publications 2018


Data on partial polyhydroxyalkanoate synthase genes (phaC) mined from Aaptos aaptos marine sponge-associated bacteria metagenome
Tan Suet May Amelia,Al-Ashraf Abdullah Amirul,Kesaven Bhubalan. Data in Brief (2018), Volume 16, February 2018, Pages 75-80

Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches
Yuko Makita, Mika Kawashima, Nyok Sean Lau, Ahmad Sofiman Othman and Minami Matsui. BMC Genomics (2018), 19(Suppl 1):922


Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia
G. Veera Singham, Ahmad Sofiman Othman, Chow-Yang Lee. PLOS One (2017),

Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2
Sim, P.-F., Furusawa, G., Teh, A.-H.Scientific Reports (2017), 7(1),13656

A Marine Actinomycete Rescues Caenorhabditis elegans from Pseudomonas aeruginosa Infection through Restitution of Lysozyme 7
Siti N. Fatin, Tan Boon-Khai, Alexander Chong Shu-Chien, Melati Khairuddean and Amirul Al-Ashraf Abdullah. Frontiers in Microbiology (2017),

Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment
Hema Ramachandran,Nur Asilla Hani Shafie, Kumar Sudesh, Mohamad Noor Azizan, Mohamad Isa Abdul Majid, Al-Ashraf Abdullah Amirul.Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology (2017), pp. 1-12

Draft genome sequence of halophilic Hahella sp. strain CCB-MM4, isolated from Matang Mangrove Forest in Perak, Malaysia
Ka-Kei Sam, Nyok Sean Lau, Go Furusawa, Al-Ashraf Abdullah Amirul..Genome Announcements. (2017), 5(42),e01147-17

Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest
Moh, T.H., Furusawa, G., Amirul, A.A.-A.International Journal of Systematic and Evolutionary Microbiology (2017), 67(10),002258, pp. 4089-4094.

Synthesis of poly(3-hydroxybutyrate) with high 4HB composition and PHA content using 1,4-butanediol and 1,6-hexanediol for medical application
Hambali Norhafini, L. Thinagaran, K. Shantini, Kai-Hee Huong, Ishak Muhammad Syafiq, Kesaven Bhubalan, A. A. Amirul. Journal of Polymer Research (2017), 24 (189)

Effect of dietary lipid source on expression of lipid metabolism genes and tissue lipid profile in juvenile spiny lobster Sagmariasus verreauxi
Shu-Chien A.C., Han W.-Y., Carter C.G., Fitzgibbon Q.P., Simon C.J., Battaglene S.C., Codabaccus B.M., Kuah M.-K., Ventura T.Aquaculture (2017), 479:342-351

Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7
Nanthini, J., Ong, S.Y., Sudesh, K..Gene (2017), 628, pp. 146-155

Biodegradation of Natural Rubber and Natural Rubber Products by Streptomyces sp. Strain CFMR 7
Nanthini, J., Sudesh, K.Journal of Polymers and the Environment (2017), 25(3), pp. 606-616

En route to economical eco-friendly solvent system in enhancing sustainable recovery of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer

Nik Murniati Nik Man Irdahayu, Kannusamy Shantini, kai-Hee Huong, Sevakumaran Vigneswari, Nursolehah Abdul Aziz, Mohd. Noor Mohd. Azizan, Al-Ashraf Abdullah Amirul. Engineering in Life Sciences (2017), 17,1050-1059

Microbial-based synthesis of highly elastomeric biodegradable poly(3-hydroxybutyrate-co-4-hydroxybutyrate) thermoplastic
Huong K-H, Teh C.-H, Amirul A.-A.A.International Journal of Biological Macromolecules (2017), 101:983-995

Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia.
Moh, T.H., Lau, N.-S., Furusawa, G., Amirul, A.-A.A..Standards in Genomic Sciences (2017), 12(1),36

Pilot scale production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) biopolymers with high molecular weight and elastomeric properties
Huong K-H, Azuraini M.J., Aziz N.A., Amirul A.-A.A.Journal of Bioscience and Bioengineering (2017), 124:76-83

