of Beijing and Manila family strains of Mycobacterium tuberculosis. Genome Announc. 2(6):e01135-14.
Geib, S.M., Calla, B., Hall, B., Hou, S., & Manoukis, N.C. 2014. Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics. 15:942.

Mukhametov, A., Newhouse, E.I., Ab Aziz, N., Saito, J.A., & Alam, M. 2014. Allosteric pocket of the dengue virus (serotype 2) NS2B/NS3 protease: In silico ligand screening and molecular dynamics studies of inhibition. J Mol Graph Model. 52:103-113.
Jamil, F., Teh, A.H., Schadich, E., Saito, J.A., Najimudin, N., & Alam, M. 2014. Crystal structure of truncated hemoglobin from an extremely thermophilic and acidophilic bacterium. J Biochem. 156(2):97-106.
Saw, J.H., Schatz, M., Brown, M.V., Kunkel, D.D., Foster, J.S., Shick, H., Christensen, S., Hou, S., Wan, X., & Donachie, S.P. 2013. Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai’i. PLoS One. 8(10):e76376.
Mchunu, N.P., Permaul, K., Abdul Rahman, A.Y., Saito, J.A., Singh, S., & Alam, M. 2013. Xylanase superproducer: genome sequence of a compost-loving thermophilic fungus, Thermomyces lanuginosus strain SSBP. Genome Announc. 1(3) e00388-13.
Mchunu, N.P., Permaul, K., Alam, M., & Singh, S. 2013. Carbon utilization of a thermophilic fungus, Thermomyces lanuginosus using phenotypic microarray. Adv Biosci Biotech. 4:24-32.
Abdul Rahman, A.Y., Usharraj, A.O., Misra, B.B., Thottathil, G.P., Jayasekaran, K., Feng, Y., Hou, S., Ong, S.Y., Ng, F.L., Lee, L.S., Tan, H.S., Muhd Sakaff, M.K.L., Teh, B.S., Khoo, B.F., Badai, S.S., Ab Aziz, N., Yuryev, A., Knudsen, B., Dionne-Laporte, A., Mchunu, N.P., Yu, Q., Langston, B.J., Freitas, T.A.K., Young, A.G., Chen, R., Wang, L., Najimudin, N., Saito, J.A., & Alam, M. 2013. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics. 14:75.
Ong, S.Y., Pratap, C.B., Wan, X., Hou, S., Abdul Rahman, A.Y., Saito, J.A., Nath, G., & Alam, M. 2013. The genomic blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12. Stand Genomic Sci. 7(3):483-496.
Islam, M.S., Haque, M.S., Islam, M.M., Emdad, E.M., Halim, A., Hossen, Q.M.M., Hossain, M.Z., Ahmed, B., Rahim, S., Rahman, M.S., Alam, M.M., Hou, S., Wan, X., Saito, J.A., & Alam, M. 2012. Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. BMC Genomics. 13:493.
Wang, J., Na, J.K., Yu, Q., Gschwend, A.R., Han, J., Zeng, F., Aryal, R., Vanburen, R., Murray, J.E., Zhang, W., Navajas-Pérez, R., Feltus, F.A., Lemke, C., Tong, E.J., Chen, C., Man Wai, C., Singh, R., Wang, M.L., Min, X.J., Alam, M., Charlesworth, D., Moore, P.H., Jiang, J., Paterson, A.H., & Ming, R. 2012. Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc Natl Acad Sci USA. 109:13710-13715.
Saw, J.H.W., Yuryev, A., Kanbe, M., Hou, S., Young, A.G., Aizawa, S.I., & Alam, M. 2012. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium. Stand Genomic Sci. 6(1):84-93.
Ong, S.Y., Pratap, C.B., Wan, X., Hou, S., Abdul Rahman, A.Y., Saito, J.A., Nath, G., & Alam, M. 2012. Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12. J Bacteriol. 194(8):2115-2116.
Teh, B.S., Abdul Rahman, A.Y., Saito, J.A., Hou, S., & Alam, M. 2012. Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1. J Bacteriol. 194(5):1240.
Muhd Sakaff, M.K.L., Abdul Rahman, A.Y., Saito, J.A., Hou, S., & Alam, M. 2012. Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5. J Bacteriol. 194(5):1239.
Teh, A.H., Saito, J.A., Baharuddin, A., Tuckerman, J.R., Newhouse, J.S., Kanbe, M., Newhouse, E.I., Rahim, R.A., Favier, F., Didierjean, C., Sousa, E.H., Stott, M.B., Dunfield, P.F., Gonzalez, G., Gilles-Gonzalez, M.A., Najimudin, N., & Alam, M. 2011. Hell’s Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin. FEBS Lett. 585:3250-3258.
Yu, Q., Tong, E., Skelton, R.L., Bowers, J.E., Jones, M.R., Murray, J.E., Hou, S., Guan, P., Acob, R.A., Luo, M.C., Moore, P.H., Alam, M., Paterson, A.H., & Ming, R. 2009. A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics. 10:371.
Wan, X., Tuckerman, J.R., Saito, J.A., Freitas, T.A.K., Newhouse, J.S., Denery, J.R., Galperin, M.Y., Gonzalez, G., Gilles-Gonzalez, M.-A., & Alam, M. 2009. Globins synthesize the second messenger bis-(3′-5′)-cyclic diguanosine monophosphate in bacteria. J Mol Biol. 388:262-270.
Fritzinger, D.C., Hew, B.E., Lee, J.Q., Newhouse, J., Alam, M., Ciallella, J.R., Bowers, M., Gorsuch, W.B., Guikema, B.J., Stahl, G.L., & Vogel, C.W. 2008. Derivatives of human complement component C3 for therapeutic complement depletion: a novel class of therapeutic agents. Adv Exp Med Biol. 632:293-307.
