Research Output

Genomics Cluster Output:

The Genomics Facility has been steadily generating Next-Generation Sequencing NGS data using the Illumina MiSeq and as of September 2016, close to 1TB of data has been generated from 151 runs (Below graph for details), which resulted in 87 publications (list below).  In hope to increase these numbers, we are happy to have more collaborations, internally and externally.

If you are interested, please do not hesitate to contact us.

2015

70. Phuong N. Tran, Nicholas E. H. Tan, Yin Peng Lee, Han Ming Gan, Steven J. Polter, Lucas K. Dailey, André O. Hudson, Michael A. Savka. 2015. Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans). Genome Announcements. Link

69. Yaakop AS, Chan KG, Gan HM, Goh KM. 2015. Draft Genome Sequence of Yellow Pigmented Jeotgalibacillus alimentarius JY-13T, the First Halophile Strain of the Genus Jeotgalibacillus. Genome Announcements. Link

68. Austin CM, Tan MH, Croft LJ, Hammer MP, Gan HM. 2015. Whole genome sequencing of the Asian arowana (Scleropages formosus) provides insights into the evolution of ray-finned fishes. Genome Biology and Evolution . Link

67. Tan MH, Gan HM, Lee YP, Croft LJ, Schultz MB, Miller AD, Austin CM. 2015. First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase. Organisms Diversity & Evolution. Link

66. Brandon-Mong GJ, Gan HM, Sing KW, Lee PS, Lim PE, Wilson JJ. 2015. DNA metabarcoding of insects and allies: An evaluation of primers and pipelines. Bulletin of Entomological Research. Link

65. Chua, P., Har, Z. M., Austin, C.M., Yule, C.M., Dykes, G.A., and Lee, S.M. 2015. Genome Sequencing and annotation of Aeromonas sp. HZM. Genomics Data. Link

64. Chua, P., Har, Z. M., Austin, C.M., Yule, C.M., Dykes, G.A., and Lee, S.M. 2015. Genome Sequencing and annotation of Cellulomonas sp. HZM. Genomics Data. Link

63. Elsa Froufea, Han Ming Gan, Yin Peng Lee, João Carneiro, Simone Varandas, Amílcar Teixeira, Alexandra Zieritz, Ronaldo Sousa, Manuel Lopes-Lima. 2015. The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae). Mitochondrial DNA. Link

62. Kian Mau Goh, Kok-Gan Chan, Amira Suriaty Yaakop, Chia Sing Chan, Robson Ee, Wen-Si Tan, Han Ming Gan. 2015. Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil. Genome Announcements. Link

61. Wilhelm Wei Han Eng, Han Ming Gan, Huan You Gan, André O. Hudson, Michael A. Savka. 2015. Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344. Genome Announcements. Link

60. Gan HY, Gan HM, Savka MA, Triassi AJ, Wheatley MS, Naqvi KF, Foxhall TE, Anauo MJ, Baldwin ML, Burkhardt RN, O’Bryon IG, Dailey LK, Busairi NI, Keith RC, Khair MHMM, Rasul MZM, Rosdi NAM, Mountzouros JR, Rhoads AC, Selochan MA, Tautanov TB, Polter SJ, Marks KD, Caraballo AA, Hudson AO. 2015. Whole-genome sequencing and annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (bird’s eye chili) and Capsicum chinense (yellow lantern chili), respectively. Genome Announcements. Link

59. Urszula Krzeminska, Robyn Wilson, Sadequr Rahman, Beng Kah Song, Sampath Seneviratne, Han Ming Gan & Christopher M. Austin. 2015. Mitochondrial genomes of the jungle crow Corvus macrorhynchos (Passeriformes: Corvidae) from shed feathers and a phylogenetic analysis of genus Corvus using mitochondrial protein-coding genes. Mitochondrial DNA. Link

58. M. E. Torres, T. Cox, W.-L. Hong, J. McManus, J. C. Sample, C. Destrigneville, H. M. Gan, H. Y. Gan, J. W. Moreau. 2015. Crustal fluid and ash alteration impacts on the biosphere of Shikoku Basin sediments, Nankai Trough, Japan. Geobiology. Link