Insecticide resistance and resistance mechanisms in bed bugs, Cimex spp. (Hemiptera: Cimicidae)
Dang, K., Doggett, S.L. , Veera Singham, G., Lee, C.-Y.Parasites and Vectors (2017), doi:10.1186/s13071-017-2232-3

Exploring the Potential of 1-Pentanol and Oleic Acid for Optimizing the Production of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Copolymer by Cupriavidus sp. USMAA1020
Huong K.-H., Amirul A.A., Shantini K., Sharmini R. Arabian Journal for Science and Engineering (2017), 42 (6), pp. 2313-2320

Combination of 4-Hydroxybutyrate Carbon Precursors as Substrate for Simultaneous Production of P(3HB-co-4HB) and Yellow Pigment by Cupriavidus sp. USMAHM13
I. Iszatty,O. Noor Aidda,R. Hema,A. A. Amirul. Arabian Journal for Science and Engineering (2017), 42 (6), pp. 2303–2311

Enhanced degradation of polyhydroxyalkanoates (PHAs) by newly isolated Burkholderia cepacia DP1 with high depolymerase activity
Azami, N.A., Wirjon, I.A., Kannusamy, S., Teh, A.-H., Abdullah, A.A.-A. 3 Biotech (2017), doi: 10.1007/s13205-017-0716-7

Enhanced production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer and antimicrobial yellow pigmentation from Cupriavidus sp. USMAHM13 with antibiofilm capability
Ismail, I., Gurusamy, T.P., Ramachandran, H., Al-Ashraf Amirul, A. Preparative Biochemistry and Biotechnology (2017), 47,388-396

Effects of Different Surfaces and Insecticide Carriers on Residual Insecticide Bioassays Againts Bed Bugs, Cimex spp. (Hemiptera: Cimicidae)
Kai Dang, G. Veera Singham, Stephen L. Doggett, David G. Lilly and Chow-Yang Lee.2017. Journal of Economic Entomology, 1-9

Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis
Yuko Makita, Kiaw Kiaw Ng, G. Veera Singham, Mika Kawashima, Hideki Hirakawa, Shushei Sato, Ahmad Sofiman Othman, Minami Matsui.2017. DNA Research, 1-11

synthesis of high 4-hydroxybutyrate copolymer by Cupriavidus sp. transformants using one-stage cultivation and mixed precursor substrates strategy
Syafiq I.M., Bhubalan K., Huong K.-H., Vigneswari S., Amirul A.A., Shantini K., Aziz N.A. 2017. Enzyme and Microbial Technology,98,1-8

Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway
Go Furusawa, Nyok-Sean Lau, Suganthi Appalasamy, Amirul Al-Ashraf Abdullah. Microbiology Open (2017), doi: 10.1002/mbo3.405

Crystallization and X-ray crystallographic analysis of recombinant TylP, a putative γ-butyrolactone receptor protein from Streptomyces fradiae
Mohd-Sharif N., Shaibullah S., Baharum S.N., Ng C.L., Givajothi V., Tan C.-S., Ho K.L., Teh A.-H., Waterman J. Acta Cryst. F (2017), 73,109-115

Genome feautures of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3

Nyok-Sean Lau, Ka-Kei Sam, Abdullah Al-Ashraf Amirul. 2017. Standards in Genomic Sciences, doi:10.1186/s40793-017-0232-8

Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of matang mangrove forest, malaysia
Balachandra Dinesh, Go Furusawa, A. A. Amirul. 2017. Archives of Microbiology, 199-63-67

Complete genome sequences of three Cupriavidus strains isolated from various Malaysian environments
Shafie N.A.H., Lau N.-S., Amirul A.A., Ramachandran H.2017. Genome Announcements (2017), doi: 10.1128/genomeA.01498-16

A fed-batch strategy to produce high poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) terpolymer yield with enhanced mechanical properties in bioreactor
Nursolehah Abd Aziz, Kai-Hee Huong, Coswald Stephen Sipaut, A. A. Amirul. Bioprocess and Biosystems Engineering (2017), 40,1643-1656


The rubber tree genome shows expansion of gene family associated with rubber biosynthesis

Nyok-Sean Lau,Yuko Makita, Mika Kawashima, Todd D. Taylor, Shinji Kondo, Ahmad Sofiman Othman,Alexander Chong Shu-Chien & Minami Matsui. 2016. Scientific Reports 6, Article number: 28594.