Shakirov, E.V., Salzberg, S.L., Alam, M., & Shippen, D.E. 2008. Analysis of Carica papaya telomeres and telomere-associated proteins: insights into the evolution of telomere maintenance in Brassicales. Trop Plant Biol. 1:202-215.
Nelson, D.R., Ming, R., Alam, M., & Schuler, M.A. 2008. Comparison of cytochrome P450 genes from six plant genomes. Trop Plant Biol. 1:216-235.
Paull, R.E., Irikura, B., Wu, P., Turano, H., Chen, N.J., Blas, A., Fellman, J.K., Gschwend, A.R., Wai, C.M., Yu, Q., Presting, G., Alam, M., & Ming, R. 2008. Fruit development, ripening and quality related genes in the papaya genome. Trop Plant Biol. 1:246-277.
Wang, J., Chen, C., Na, J.-K., Yu, Q., Hou, S., Paull, R.E., Moore, P.H., Alam, M., & Ming, R. 2008. Genome-wide comparative analysis of microsatellites in papaya. Trop Plant Biol. 1:278-292.
Suzuki, J.Y., Tripathi, S., Fermín, G.A., Jan, F.-J., Hou, S., Saw, J.H., Ackerman, C.M., Yu, Q., Schatz, M.C., Pitz, K.Y., Yépes, M., Fitch, M.M.M., Manshardt, R.M., Slightom, J.L., Ferreira, S.A., Salzberg, S.L., Alam, M., Ming, R., Moore, P.H., & Gonsalves, D. 2008. Characterization of insertion sites in Rainbow papaya, the first commercialized transgenic fruit crop. Trop Plant Biol. 1:293-309.
Saw, J.H., Mountain, B.W., Feng, L., Omelchenko, M.V., Hou, S., Saito, J.A., Stott, M.B., Li, D., Zhao, G., Wu, J., Galperin, M.Y., Koonin, E.V., Makarova, K.S., Wolf, Y.I., Rigden, D.J., Dunfield, P.F., Wang, L., & Alam, M. 2008. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol. 9(11):R161.
Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D., & Freeling, M. 2008. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids. Plant Phys. 148(4):1772-1781.
Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R., & Lisch, D. 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18:1924-1937.
Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M., & Paterson, A.H. 2008. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18:1944-1954.
Othman, R., Kiat, T.S., Khalid, N., Yusof, R., Newhouse, E.I., Newhouse, J.S., Alam, M., & Rahman, N.A. 2008. Docking of noncompetitive inhibitors into dengue virus type 2 protease: understanding the interactions with allosteric binding sites. J Chem Inf Model. 48(8):1582-1591.
Hou, S., Makarova, K.S., Saw, J.H., Senin, P., Ly, B.V., Zhou, Z., Ren, Y., Wang, J., Galperin, M.Y., Omelchenko, M.V., Wolf, Y.I., Yutin, N., Koonin, E.V., Stott, M.B., Mountain, B.W., Crowe, M.A., Smirnova, A.V., Dunfield, P.F., 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. 3:26.
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. 582(13):1840-1846.
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. 10(8):2030-2041.
Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M., & Paterson, A.H. 2008. Synteny and collinearity in plant genomes. Science. 320(5875):486-488.
Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J.H., Senin, P., Wang, W., Ly, B.V., Lewis, K.L.T., Salzberg, S.L., Feng, L., Jones, M.R., Skelton, R.L., Murray, J.E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Tang, H., Lyons, E., Paull, R.E., Michael, T.P., Wall, K., Rice, D., Albert, H., Wang, M.L., Zhu, Y.J., Schatz, M., Nagarajan, N., Acob, R.A., Guan, P., Blas, A., Wai, C.M., Ackerman, C.M., Ren, Y., Liu, C., Wang, J., Wang, J., Na, J.K., Shakirov, E.V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J.E., Gschwend, A.R., Delcher, A.L., Singh, R., Suzuki, J.Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M.J., Feltus, F.A., Porter, B., Li, Y., Burroughs, A.M., Luo, M.C., Liu, L., Christopher, D.A., Mount, S.M., Moore, P.H., Sugimura, T., Jiang, J., Schuler, M.A., Friedman, V., Mitchell-Olds, T., Shippen, D.E., dePamphilis, C.W., Palmer, J.D., Freeling, M., Paterson, A.H., Gonsalves, D., Wang, L., & Alam, M. 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 Genet Genomes. 4(2):333-341.
Saito, J.A., Freitas, T.A.K., & Alam, M. 2008. Cloning, expression, and purification of the N-terminal heme-binding domain of globin-coupled sensors. Methods Enzymol. 437:163-172.
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.
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.
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.
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.
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. Proc Natl Acad Sci USA. 101(52):18036-18041.

