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Data on whole-genome sequencing of extended-spectrum beta-lactamases producing Enterobacteriaceae isolates from Malaysia.

Gan HM, Eng WWH, Dhanoa A.

Data Brief. 2019 Jul 13;25:104257. doi: 10.1016/j.dib.2019.104257. eCollection 2019 Aug.


Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition.

Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM.

Sci Rep. 2019 Jul 24;9(1):10756. doi: 10.1038/s41598-019-47145-0.


First genomic insights into carbapenem-resistant Klebsiella pneumoniae from Malaysia.

Gan HM, Eng WWH, Dhanoa A.

J Glob Antimicrob Resist. 2019 Jul 17. pii: S2213-7165(19)30174-2. doi: 10.1016/j.jgar.2019.07.008. [Epub ahead of print]


Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia.

Yeo LF, Aghakhanian FF, Tan JSY, Gan HM, Phipps ME.

Version 3. F1000Res. 2019 Feb 11 [revised 2019 Jan 1];8:175. doi: 10.12688/f1000research.17706.3. eCollection 2019.


Mitogenome data of Nycticebus coucang insularis Robinson, 1917 (Primate: Lorisidae).

Rovie-Ryan JJ, Gani M, Lee YP, Gan HM, Abdullah MT.

Data Brief. 2019 May 25;25:104058. doi: 10.1016/j.dib.2019.104058. eCollection 2019 Aug.


The Influence of Modernization and Disease on the Gastric Microbiome of Orang Asli, Myanmars and Modern Malaysians.

Chua EG, Loke MF, Gunaletchumy SP, Gan HM, Thevakumar K, Tay CY, Young S, Aye TT, Maw WW, Aye MM, Leow AH, Azmi AN, Kalimuthu SG, Dahlan HMABD, Goh KL, Vadivelu J.

Microorganisms. 2019 Jun 14;7(6). pii: E174. doi: 10.3390/microorganisms7060174.


Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolution.

Froufe E, Bolotov I, Aldridge DC, Bogan AE, Breton S, Gan HM, Kovitvadhi U, Kovitvadhi S, Riccardi N, Secci-Petretto G, Sousa R, Teixeira A, Varandas S, Zanatta D, Zieritz A, Fonseca MM, Lopes-Lima M.

Heredity (Edinb). 2019 Jun 14. doi: 10.1038/s41437-019-0242-y. [Epub ahead of print]


MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing.

Pong LY, Parkkinen S, Dhanoa A, Gan HM, Wickremesinghe IAC, Syed Hassan S.

PeerJ. 2019 Apr 22;7:e6697. doi: 10.7717/peerj.6697. eCollection 2019.


De Novo assembly and characterisation of the greentail prawn (Metapenaeus bennettae) hepatopancreas transcriptome - identification of stress response and detoxification transcripts.

Armstrong EK, Miller AD, Mondon JA, Greenfield PA, Stephenson SA, Tan MH, Gan HM, Hook SE.

Mar Genomics. 2019 Apr 12. pii: S1874-7787(18)30272-1. doi: 10.1016/j.margen.2019.04.002. [Epub ahead of print]


Biodegradation of thiocyanate by a native groundwater microbial consortium.

Spurr LP, Watts MP, Gan HM, Moreau JW.

PeerJ. 2019 Mar 26;7:e6498. doi: 10.7717/peerj.6498. eCollection 2019.


Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4.

Gan HM, Lee MVL, Savka MA.

PeerJ. 2019 Feb 8;7:e6366. doi: 10.7717/peerj.6366. eCollection 2019.


Erratum: Author Correction: High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia.

Drewes JL, White JR, Dejea CM, Fathi P, Iyadorai T, Vadivelu J, Roslani AC, Wick EC, Mongodin EF, Loke MF, Thulasi K, Gan HM, Goh KL, Chong HY, Kumar S, Wanyiri JW, Sears CL.

NPJ Biofilms Microbiomes. 2019 Jan 9;5:2. doi: 10.1038/s41522-018-0078-x. eCollection 2019.


Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa.

Loke MF, Chua EG, Gan HM, Thulasi K, Wanyiri JW, Thevambiga I, Goh KL, Wong WF, Vadivelu J.

PLoS One. 2018 Dec 21;13(12):e0208584. doi: 10.1371/journal.pone.0208584. eCollection 2018.


High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall.

Gan HM, Lee MVJ, Savka MA.

Microbiol Resour Announc. 2018 Sep 6;7(9). pii: e01045-18. doi: 10.1128/MRA.01045-18. eCollection 2018 Sep.


Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate-reducing bacteria.

