Journal Articles

Su HJ, Hogenhout SA, Al-Sadi AM, Kuo CH* (2014) Complete chloroplast genome sequence of Omani lime (Citrus aurantiifolia) and comparative analysis within the rosids. PLoS ONE accepted. DOI: 10.1371/journal.pone.0113049

Lo WS, Chen HJ, Chen CY, Kuo CH* (2014) Complete genome sequence of Vibrio vulnificus 93U204, a bacterium isolated from diseased tilapia in Taiwan. Genome Announcements 2: e01005-14. DOI: 10.1128/genomeA.01005-14

Ku C, Lo WS, Kuo CH* (2014) Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria. Biochemical and Biophysical Research Communications 446: 927-932. DOI: 10.1016/j.bbrc.2014.03.039

Radjacommare R, Usharani R, Kuo CH, Fu H* (2014) Distinct phylogenetic relationships and biochemical properties of Arabidopsis ovarian tumor-related deubiquitinases support their functional differentiation. Frontiers in Plant Science 5: 84. DOI: 10.3389/fpls.2014.00084

Tung CH#, Cheng YR#, Lin CY, Ho JS, Kuo CH, Yu JK*, Su YH* (2014) A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. Biological Bulletin 226: 69-80. #Equal contribution.

Chang TH#, Lo WS#, Ku C, Chen LL, Kuo CH* (2014) Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biology and Evolution 6: 500-509. DOI: 10.1093/gbe/evu033 #Equal contribution.

Ku C, Lo WS, Chen LL, Kuo CH* (2014) Complete genome sequence of Spiroplasma apis B31T (ATCC 33834), a bacterium associated with May disease of honeybees (Apis mellifera). Genome Announcements 2: e01151-13. DOI: 10.1128/genomeA.01151-13

Lo WS, Ku C, Chen LL, Chang TH, Kuo CH* (2013) Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biology and Evolution 5: 1512-1523. DOI: 10.1093/gbe/evt108

Ku C, Lo WS, Chen LL, Kuo CH* (2013) Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma. Genome Biology and Evolution 5: 1151-1164. DOI: 10.1093/gbe/evt084

Lo WS, Chen LL, Chung WC, Gasparich GE, Kuo CH* (2013) Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics 14: 22. DOI: 10.1186/1471-2164-14-22

Shelomi M, Lo WS, Kimsey LS, Kuo CH* (2013) Analysis of the gut microbiota of walking sticks (Phasmatodea). BMC Research Notes 6: 368. DOI: 10.1186/1756-0500-6-368

Ku C, Chung WC, Chen LL, Kuo CH* (2013) The complete plastid genome sequence of Madagascar periwinkle Catharanthus roseus (L.) G. Don: plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids. PLoS ONE 8: e68518. DOI: 10.1371/journal.pone.0068518

Ku C, Hu JM, Kuo CH* (2013) Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE 8: e62548. DOI: 10.1371/journal.pone.0062548

Chung WC, Chen LL, Lo WS, Kuo PA, Tu J, Kuo CH* (2013) Complete genome sequence of Serratia marcescens WW4. Genome Announcements 1: e00126-13. DOI: 10.1128/genomeA.00126-13

Kuo PA, Kuo CH, Lai YK, Graumann P, Tu J* (2013) Phosphate limitation induces the intergeneric inhibition of Pseudomonas aeruginosa by Serratia marcescens isolated from paper machines. FEMS Microbiology Ecology 84: 577-587. DOI: 10.1111/1574-6941.12086

Ku C, Lo WS, Kuo CH* (2013) Horizontal transfer of potential mobile units in phytoplasmas. Mobile Genetic Elements 3: e26145. DOI: 10.4161/mge.26145

Chung WC#, Chen LL#, Lo WS, Lin CP, Kuo CH* (2013) Comparative analysis of the peanut witches¡¦-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. PLoS ONE 8: e62770. DOI: 10.1371/journal.pone.0062770 #Equal contribution.