Wan, X., Saito, J.A., Hou, S., Geib, S.M., Yuryev, A., Higa, L.M., Womersley, C.Z., & Alam, M. 2021. The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation. Commun Biol. 4(1):1232.

Zhang, M., Lv, Y., Hou, S., Liu, Y., Wang, Y., & Wan, X. 2021. Differential mucosal microbiome profiles across stages of human colorectal cancer. Life. 11(8):831.

Wang, Y., Wan, X., Wu, X., Zhang, C., Liu, J., & Hou, S. 2021. Eubacterium rectale contributes to colorectal cancer initiation via promoting colitis. Gut Pathog. 13(1):2.

Uz Zaman, K.A., Wu, X., Hu, Z., Yoshida, W., Hou, S., Saito, J., Avad, K.A., Hevener, K.E., Alumasa, J.N., & Cao, S. 2021. Antibacterial kaneoheoic acids A-F from a Hawaiian fungus Fusarium sp. FM701. Phytochemistry. 181:112545.

Wang, Y., Zhang, C., Hou, S., Wu, X., Liu, J., & Wan, X. 2020. Analyses of potential driver and passenger bacteria in human colorectal cancer. Cancer Manag Res. 12:11553-11561.

Wang, C., Wu, X., Bai, H., Zaman, K.A.U., Hou, S., Saito, J., Wongwiwatthananukit, S., Kim, K.S., & Cao, S. 2020. Antibacterial and NF-κB inhibitory lumazine peptides, aspochalasin, γ-butyrolactone derivatives, and cyclic peptides from a Hawaiian Aspergillus flavipes. J Nat Prod. 83(7):2233-2240.

Zaman, K.A.U., Hu, Z., Wu, X., Hou, S., Saito, J., Kondratyuk, T.P., Pezzuto, J.M., & Cao, S. 2020. NF-κB inhibitory and antibacterial helvolic and fumagillin derivatives from Aspergillus terreus. J Nat Prod. 83(3):730-737.

Koster, K.J., Largen, A., Foster, J.T., Drees, K.P., Qian, L., Desmond, E., Wan, X., Hou, S., & Douglas, J.T. 2018. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infect Dis. 18(1):608.

Koster, K., Largen, A., Foster, J.T., Drees, K.P., Qian, L., Desmond, E.P., Wan, X., Hou, S., & Douglas, J.T. 2018. Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii. PLoS One. 13(7):e0201146.

Hayashi, K., Busse, H.J., Golke, J., Anderson, J., Wan, X., Hou, S., Chain, P.S.G., Prescott, R.D., & Donachie, S.P. 2018. Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera. Int J Syst Evol Microbiol. 68(1):35-41.

Wan, X., Darris, M., Hou, S., & Donachie, S.P. 2017. Draft genome sequence of a novel Chitinophaga sp. strain, MD30, isolated from a biofilm in an air conditioner condensate pipe. Genome Announc. 5(42):e01161-17.