Cox TL, Gan HM, Moreau JW.

Geobiology. 2019 Mar;17(2):172-184. doi: 10.1111/gbi.12324. Epub 2018 Nov 25.


Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.

Md Zoqratt MZH, Eng WWH, Thai BT, Austin CM, Gan HM.

PeerJ. 2018 Oct 30;6:e5826. doi: 10.7717/peerj.5826. eCollection 2018.


Isolation and genomic characterization of six endophytic bacteria isolated from Saccharum sp (sugarcane): Insights into antibiotic, secondary metabolite and quorum sensing metabolism.

Parthasarathy A, Gan HM, Wong NH, Savka MA, Steiner KK, Henry KR, Hudson AO.

J Genomics. 2018 Oct 2;6:117-121. doi: 10.7150/jgen.28335. eCollection 2018.


ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements.

Tan MH, Gan HM, Lee YP, Linton S, Grandjean F, Bartholomei-Santos ML, Miller AD, Austin CM.

Mol Phylogenet Evol. 2018 Oct;127:320-331. doi: 10.1016/j.ympev.2018.05.015. Epub 2018 May 23.


Commentary: Genome Sequence of Vibrio parahaemolyticus VP152 Strain Isolated From Penaeus indicus in Malaysia.

Allnutt T, Yan CZY, Crowley TM, Gan HM.

Front Microbiol. 2018 May 1;9:865. doi: 10.3389/fmicb.2018.00865. eCollection 2018. No abstract available.


Expansion and systematics redefinition of the most threatened freshwater mussel family, the Margaritiferidae.

Lopes-Lima M, Bolotov IN, Do VT, Aldridge DC, Fonseca MM, Gan HM, Gofarov MY, Kondakov AV, Prié V, Sousa R, Varandas S, Vikhrev IV, Teixeira A, Wu RW, Wu X, Zieritz A, Froufe E, Bogan AE.

Mol Phylogenet Evol. 2018 Oct;127:98-118. doi: 10.1016/j.ympev.2018.04.041. Epub 2018 May 3.


High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?

Wilson JJ, Brandon-Mong GJ, Gan HM, Sing KW.

Mitochondrial DNA A DNA Mapp Seq Anal. 2019 Jan;30(1):60-67. doi: 10.1080/24701394.2018.1455189. Epub 2018 Mar 29.


One More Decade of Agrobacterium Taxonomy.

Gan HM, Savka MA.

Curr Top Microbiol Immunol. 2018;418:1-14. doi: 10.1007/82_2018_81. Review.


Temporal changes in arthropod activity in tropical anthropogenic forests.

Brandon-Mong GJ, Littlefair JE, Sing KW, Lee YP, Gan HM, Clare EL, Wilson JJ.

Bull Entomol Res. 2018 Dec;108(6):792-799. doi: 10.1017/S000748531800010X. Epub 2018 Feb 14.


Genome Sequence of Serratia marcescens subsp. sakuensis Strain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis).

Cheng TH, Saidin J, Danish-Daniel M, Gan HM, Mat Isa MN, Abu Bakar MF, Ismail N.

Genome Announc. 2018 Feb 8;6(6). pii: e00022-18. doi: 10.1128/genomeA.00022-18.


Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly.

Tan MH, Austin CM, Hammer MP, Lee YP, Croft LJ, Gan HM.

Gigascience. 2018 Mar 1;7(3):1-6. doi: 10.1093/gigascience/gix137.


Climate-driven mitochondrial selection: A test in Australian songbirds.

Lamb AM, Gan HM, Greening C, Joseph L, Lee YP, Morán-Ordóñez A, Sunnucks P, Pavlova A.

Mol Ecol. 2018 Feb;27(4):898-918. doi: 10.1111/mec.14488. Epub 2018 Feb 12.


High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia.

Drewes JL, White JR, Dejea CM, Fathi P, Iyadorai T, Vadivelu J, Roslani AC, Wick EC, Mongodin EF, Loke MF, Thulasi K, Gan HM, Goh KL, Chong HY, Kumar S, Wanyiri JW, Sears CL.

NPJ Biofilms Microbiomes. 2017 Nov 29;3:34. doi: 10.1038/s41522-017-0040-3. eCollection 2017. Erratum in: NPJ Biofilms Microbiomes. 2019 Jan 9;5:2.


Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis.

Gan HM, Thomas BN, Cavanaugh NT, Morales GH, Mayers AN, Savka MA, Hudson AO.

PeerJ. 2017 Nov 14;5:e4030. doi: 10.7717/peerj.4030. eCollection 2017.


