(*Corresponding Author; ^equal contribution; lab members)

(43) H. Zhang, S. Yoshizawa, Y. Sun, Y. Huang, X. Chu, J.M. González, J. Pinhassi, H. Luo*. 2019. Repeated Evolutionary Transitions of Flavobacteria from Marine to Non-Marine Habitats. Environmental Microbiology (in press)

(42) G. Yu*^, Y. Jiang^, J. Wang, H. Zhang, and H. Luo*. 2018. BMC3C: Binning Metagenomic Contigs using Codon usage, sequence Composition and read Coverage. Bioinformatics 34 (24):4172-4179

(41)  Y. Sun and H. Luo*. 2018. Homologous recombination in core genomes facilitates marine bacterial adaptation. Applied and Environmental Microbiology 84 (11): e02545-17 (selected as a “Spotlight” article by the journal)

(40) F.L. Hellweger*, Y. Huang, H. Luo*. 2018. Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model. The ISME Journal 12 (5):1180-1187

(39) W. Xie*, H. Luo, S.K. Murugapiran, J.A. Dodsworth, S. Chen, Y. Sun, B.P. Hedlund, P. Wang, H. Fang, M. Deng, and C. Zhang*. 2018. Localized high abundance of Marine group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environmental Microbiology 20 (2):734-754

(38) H. Long^, W. Sung^, S. Kucukyildirim^, E. Williams, S. Miller, W. Guo, C. Patterson, C. Gregory, C. Strauss, C. Stone, C. Berne, D. Kysela, W.R. Shoemaker, M. Muscarella, H. Luo, J.T. Lennon, Y.V. Brun, and M. Lynch*. 2018. Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology & Evolution 2 (2):237-240

(37) H. Luo*^, Y. Huang^, R. Stepanauskas, and J. Tang. 2017. Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes. Nature Microbiology 2:17091

(36) H.A. Bullock*, H. Luo, W.B. Whitman. 2017. Evolution of dimethylsulfoniopropionate metabolism in marine phytoplankton and bacteria. Frontiers in Microbiology 8:637

(35) Y. Sun, Y. Zhang, J.T. Hollibaugh, and H. Luo*. 2017. Ecotype diversification of an abundant Roseobacter lineage. Environmental Microbiology 19(4):1625-1638

(34) Y. Sun, K.E. Powell, W. Sung, M. Lynch, M.A. Moran, and H. Luo*. 2017. Spontaneous mutations of a model heterotrophic marine bacterium. The ISME Journal 11(7):1713-1718

(33) W. Zhang, W. Ding, B. Yang, R. Tian, S. Gu, H. Luo, and P-Y Qian*. 2016. Genomic and transcriptomic evidence for carbohydrate consumption among microorganisms in a cold seep brine pool. Frontiers in Microbiology 7:1825

(32) H. Luo*, Y. Sun, J.T. Hollibaugh, and M.A. Moran. 2016. Low genome content diversity of marine planktonic Thaumarchaeota. Environmental Microbiology Reports 8(4):501-507

(31) Y. Zhang, Y. Sun, N. Jiao, R. Stepanauskas, and H. Luo*. 2016. Ecological genomics of the uncultivated marine Roseobacter lineage CHAB-I-5. Applied and Environmental Microbiology 82(7):2100-2111

(30) H. Luo*, L. Thompson, U. Stingl, and A.L. Hughes. 2015. Selection maintains low genomic GC content in marine SAR11 lineages. Molecular Biology and Evolution 32 (10): 2738-2748

(29) H. Luo and M.A. Moran*. 2015. How do divergent ecological strategies emerge among marine bacterioplankton lineages? Trends in Microbiology 23(9):577-584

(28) J.M. Labonté, B.K. Swan, B. Poulos, H. Luo, S. Koren, S.J. Hallam, M.B. Sullivan, T. Woyke, K.E. Wommack, and R. Stepanauskas*. 2015. Single cell genomics-based analysis of virus-host interactions in marine surfacebacterioplankton. The ISME Journal 9(11):2386-2399

(27) H. Luo*. 2015. The use of evolutionary approaches to understand single cell genomes. Frontiers in Microbiology 6: 191

(26) H. Luo*. 2015. Evolutionary origin of a streamlined marine bacterioplankton lineage. The ISME Journal 9(6):1423-1433


Before CUHK

(25) B.P. Durham, S. Sharma, H. Luo, C.B. Smith, S.A. Amin, S.J. Bender, S.P. Dearth, B.A.S. Van Mooy, S.R. Campagna, E.B. Kujawinski, E.V. Armbrust, and M.A. Moran*. 2015. Cryptic carbon and sulfur cycling between surface ocean plankton. Proc. Natl. Acad. Sci. USA 112 (2): 453-457

(24) H. Luo and M.A. Moran*. 2014. Evolutionary ecology of the marine Roseobacter clade. Microbiology and Molecular Biology Reviews 78 (4): 573-587

(23) H. Luo*. 2014. New computational methodologies to understand microbial diversity. Encyclopedia of Metagenomics. Karen E. Nelson, ed. Springer. ISBN 978-1-4614-4676-7

(22) M. Lin, M.V. Kitahara, H. Luo, D. Tracey, J. Geller, F. Hironobu, D.J. Miller, and C.A. Chen. 2014. Mitochondrial genome rearrangements in the Scleractinia / Corallimorpharia complex: implications for coral phylogeny. Genome Biology and Evolution 6 (5): 1086-1095