 Comparative genome analyses of novel Mangrovimonas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes

Balachandra Dinesh, Nyok-Sean Lau, Go Furusawa, Seok-Won Kim, Todd D. Taylor, Swee Yeok Foong, Alexander Chong Shu-Chien. 2016. Marine Genomics, 25 (2016), 115-121.

Discovery Of a new polyhydroxyalkanoate synthase from limestone soil through metagenomic approach

Yen Teng Tai, Choon Pin Foong, Nazalan Najimudin, Kumar Sudesh. 2016. Journal of Bioscience and Bioengineering, 121, 355-364.

Crystal Structure Of Anoxybacillus α-amylase Provides Insights Into Maltose Binding Of A New Glycosyl Hydrolase Subclass
Kian Piaw Chai, Noor Farhan Binti Othman. Aik-Hong Teh, Kok Lian Ho, Kok-Gan Chan, Mohd Shahir Shamsir, Kian Mau Goh & Chyan Leong Ng.    2016. Scientific Report, 6, Article number:23126.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human c1ORF123 protein
Rahaman, S.N.A, Yusop, J.M., Mohamed-Hussein, Z.-A, Ho, K.L., Teh, A.-H, Waterman, J., Ng, C.L.. 2016. Acta Cryst. F, 72, 207-213.

simultaneous dual syringe electrospinning system using benign solvent to fabricate nanofibrous P(3HB-co-4HB)/ collagen peptides construct as potential leave-on wound dressing
S. Vigneswari, V. Murugaiyah, G. Kaur, H.P.S. Abdul Khalil, A.A. Amirul. 2016. Materials Science and Engineering C, 66, 147-155.

Identification of a new polyhydroxyalkanoate (PHA) producer Aquitalea sp. USM4 (JCM 19919) and characterization of its PHA synthase
Lee-Mei Ng, Kumar Sudesh.2016. Journal of Bioscience and Bioengineering (2016). doi:10.1016/j.jbiosc.2016.03.024
Identification of differentially expressed genes and signalling pathways in bark of Hevea brasiliensis seedlings associated with secondary laticifer differentiation using gene expression microarray
Swee Cheng Loh,  Gincy P. Thottathil, Ahmad Sofiman Othman.2016. Plant Physiology and Biochemistry,107, 45-55

A fatty acyl desaturase (fads2) with dual ∆6 and ∆5 activities from the freshwater carnivorous striped snakehead Channa striata
Kuah M.-K., Shu-Chien A.C., Jaya-Ram A.2016. Comparative Biochemistry and Physiology -Part A, 201,146-155

Effects of polyhydroxyalkanoate degradation on soil microbial community
Ong S.Y., Sudesh K..2016. Polymer Degradation and Stability, 131,9-19

Biodegradation of Natural Rubber and Natural Rubber Products by Streptomyces sp. Strain CFMR 7
Nanthini J., Sudesh K..2016. Journal of Polymers and the Environment, 1-11

Synthesis, structures and antibacterial studies of non-functionalized and nitrile-functionalized bis-benzimidazolium salts and respective dinuclear silver(I)-N-heterocyclic carbene complexes
Haziz U.F.M., Haque R.A., Razali M.R., Amirul A.A., Shaheeda N..2016. Polyhedron, 117,628-636

New non-functionalized and nitrile-functionalized benzimidazolium salts and their silver(I) complexes: Synthesis, crystal structures and antibacterial studies
Haque R.A., Haziz U.F.M., Razali M.R., Abdullah A.A.-A., Shaheeda N..2016. Polyhedron, 109,208-217

Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia
Dinesh B., Furusawa G., Amirul A.A..2016. Archives of Microbiology, 1-5
Biomacromolecule immobilization: grafting of fish-scale collagen peptides onto aminolyzed P(3HB-co-4HB) scaffolds as a potential wound dressing
S Vigneswari, V Murugaiyah, G Kaur, H P S Abdul Khalil, and A A Amirul.2016. Biomedical Materials, 11,5

Synthesis of a palladium(II) complex of a N-heterocyclic carbene via transmetalation: crsytal structure and antibacterial studies
S Vigneswari, V Murugaiyah, G Kaur, H P S Abdul Khalil, and A A Amirul.2016. Transition Metal Chemistry, 41,715-781

Sequencing crop genomes: A gateway to improve tropical agriculture
Thottathil G.P., Jayasekaran K., Othman A.S..2016. Tropical Life Sciences Research, 1,93-114


Cloning, expression, purification, characterization, crystallization and X-ray crystallographic analysis of recombinant Der f 21 (rDer f 21) from Dermatophagoides farinae
S. L. Pang, K. L. Ho, J. Waterman, A.-H. Teh, F. T. Chew and C. L. Ng. 2015. Acta Crystallographica Section F: Structural Biology Communications 71, 1396–1400 (2015).

Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia.
Beng Soon Teh, Nyok-Sean Lau, Fui Ling Ng, Ahmad Yamin Abdul Rahman, Xuehua Wan, Jennifer A. Saito, Shaobin Hou, Aik-Hong Teh, Nazalan Najimudin, and Maqsudul Alam. 2015. Standards in Genomic Sciences, , 10(2015), 76

Calcium is required for ixotrophy of Aureispira sp. CCB-QB1.
Furusawa, G., Hartzell, P. L., & Navaratnam, V. 2015. Microbiology , 161(10), 1933-1941

Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang, Malaysia
Jayaram Nanthini, Kim-Hou Chia, Gincy P. Thottathil, Todd D. Taylor, Shinji Kondo, Nazalan Najimudin, Primo Baybayan, Siddharth Singh, Kumar Sudesh. 2015. Journal of Biotechnology , 214(2015), 47-48

Cyanobacteria: Photoautotrophic Microbial Factories for the Sustainable Synthesis of Industrial Products
Nyok-Sean Lau, Minami Matsui, Amirul Al-Ashraf Abdullah. 2015. BioMed Research International  Volume 2015 (2015), Article ID 754934, 9 pages

Open and Lys–His hexacoordinated closed structures of a globin with swapped proximal and distal sites
Teh AH, Saito JA, Najimudin N, Alam M. 2015. Scientific Reports 5, 11407 (2015).

Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis
Teh AH, Makino M, Hoshino T, Baba S, Shimizu N, Yamamoto M, Kumasaka T. 2015. Acta Crystallographica Section D: Biological Crystallography 71, 1392–1399 (2015).

Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1
Furusawa G, Lau NS, Shu-Chien AC, Jaya-Ram A, Al-Ashraf AA. 2015. Marine Genomics, 19 (2015), 39-44.
Genetic relatedness of Candida albicans bloodstream infection clinical isolates in Malaysia
Saranpal C.-S., Lim C.S.Y., Chong P.P., Ng K.P. 2015. Malaysian Journal of Microbiology,11,294-299
Characteristics of limestone soil collected from Gunung Lang, Perak and metagenomic analysis of the soil microbial community
Shantini K., Yahya A.R.M., Amirul A.A.. 2015. Applied Biochemistry and Biotechnology,11,373-382

Influence of feeding and controlled dissolved oxygen level on the production of poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Copolymer by Cupriavidus sp. USMAA2-4 and its characterization
Tai Y.T., Najimudin N., Sudesh K. 2015. Malaysian Journal of Microbiology,5,doi:10.1038/srep11407

Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang, Malaysia
Nanthini J., Chia K.-H., Najimudin N., Sudesh K., Thottathil G.P., Taylor T.D., Kondo S., Baybayan P., Singh S. 2015. Journal of Biotechnology,214,47-48


Identification of new rubber-degrading bacterial strains from aged latex
Chia, K.-H., Nanthini, J., Thottathil, G.P., Najimudin, N., Hakim Mas Haris, M.R., Sudesh, K. 2014. Polymer Degradation and Stability, 109 (2014), 354-361.