In Situ Stimulation of Thiocyanate Biodegradation through Phosphate Amendment in Gold Mine Tailings Water.

Watts MP, Gan HM, Peng LY, Lê Cao KA, Moreau JW.

Environ Sci Technol. 2017 Nov 21;51(22):13353-13362. doi: 10.1021/acs.est.7b04152. Epub 2017 Nov 8.


Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity.

Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis-Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P.

Mol Ecol. 2017 Nov;26(22):6253-6269. doi: 10.1111/mec.14368. Epub 2017 Nov 8.


More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae).

Gan HM, Tan MH, Lee YP, Schultz MB, Horwitz P, Burnham Q, Austin CM.

Mol Phylogenet Evol. 2018 Jan;118:88-98. doi: 10.1016/j.ympev.2017.09.022. Epub 2017 Sep 28.


De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read.

Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, Pavlova A, Gan HM.

Gigascience. 2017 Aug 1;6(8):1-6. doi: 10.1093/gigascience/gix063.


Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains TT6675 and TT9097 Employed in the Isolation and Characterization of a Giant Phage Mutant Collection.

Gan HM, Eng WWH, Barton MK, Adams LE, Samsudin NA, Bartl AJ, Hudson AO, Savka MA, Thomas JA.

Genome Announc. 2017 Aug 24;5(34). pii: e00857-17. doi: 10.1128/genomeA.00857-17.


Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia.

Gan HM, Rajasekaram G, Eng WWH, Kaniappan P, Dhanoa A.

Genome Announc. 2017 Aug 10;5(32). pii: e00768-17. doi: 10.1128/genomeA.00768-17.


In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas.

Tran PN, Savka MA, Gan HM.

Front Microbiol. 2017 Jul 12;8:1296. doi: 10.3389/fmicb.2017.01296. eCollection 2017.


Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins.

Daniel DS, Gan HM, Lee SM, Dykes GA, Rahman S.

Genome Announc. 2017 Jun 15;5(24). pii: e00553-17. doi: 10.1128/genomeA.00553-17.


Characterization of an autotrophic bioreactor microbial consortium degrading thiocyanate.

Watts MP, Spurr LP, Gan HM, Moreau JW.

Appl Microbiol Biotechnol. 2017 Jul;101(14):5889-5901. doi: 10.1007/s00253-017-8313-6. Epub 2017 May 16.


New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing.

Foo SM, Eng WWH, Lee YP, Gui K, Gan HM.

Genome Announc. 2017 May 11;5(19). pii: e00302-17. doi: 10.1128/genomeA.00302-17.


Changes in rumen protozoal community by condensed tannin fractions of different molecular weights from a Leucaena leucocephala hybrid in vitro.

Saminathan M, Gan HM, Abdullah N, Wong CMVL, Ramiah SK, Tan HY, Sieo CC, Ho YW.

J Appl Microbiol. 2017 Jul;123(1):41-53. doi: 10.1111/jam.13477. Epub 2017 Jun 9.


Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing.

Aziz SA, Clements GR, Peng LY, Campos-Arceiz A, McConkey KR, Forget PM, Gan HM.

PeerJ. 2017 Apr 12;5:e3176. doi: 10.7717/peerj.3176. eCollection 2017.


Genetic diversity of Enterococcus faecalis isolated from environmental, animal and clinical sources in Malaysia.

Daniel DS, Lee SM, Gan HM, Dykes GA, Rahman S.

J Infect Public Health. 2017 Sep - Oct;10(5):617-623. doi: 10.1016/j.jiph.2017.02.006. Epub 2017 Feb 21.


Genomic characterization of eight Ensifer strains isolated from pristine caves and a whole genome phylogeny of Ensifer (Sinorhizobium).

Kumar HK, Gan HM, Tan MH, Eng WW, Barton HA, Hudson AO, Savka MA.

J Genomics. 2017 Jan 18;5:12-15. doi: 10.7150/jgen.17863. eCollection 2017.


Phylogeography of red muntjacs reveals three distinct mitochondrial lineages.

Martins RF, Fickel J, Le M, van Nguyen T, Nguyen HM, Timmins R, Gan HM, Rovie-Ryan JJ, Lenz D, Förster DW, Wilting A.

BMC Evol Biol. 2017 Jan 26;17(1):34. doi: 10.1186/s12862-017-0888-0.


Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish.

Pavlova A, Gan HM, Lee YP, Austin CM, Gilligan DM, Lintermans M, Sunnucks P.

Heredity (Edinb). 2017 May;118(5):466-476. doi: 10.1038/hdy.2016.120. Epub 2017 Jan 4.

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