(21) B.P. Durham, J. Grote, K.A. Whittaker, S.J. Bender, H. Luo, S.L. Grim, J.M. Brown, J.R. Casey, A. Dron, L. Florez-Leiva, A. Krupke, C.M. Luria, A.H. Mine, S. Pather, A. Talarmin, E.K. Wear, T.S. Weber, J.M. Wilson, M.J. Church, E.F. DeLong, D.M. Karl, G.F. Steward, J.M. Eppley, N.C.Kyrpides, S. Schuster, and M.S. Rappe*. 2014. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Standards in Genomic Sciences 9:632-645

(20) H. Luo, B.K. Swan, R. Stepanauskas, A.L. Hughes, and M.A. Moran*. 2014. Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. The ISME Journal 8:1428-1439

(19) H. Luo, B.K. Swan, R. Stepanauskas, A.L. Hughes, and M.A. Moran*. 2014. Comparing effective population sizes of dominant marine Alphaproteobacteria lineages. Environmental Microbiology Reports 6 (2): 167-172

(18) H. Luo*, B.B. Tolar, B.K. Swan, C.L. Zhang, R. Stepanauskas, M.A. Moran, and J.T. Hollibaugh*. 2014. Single cell genomics shedding light on marine Thaumarchaeota diversification. The ISME Journal 8: 732-736

(17) H. Luo, M. Csuros, A.L. Hughes, and M.A. Moran*. 2013. Evolution of divergent life history strategies in marine Alphaproteobacteria. mBio 4 (4): e00373-13

(16) B.K. Swan, B. Tupper, A. Sczyrba, F.M. Lauro, M. Martinez-Garcia, J.M. Gonzalez, H. Luo, J.J. Wright, Z. C. Landry, N.W. Hanson, B. Thompson, N.J. Poulton, P. Schwientek, S.G. Acinas, S.J. Giovannoni, M.A. Moran, S.J. Hallam, R.Cavicchioli, T. Woyke, and R. Stepanauskas*. 2013. Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean. Proc. Natl. Acad. Sci. USA 110 (28):11463-11468

(15) H. Luo and M.A. Moran*. 2013 Assembly-free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton. Environmental Microbiology Reports 5 (5): 686-696

(14) N. Akram, J. Palovaara, J. Forsberg, M.V. Lindh, D.L. Milton, H. Luo, J.M. Gonzalez, and J. Pinhassi*. 2013. Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp. AND4. Environmental Microbiology 15 (5): 1400-1415

(13) M.A. Moran*, B. Satinsky, S.M. Gifford, H. Luo, A. Rivers, L. Chan, J. Meng, B.P. Durham, C. Shen, V.A.Varaljay, C.B. Smith, P.L. Yager, and B.M. Hopkinson. 2013. Sizing up metatranscriptomics. The ISME Journal 7: 237-243

(12) H. Luo* and A.L. Hughes. 2012. dN/dS does not show positive selection drives separation of polar-tropical SAR11 populations. Molecular Systems Biology 8:625

(11) H. Luo*. 2012. Predicted protein subcellular localization in dominant surface ocean bacterioplankton. Applied and Environmental Microbiology 78 (18): 6550-6557

(10) H. Luo, W. Arndt, Y. Zhang, G. Shi, M. Alekseyev, J. Tang, A.L. Hughes*, and R. Friedman. 2012. Phylogenetic analysis of genome rearrangements among five mammalian orders. Molecular Phylogenetics and Evolution 65 (3): 871-882

(9) H. Luo, A. Loytynoja, and M.A. Moran*. 2012. Genome content of uncultivated marine roseobacters in the surface ocean. Environmental Microbiology 14 (1): 41-51

(8) H. Luo, R. Friedman, J. Tang, and A.L. Hughes*. 2011. Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus. Molecular Biology and Evolution 28 (10): 2751-2760

(7) H. Luo*^, H. Zhang^, R.A. Long, and R. Benner. 2011. Depth distributions of alkaline phosphatase and phosphonate utilization genes in the North Pacific Subtropical Gyre. Aquatic Microbial Ecology 62: 61-69 (recommended by Faculty of 1000, http://f1000.com/prime/13445998)

(6) H. Luo, J. Tang, R. Friedman, and A.L. Hughes*. 2011. Ongoing purifying selection on the intergenic spacers in the Group A Streptococcus. Infection, Genetics and Evolution 11 (2): 343-348

(5) J. Shi, Y. Zhang, H. Luo, and J. Tang*. 2010. Using jackknife to assess the quality of gene order phylogenies. BMC Bioinformatics 11:168

(4) H. Luo*, R. Benner, R. A. Long, and J. Hu. 2009. Subcellular localization of marine bacterial alkaline phosphatases. Proc. Natl. Acad. Sci. USA 106 (50): 21219-21223

(3) H. Luo*, Z. Sun, W. Arndt, J. Shi, R. Friedman, and J. Tang. 2009. Gene order phylogeny and the evolution of methanogens. PLoS ONE 4 (6): e6069

(2) H. Luo, J. Shi, W. Arndt, J. Tang, and R. Friedman*. 2008. Gene order phylogeny of the genus Prochlorococcus. PLoS ONE 3 (12): e3837

(1) B. Huang, L. Ou, H. Hong*, H. Luo, and D. Wang. 2005. Bioavailability of dissolved organic phosphorus compounds to typical harmful dinoflagellate Prorocentrum donghaiense Lu. Marine Pollution Bulletin 51: 838-844