Wan, X., Saito, J.A., Newhouse, J.S., Hou, S., & Alam, M. 2017. The importance of conserved amino acids in heme-based globin-coupled diguanylate cyclases. PLoS One. 12(8):e0182782.

Wan, X., Koster, K., Qian, L., Desmond, E., Brostrom, R., Hou, S., & Douglas, J. 2017. Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis. PLoS One. 12(4):e0175330.

Wang, Y., Zhang, C., Zhang, S., Zhao, Z., Wang, J., Song, J., Wang, Y., Liu, J., & Hou, S. 2017. Kanglaite sensitizes colorectal cancer cells to Taxol via NF-κB inhibition and connexin 43 upregulation. Sci Rep. 7:1280.

Wan, X., Hou, S., Hayashi, K., Anderson, J., & Donachie, S.P. 2016. Genome sequence of Rheinheimera salexigens sp. nov. isolated from a fishing hook off O’ahu, Hawai’i. Genome Announc. 4(6):e01390-16.

Wan, X., Hou, S., Burns, S.L., Saito, J.A., & Donachie, S.P. 2016. Draft genome sequence of a novel Marinobacter sp. strain from Honolulu Harbor, Hawai’i. Genome Announc. 4(6):e01354-16.

Wan, X., Lee, A.J., Hou, S., Ushijima, B., Nguyen, Y.P., Thawley, J.A., & Donachie, S.P. 2016. Draft genome sequence of Piscirickettsia litoralis, isolated from seawater. Genome Announc. 4(6):e01252-16.

Wan, X., Miller, J.M., Rowley, S.J., Hou, S., & Donachie, S.P. 2016. Draft genome sequence of a novel Luteimonas sp. strain from coral mucus, Hawai’i. Genome Announc. 4(6):e01228-16.

Wan, X., Dasilveira, L., Hou, S., Saito, J.A., & Donachie, S.P. 2016. Draft genome sequence of Terasakiispira papahanaumokuakeensis PH27AT, a spiral bacterium from the Northwestern Hawaiian Islands. Genome Announc. 4(5):e01166-16.

Wan, X., Hou, S., Saito, J.A., Kaneshiro, K.Y., & Donachie, S.P. 2015. Genome sequence of Flavobacterium akiainvivens IK-1T, isolated from decaying Wikstroemia oahuensis, an endemic Hawaiian shrub. Genome Announc. 3(5):e01222-15.

Teh, B.S., Lau, N.S., Ng, F.L., Abdul Rahman, A.Y., Wan, X., Saito, J.A., Hou, S., Teh, A.H., Najimudin, N., & Alam, M. 2015. Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. Stand Genomic Sci. 10:76.

Teh, A. H., Saito, J.A., Najimudin, N., & Alam, M. 2015. Open and Lys-His hexacoordinated closed structures of a globin with swapped proximal and distal sites. Sci Rep. 5:11407.

Wan, X., Hou, S., Phan, N., Malone Moss, J.S., Donachie, S.P., & Alam, M. 2015. Draft genome sequence of Pantoea anthophila strain 11-2 from hypersaline Lake Laysan, Hawaii. Genome Announc. 3(3):e00321-15.

Wan, X., Qian, L., Hou, S., Drees, K.P., Foster, J.T., & Douglas, J.T. 2014. Complete genome sequences of Beijing and Manila family strains of Mycobacterium tuberculosis. Genome Announc. 2(6):e01135-14.

Geib, S.M., Calla, B., Hall, B., Hou, S., & Manoukis, N.C. 2014. Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. BMC Genomics. 15:942.

Mukhametov, A., Newhouse, E.I., Ab Aziz, N., Saito, J.A., & Alam, M. 2014. Allosteric pocket of the dengue virus (serotype 2) NS2B/NS3 protease: In silico ligand screening and molecular dynamics studies of inhibition. J Mol Graph Model. 52:103-113.

Jamil, F., Teh, A.H., Schadich, E., Saito, J.A., Najimudin, N., & Alam, M. 2014. Crystal structure of truncated hemoglobin from an extremely thermophilic and acidophilic bacterium. J Biochem. 156(2):97-106.

Saw, J.H., Schatz, M., Brown, M.V., Kunkel, D.D., Foster, J.S., Shick, H., Christensen, S., Hou, S., Wan, X., & Donachie, S.P. 2013. Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai’i. PLoS One. 8(10):e76376.

