2008

• 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.
• 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 Genetics and Genomes.  4:333-341.
• 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.
• Nardini, M., Pesce, A., Thijs, L., Saito, J.A., Dewilde, S., Alam, M., Ascenzi, P., Coletta, M., Ciaccio, C., Moens, L., & Bolognesi, M.  2008.  Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity.  EMBO Rep.  9(2):157-163.
• 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.

2007

• 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.
• Thijs, L., Vinck, E., Bolli, A., Trandafir, F., Wan, X., Hoogewijs, D., Coletta, M., Fago, A., Weber, R.E., Van Doorslaer, S., Ascenzi, P., Alam, M., Moens, L. & Dewilde, S.  2007.  Characterization of a globin coupled sensor with a gene regulating function.  J Biol Chem.  282(52):37325-37340.
• 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.

2006

• Donachie, S.P., Bowman, J.P. & Alam, M.  2006.  Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake.  Int J Syst Evol Microbiol. 56(Pt 3):563-567.

2005

• Shibata, S., Alam, M., & Aizawa, S-I.  2005.  Flagellar Filaments of the Deep-sea Bacteria Idiomarina loihiensis Belong to a Family Different from those of Salmonella typhimurium.  J Mol Biol.  352:510-516.
• Donachie, S. P., Bowman, J. P., On, S. L. W., & Alam, M.  2005.  Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter.  Int J Syst Evol Microbiol.  55(Pt 3):1271-1277.
• 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.

2004

• 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.
• Donachie, S.P., Bowman, J.P., & Alam, M.  2004.  Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga-Flavobacterium-Bacteroides group bacterium from an Hawaiian hypersaline lake.  Int J Syst Evol Microbiol. 54: 935-940.
• 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.

2003

• 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.

2002

• Donachie, S.P., Christenson, B.W., Kunkel, D.D., Malahoff, A., & Alam, M.  2002.  Microbial community in acidic hydrothermal waters of volcanically active White Island, New Zealand.  Extremophiles.  6(5):419-425.
• Malahoff, A., Gregory, T., Bossuyt, A., Donachie, S., & Alam, M.  2002.  A seamless sytem for the collection and cultivation of extremophiles from deep-ocean hydrothermal vents.  IEEE J Ocea. Eng.  27:862-869.
• 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.

2001

• 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.

2000

• 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.

1999

• 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.

1998

• 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.
• Brooun, A., Bell, J., Freitas, T., Larsen, R.W., & Alam, M.  1998.  An archaeal aerotaxis transducer combines subunit I core structures of eukaryotic cytochrome c oxidase and eubacterial methyl-accepting chemotaxis proteins.  J Bacteriol.  180(7):1642-1646.
• Muthyala, R.S., Alam, M., & Liu, R.S.  1998.  Alkylated Azulenic Retinal and Bacteriorhodopsin Analogs.  Tetrahedron Letters.  39:5-8.
• Bell, J.R., Muthyala, R.S., Larsen, R.W., Alam, M., & Liu, R.S.  1998.  Photoactivities of the Red-Shifted Azulenic Bacteriorhodopsin Analogues.  J Phys Chem.  102:5481-5483.

1997

• Yu, H.S. & Alam, M.  1997.  An agarose-in-plug bridge method to study chemotaxis in the Archaeon Halobacterium salinarium.  FEMS Microbiol Lett.  156:256-269.
• Brooun, A., Zhang, W., & Alam, M.  1997.  Primary structure and functional studies of the soluble transducer HtrXI from the Archaeon Halobacterium salinarium.  J Bacteriol.  179:2963-2968.
• Zhu, J., Spudich, E.N., Alam, M., & Spudich, J.L.  1997.  Effects of substitutions D73E, D73N, D103N and V106M on signaling and pH titration of sensory rhodopsin II.  Photochem Photobiol.  66(6):788-791.
• Spudich, E.N., Zhang, W., Alam, M., & Spudich, J.L.  1997.  Constitutive signaling by the phototaxis receptor sensory rhodopsin II from disruption of its protonated Schiff base-Asp-73 interhelical salt bridge.  Proc Natl Acad Sci USA.  94:4960-4965.

1996

• Zhang, W., Brooun, A., McCandless, J., Banda, P., & Alam, M.  1996.  Signal Transduction in the Archaeon Halobacterium salinarum is processed through three subfamilies of thirteen soluble and membrane-bound transducer proteins.  Proc Natl Acad Sci USA.  93: 4649-4654.
• Zhang, W., Brooun, A., Mueller, M.M., & Alam, M.  1996.  The primary structures of the Archaeon Halobacterium salinarum blue light receptor sensory rhodpsin II and its transducer, a methyl-accepting protein.  Proc Natl Acad Sci USA.  93:8320-8235.

1994

• Nordmann, B., Lebert, M.R., Alam, M., Nitz, S., Kollmannsberger, H., Oesterhelt, D., & Hazelbauer, G.L.  1994.  Identification of volatile forms of methyl groups released by Halobacterium halobium.  J Biol Chem.  269:16449-16454.

1991

• Alam, M. & Hazelbauer, G.L.  1991.  Structural features of methyl-accepting taxis proteins conserved between archaeabacteria and eubacteria revealed by antigenic cross-reaction.  J Bacteriol.  173:5837-5842.
• Marwan, W., Alam, M., & Oesterhelt, D.  1991.  Rotation and switching of the flagellar motor assembly in Halobacterium halobium.  J Bacteriol.  173(6):1971-1977.

1990

• Sundberg, S.A., Alam, M., Lebert, M., Spudich, J.L, Oesterhelt, D., & Hazelbauer, G.L.  1990.  Characterization of Halobacterium halobium mutants defective in taxis.  J Bacteriol.  172(5):2328-2335.

1989

• Alam, M., Lebert, M., Oesterhelt, D., & Hazelbauer, G.L.  1989.  Methyl-accepting taxis proteins in Halobacterium halobium.  EMBO J.  8(2):631-639.

1987

• Alam, M. & Oesterhelt, D.  1987.  Purification, reconstitution and polymorphic transition of halobacterial flagella.  J Mol Biol.  194(3):495-499.

1986

• Sundberg, S.A., Alam, M., & Spudich, J.L.  1986.  Excitation signal processing time in Halobacterium halobium phototaxis.  J Biophys.  50:895-900.

1984

• Alam, M., Claviez, M., Oesterhelt, D., & Kessel, M.  1984.  Flagellar and motility behavior of square bacteria.  EMBO J.  3:2899-2903. This paper was reviewed in the News and Views section. Nature. 1985. 313:183.
• Alam, M. & Oesterhelt, D.  1984.  Morphology, function and isolation of halobacterial flagella.  J Mol Biol.  176:459-475. This paper was reviewed in the News and Views section in Nature. 1984. 310:367.

1983

• Alam, M.  1983.  Chemosensory behavior of marine luminescent bacteria.  FEMS Microbiol Lett.  17:291-293.

1982

• Alam, M. & Glagolev, A.N.  1982. delta mu H+-sensing in taxis of Vibrio harveyi. FEBS Lett. 143(1):144-146.

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