57. Amira Suriaty Yaakop, Kok-Gan Chan, Han Ming Gan, Kian Mau Goh. 2015. Draft genome of Jeotgalibacillus campisalis SF-57T, a moderate halophilic bacterium isolated from marine saltern. Marine Genomics. Link

56. Steven J. Polter, Alexander A. Caraballo, Yin P. Lee, Wilhelm W. H. Eng, Han M. Gan, Matthew S. Wheatley, Michael A. Savka, Bolaji N. Thomas, André O. Hudson. 2015. Isolation, Identification, Whole-Genome Sequencing, and Annotation of Four Bacillus Species, B. anthracis RIT375, B. circulans RIT379, B. altitudinis RIT380, and B. megaterium RIT381, from Internal Stem Tissue of the Insulin Plant Costus igneus. Genome Announcements. Link

55. Frédéric Grandjean, Mun Hua Tan, Huan You Gan, Han Ming Gan, Christopher M. Austin. 2015. The complete mitogenome of the endangered white-clawed freshwater crayfish Austropotamobius pallipes (Lereboullet, 1858) (Crustacea: Decapoda: Astacidae). Mitochondrial DNA. Link

54. Yin Peng Lee, Han Ming Gan, Mun Hua Tan, Isabelle Lys, Rachel Page, Beatrice Dias Wanigasekera, Christopher M. Austin. 2015. The complete mitogenome of the New Zealand freshwater crayfish Paranephrops planifrons (White, 1842) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

53. Mun Hua Tan, Han Ming Gan, Mark B. Schultz, Christopher M. Austin. 2015. MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Molecular Phylogenetics and Evolution. Link

52. Christopher M. Austin, Mun Hua Tan, Laurence J. Croft, Mark G. Meekan, Huan You Gan, Han Ming Gan. 2015. The complete mitogenome of the bluespotted ribbontail ray Taeniura lymma (Forsskål, 1775) (Elasmobranchii: Myliobatiformes: Dasyatidae). Mitochondrial DNA. Link

51. Huan You Gan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2015. The complete mitogenome of the Australian freshwater shrimp Paratya australiensis (Kemp, 1917) (Crustacea: Decapoda: Atyidae). Mitochondrial DNA. Link

50. Huan You Gan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2015. The complete mitogenome of the rock pool prawn Palaemon serenus (Heller, 1862) (Crustacea: Decapoda: Palaemonidae). Mitochondrial DNA. Link

49. Han Ming Gan, Huan You Gan, Mun Hua Tan, Shane S. Penny, Richard C. Willan, Christopher M. Austin. 2015. The complete mitogenome of the giant clam Tridacna squamosa (Heterodonta: Bivalvia: Tridacnidae). Mitochondrial DNA. Link

48. Han Ming Gan, Mun Hua Tan, Huan You Gan, Yin Peng Lee, Christopher M. Austin. 2015. The complete mitogenome of the Norway lobster Nephrops norvegicus (Linnaeus, 1758) (Crustacea: Decapoda: Nephropidae). Mitochondrial DNA. Link

47. Han Ming Gan, Huan You Gan, Yin Peng Lee, Frédéric Grandjean, Christopher M. Austin. 2015. The complete mitogenome of the invasive spiny-cheek crayfish Orconectes limosus (Rafinesque, 1817) (Crustacea: Decapoda: Cambaridae). Mitochondrial DNA. Link

46. Christopher M. Austin, Mun Hua Tan, Huan You Gan, Han Ming Gan. 2015. The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

45. Han Ming Gan, Huan You Gan, Nurul H. Ahmad, Nazrin A. Aziz, André O. Hudson, Michael A. Savka. 2015. Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family. Frontiers in Cellular and Infection Microbiology. Link

2014

44. Huan You Gan, Han Ming Gan, Mun Hua Tan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the hermit crab Clibanarius infraspinatus (Hilgendorf, 1869), (Crustacea; Decapoda; Diogenidae) - a new gene order for the Decapoda. Mitochondrial DNA. Link

43. Han Ming Gan, Mun Hua Tan, Yin Peng Lee, Michael P. Hammer, Christopher M. Austin. 2014. The complete mitogenome of the minute mudskipper, Periophthalmus minutus Eggert, 1935 (Perciformes: Gobiidae: Oxudercinae). Mitochondrial DNA. Link