Mchunu, N.P., Permaul, K., Abdul Rahman, A.Y., Saito, J.A., Singh, S., & Alam, M. 2013. Xylanase superproducer: genome sequence of a compost-loving thermophilic fungus, Thermomyces lanuginosus strain SSBP. Genome Announc. 1(3) e00388-13.

Mchunu, N.P., Permaul, K., Alam, M., & Singh, S. 2013. Carbon utilization of a thermophilic fungus, Thermomyces lanuginosus using phenotypic microarray. Adv Biosci Biotech. 4:24-32.

Ong, S.Y., Pratap, C.B., Wan, X., Hou, S., Abdul Rahman, A.Y., Saito, J.A., Nath, G., & Alam, M. 2013. The genomic blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12. Stand Genomic Sci. 7(3):483-496.

Saw, J.H.W., Yuryev, A., Kanbe, M., Hou, S., Young, A.G., Aizawa, S.I., & Alam, M. 2012. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium. Stand Genomic Sci. 6(1):84-93.

Ong, S.Y., Pratap, C.B., Wan, X., Hou, S., Abdul Rahman, A.Y., Saito, J.A., Nath, G., & Alam, M. 2012. Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12. J Bacteriol. 194(8):2115-2116.

Teh, B.S., Abdul Rahman, A.Y., Saito, J.A., Hou, S., & Alam, M. 2012. Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1. J Bacteriol. 194(5):1240.

Muhd Sakaff, M.K.L., Abdul Rahman, A.Y., Saito, J.A., Hou, S., & Alam, M. 2012. Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5. J Bacteriol. 194(5):1239.

Yu, Q., Tong, E., Skelton, R.L., Bowers, J.E., Jones, M.R., Murray, J.E., Hou, S., Guan, P., Acob, R.A., Luo, M.C., Moore, P.H., Alam, M., Paterson, A.H., & Ming, R. 2009. A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics. 10:371.

Wan, X., Tuckerman, J.R., Saito, J.A., Freitas, T.A.K., Newhouse, J.S., Denery, J.R., Galperin, M.Y., Gonzalez, G., Gilles-Gonzalez, M.-A., & Alam, M. 2009. Globins synthesize the second messenger bis-(3′-5′)-cyclic diguanosine monophosphate in bacteria. J Mol Biol. 388:262-270.

Shakirov, E.V., Salzberg, S.L., Alam, M., & Shippen, D.E. 2008. Analysis of Carica papaya telomeres and telomere-associated proteins: insights into the evolution of telomere maintenance in Brassicales. Trop Plant Biol. 1:202-215.

Nelson, D.R., Ming, R., Alam, M., & Schuler, M.A. 2008. Comparison of cytochrome P450 genes from six plant genomes. Trop Plant Biol. 1:216-235.

Paull, R.E., Irikura, B., Wu, P., Turano, H., Chen, N.J., Blas, A., Fellman, J.K., Gschwend, A.R., Wai, C.M., Yu, Q., Presting, G., Alam, M., & Ming, R. 2008. Fruit development, ripening and quality related genes in the papaya genome. Trop Plant Biol. 1:246-277.

Wang, J., Chen, C., Na, J.-K., Yu, Q., Hou, S., Paull, R.E., Moore, P.H., Alam, M., & Ming, R. 2008. Genome-wide comparative analysis of microsatellites in papaya. Trop Plant Biol. 1:278-292.

Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D., & Freeling, M. 2008. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids. Plant Phys. 148(4):1772-1781.

Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R., & Lisch, D. 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18:1924-1937.

Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M., & Paterson, A.H. 2008. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18:1944-1954.

Othman, R., Kiat, T.S., Khalid, N., Yusof, R., Newhouse, E.I., Newhouse, J.S., Alam, M., & Rahman, N.A. 2008. Docking of noncompetitive inhibitors into dengue virus type 2 protease: understanding the interactions with allosteric binding sites. J Chem Inf Model. 48(8):1582-1591.

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. 582(13):1840-1846.

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. 10(8):2030-2041.

Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M., & Paterson, A.H. 2008. Synteny and collinearity in plant genomes. Science. 320(5875):486-488.

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 Genet Genomes. 4(2):333-341.

Saito, J.A., Freitas, T.A.K., & Alam, M. 2008. Cloning, expression, and purification of the N-terminal heme-binding domain of globin-coupled sensors. Methods Enzymol. 437:163-172.

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.

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.