Chen LL#, Chung WC#, Lin CP, Kuo CH* (2012) Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PLoS ONE 7: e34407. DOI: 10.1371/journal.pone.0034407 #Equal contribution.

McGaugh SE*, Bowden RM, Kuo CH, Janzen FJ (2011) Field-measured heritability of the threshold for sex determination in a turtle with temperature dependent sex determination. Evolutionary Ecology Research 13: 75-90.

Ochman H*, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn B, Hugenholtz P (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biology 8: e1000546. DOI: 10.1371/journal.pbio.1000546

Kuo CH, Ochman H* (2010) The extinction dynamics of bacterial pseudogenes. PLoS Genetics 6: e1001050. DOI: 10.1371/journal.pgen.1001050

Joseph SJ, Fernandez-Robledo JA, Gardner MJ, El-Sayed NM, Kuo CH, Schott EJ, Wang H, Kissinger JC*, Vasta GR* (2010) The alveolate Perkinsus marinus: biological insights from EST gene discovery. BMC Genomics 11: 228. DOI: 10.1186/1471-2164-11-228

Kuo CH, Ochman H* (2009) Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biology Direct 4: 35. DOI: 10.1186/1745-6150-4-35

Kuo CH, Ochman H* (2009) Deletional bias across the three domains of life. Genome Biology and Evolution 1: 145-152. DOI: 10.1093/gbe/evp016

Kuo CH, Moran NA, Ochman H* (2009) The consequences of genetic drift for bacterial genome complexity. Genome Research 19: 1450-1454. DOI: 10.1101/gr.091785.109

Kuo CH, Ochman H* (2009) The fate of new bacterial genes. FEMS Microbiology Reviews 33: 38-43. DOI: 10.1111/j.1574-6976.2008.00140.x

Kuo CH*, Wares JP, Kissinger JC (2008) The apicomplexan whole genome phylogeny: an analysis of incongruence among gene trees. Molecular Biology and Evolution 25: 2689-2698. DOI: 10.1093/molbev/msn213

Kuo CH*, Kissinger JC (2008) Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria. BMC Evolutionary Biology 8: 108. DOI: 10.1186/1471-2148-8-108

Kuo CH*, Avise JC (2008) Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci? Genetica 132: 219-225. DOI: 10.1007/s10709-007-9167-0

Kuo CH*, Corby-Harris V, Promislow DEL (2008) The unavoidable costs and unexpected benefits of parasitism: population and metapopulation models of parasite-mediated competition. Journal of Theoretical Biology 250: 244-256. DOI: 10.1016/j.jtbi.2007.10.004

Kuo CH*, Janzen FJ (2007) Longevity, overlapping generations, and conservation of turtle populations. Turtle and Tortoise Newsletter 11: 18-23.

Kuo CH*, Avise JC (2005) Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica 124: 179-186. DOI: 10.1007/s10709-005-2095-y

Kuo CH*, Janzen FJ (2004) Genetic effects of a persistent bottleneck on a natural population of ornate box turtles (Terrapene ornata). Conservation Genetics 5: 425-437. DOI: 10.1023/B:COGE.0000041020.54140.45

Kuo CH*, Janzen FJ (2003) BottleSim: a bottleneck simulation program for long-lived species with overlapping generations. Molecular Ecology Notes 3: 669-673. DOI: 10.1046/j.1471-8286.2003.00532.x

Book Chapters

Kuo CH, Ochman H*, Raghavan R (2011) The genomics of Escherichia coli and beyond. In: The Population Genetics of Bacteria: a Tribute to Thomas S. Whittam. Eds. S. Walk and P. Feng. American Society for Microbiology Press. ISBN: 978-1-55581-535-6.

Kissinger JC*, Kuo CH (2007) Evolution and comparative genomics of Toxoplasma gondii. In: Toxoplasma: Molecular and Cellular Biology. Eds. J. Ajioka and D. Soldati. Horizon Press. ISBN: 978-1-904933-34-2.

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