42. Huan You Gan, Mohd Ezhar Mohd Noor, Nur Azna Saari, Najiah Musa, Baharim Mustapha, Gires Usup, Muhd Danish-Daniel. 2014. Genome Sequence of Vibrio campbellii Strain UMTGB204, a Marine Bacterium Isolated from a Green Barrel Tunicate. Genome Announcements. Link

41. Mohd Asrore Mohd Shaufi, Chin Chin Sieo, Chun Wie Chong, Han Ming Gan, Yin Wan Ho. 2014. Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses. Gut pathogens. Link

40. Huan You Gan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitochondrial genome of the bass yabby Trypaea australiensis Dana 1852, (Crustacea; Decapoda; Callianassidae) - a new gene order for the Decapoda. Mitochondrial DNA. Link

39. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura). Mitochondrial DNA. Link

38. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. Milne-Edwards, 1853 (Crustacea: Decapoda: Grapsoidea). Mitochondrial DNA. Link

37. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the ghost crab Ocypode ceratophthalmus (Pallas, 1772) (Crustacea: Decapoda: Ocypodidae). Mitochondrial DNA. Link

36. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae). Mitochondrial DNA. Link

35. Kien-Pong Yap, Han Ming Gan, Cindy Shuan Ju Teh, Lay Ching Chai and Kwai Lin Thong. 2014. Comparative genomics of closely related Salmonella enterica serovar Typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements. BMC Genomics. Link

34. Huan You Gan, Han Ming Gan, Alexander Mario Tarasco, Nurfatini Idayu Busairi, Hazel A. Barton, André O. Hudson, Michael A. Savka. 2014. Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico. Genome Announcements. Link

33. Joanita Sulaiman, Han Ming Gan, Wai-Fong Yin and Kok-Gan Chan. 2014. Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine. Frontiers in Microbiology. Link

32. Han Ming Gan, Mun Hua Tan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca). Mitochondrial DNA. Link

31. Han Ming Gan, Mun Hua Tan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the river blackfish, Gadopsis marmoratus (Richardson, 1848) (Teleostei: Percichthyidae). Mitochondrial DNA. Link

30. Alexander J. Triassi, Matthew S. Wheatley, Michael A. Savka, Han Ming Gan, Renwick C. J. Dobson and André O. Hudson. 2014. L,L-diaminopimelate aminotransferase (DapL): A putative target for the development of narrow-spectrum antibacterial compounds. Frontiers in Microbiology. Link

29. Christopher M. Austin, Mun Hua Tan, Yin Peng Lee, Laurence J. Croft, Mark G. Meekan & Han Ming Gan. 2014. The complete mitogenome of the cow tail ray Pastinachus atrus (Macleay, 1883) (Elasmobranchii; Myliobatiformes; Dasyatidae). Mitochondrial DNA. Link

28. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae). Mitochondrial DNA. Link

27. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the Morton Bay bug Thenus orientalis (Lund, 1793) (Crustacea: Decapoda: Scyllaridae) from a cooked sample and a new mitogenome order for the Decapoda. Mitochondrial DNA. Link

26. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae). Mitochondrial DNA. Link

25. Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Christopher M. Austin. 2014. The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae). Mitochondrial DNA. Link

24. Urszula Krzeminska, Robyn Wilson, Sadequr Rahman, Beng Kah Song, Han Ming Gan, Mun Hua Tan & Christopher M. Austin. 2014. The complete mitochondrial genome of the invasive house crow Corvus splendens (Passeriformes: Corvidae). Mitochondrial DNA. Link

23. Han Ming Gan, Mun Hua Tan, Christopher M. Austin. 2014. The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

22. Han Ming Gan, Mun Hua Tan, Huan You Gan, Yin Peng Lee, Mark B. Schultz & Christopher M. Austin. 2014. The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

21. Huan You Gan, Han Ming Gan, Michael A. Savka, Alexander J. Triassi, Matthew S. Wheatley, Lawrence B. Smart, Eric S. Fabio, André O. Hudson. 2014. Whole-genome sequences of 13 endophytic bacteria isolated from shrub willow (salix) grown in geneva, new york. Genome Announcements. Link

20. Christopher M. Austin, Mun Hua Tan, Yin Peng Lee, Laurence J. Croft, Han Ming Gan. 2014. The complete mitogenome of the Murray Cod, Maccullochella peelii (Mitchell, 1838) (Teleostei: Percichthyidae). Mitochondrial DNA. Link

19. Christopher M. Austin, Mun Hua Tan, Yin Peng Lee, Laurence J. Croft, Mark G. Meekan, Simon J. Pierce & Han Ming Gan. 2014. The complete mitogenome of the whale shark parasitic copepod Pandarus rhincodonicus norman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae) - a new gene order for the copepoda. Mitochondrial DNA. Link

18. Han Ming Gan, Mun Hua Tan, Yin Peng Lee, Mark B. Schultz & Christopher M. Austin. 2014. The complete mitogenome of the Australian land crayfish Engaeus lyelli (Clark 1936) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

17. Han Ming Gan, Mun Hua Tan, Binh Thanh Thai & Christopher M. Austin. 2014. The complete mitogenome of the marine bivalve Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae). Mitochondrial DNA. Link

16. Han Ming Gan, Mun Hua Tan & Christopher M. Austin. 2014. The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens, 1868) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

15. Han Ming Gan, Mun Hua Tan, Rury Eprilurahman & Christopher M. Austin. 2014. The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA. Link

14. Han Ming Gan, Mun Hua Tan & Christopher M. Austin. 2014. The complete mitogenome of the Macquarie perch, Macquaria australasica Cuvier, 1830 (Teleostei: Percichthyidae). Mitochondrial DNA. Link

13. Y. M. Wong, J. C. Juan, H. M. Gan, C. M. Austin. 2014. Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge. Genome Announcements. Link

12. Kian Mau Goh, Han Ming Gan, Kok-Gan Chan, Giek Far Chan, Saleha Shahar, Chun Shiong Chong, Ummirul Mukminin Kahar, Kian Piaw Chai. 2014. Analysis of Anoxybacillus Genomes from the Aspects of Lifestyle Adaptations, Prophage Diversity, and Carbohydrate Metabolism. PLoS ONE. Link

11. Yee Meng Wong, Joon Ching Juan, Han Ming Gan, Christopher M. Austin. 2014. Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge. Genome Announcements. Link

10. Yee Meng Wong, Joon Ching Juan, Han Ming Gan, Christopher M. Austin. 2014. Draft Genome Sequence of Clostridium sp. Strain Ade. TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge. Genome Announcements. Link

9. Han Ming Gan, Alexander J. Triassi, Matthew S. Wheatley, Michael A. Savka, André O. Hudson. 2014. High-Quality Draft Whole-Genome Sequences of Three Strains of Enterobacter Isolated from Jamaican Dioscorea cayenensis (Yellow Yam). Genome Announcements. Link

8. Han Ming Gan, Mark B Schultz and Christopher M Austin. 2014. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evolutionary Biology. Link

7. Christopher M. Austin, Mun Hua Tan, Laurence J. Croft & Han Ming Gan. 2014. The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

6. Christopher M. Austin, Mun Hua Tan, Laurence J. Croft & Han Ming Gan. 2014. The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. Link

5. Patric Chua, Hye-Seung Yoo, Han Ming Gan, Sui-Mae Lee. 2014. Draft Genome Sequences of Two Cellulolytic Paenibacillus sp. Strains, MAEPY1 and MAEPY2, from Malaysian Landfill Leachate. Genome Announcements. Link

4. Yoong Kit Aw, Kuan Shion Ong, Catherine M. Yule, Han Ming Gan, Sui Mae Lee. 2014. Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil. Genome Announcements. Link

3. Muhd Danish-Daniela, Huan You Gan, Han Ming Gan, Nur Azna Saari, Gires Usup. 2014. Genome Sequence of Nitratireductor basaltis Strain UMTGB225, a Marine Bacterium Isolated from a Green Barrel Tunicate in Bidong Island, Malaysia. Genome Announcements. Link

2. Kuan Shion Ong, Yoong Kit Aw, Han Ming Gan, Catherine M. Yule, Sui Mae Lee. 2014. Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil. Genome Announcements. Link

2013

1. Han Ming Gan, André O Hudson, Ahmad Yamin Abdul Rahman, Kok Gan Chan and Michael A Savka. 2013. Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation. BMC Genomics. Link