Chemopreventive effects of standardized papaya leaf fraction on oxidatively stressed human liver cells
S.-A. Tan, L. Goya, S. Ramanathan, S.F. Sulaiman, M. Alam, V. Navaratnam. 2014. Food Research International, 64 (2014) 387-395.

Allosteric pocket of the dengue virus (serotype 2) NS2B/NS3 protease: In silico ligand screening and molecular dynamics studies of inhibition
A. Mukhametov, E.I. Newhouse, N.A. Aziz, J.A. Saito, M. Alam. 2014. Journal of Molecular Graphics and Modelling, 52 (2014) 103-113.

Crystal structure of truncated hemoglobin from an extremely thermophilic and acidophilic bacterium
Farrukh Jamil,*, Aik-Hong Teh, Ermin Schadich, Jennifer A. Saito, Nazalan Najimudin, and Maqsudul Alam. 2014. J Biochem (2014) doi: 10.1093/jb/mvu023

Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater

Foong C.P., Lau N.-S., Matsui M., Sudesh K., Deguchi S., Toyofuku T., Taylor T.D. 2014. BMC Microbiology  doi:10.1186/s12866-014-0318-z


Draft genome sequence of the rubber tree Hevea brasiliensis
Ahmad Yamin Abdul Rahman, Abhilash O. Usharraj, Biswapriya B. Misra, Gincy P. Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Feong Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz, Anton Yuryev, Bjarne Knudsen, Alexandre Dionne-Laporte, Nokuthula P. Mchunu, Qingyi Yu, Brennick J. Langston, Tracey Allen K. Freitas, Aaron G. Young, Rui Chen, Lei Wang, Nazalan Najimudin, Jennifer A. Saito, and Maqsudul Alam. 2013. BMC Genomics, 14:75. ( Rubber Tree Genome Browser (

Xylanase superproducer: Genome sequence of a compost-loving thermophilic fungus, Thermomyces lanuginosus strain SSBP
Mchunu N.P., Permaul K., Singh S., Saito J.A., Alam M., Abdul Rahman A.Y. 2013. Genome Announcements, 3,doi: 10.1128/genomeA.00388-13

The genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12

Ong S.Y., Rahman A.Y.A., Saito J.A., Pratap C.B., Nath G., Wan X., Hou S., Alam M. 2013. Standards in Genomic Sciences, 7,483-496

Crystal structure of a compact α-amylase from Geobacillus thermoleovorans

Mok S.-C., Teh A.-H., Saito J.A., Najimudin N., Alam M. 2013. Enzyme and Microbial Technology, 53,46-54


Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5
Muhd Khairul Luqman Muhd Sakaff, Ahmad Yamin Abdul Rahman, Jennifer A. Saito, Shaobin Hou, and Maqsudul Alam. 2012. Journal of Bacteriology. 194(5):1239.

Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1
Beng Soon Teh, Ahmad Yamin Abdul Rahman, Jennifer A. Saito, Shaobin Hou, and Maqsudul Alam. 2012. Journal of Bacteriology. 194(5):1240.

Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium
Jimmy H. W. Saw, Anton Yuryev, Masaomi Kanbe, Shaobin Hou, Aaron G. Young, Shin-Ichi Aizawa, and Maqsudul Alam. 2012. Standards in Genomic Sciences, 6(1):84-93.

Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12
Su Yean Ong, Chandra Bhan Pratap, Xuehua Wan, Shaobin Hou, Ahmad Yamin Abdul Rahman, Jennifer A. Saito, Gopal Nath, and Maqsudul Alam. 2012. Journal of Bacteriology, 194(8):2115-2116.

Protective effects of papaya extracts on tert-butyl hydroperoxide mediated oxidative injury to human liver cells (an in-vitro study)
Sheri-Ann Tan, Sonia Ramos, Maria Angeles Martin, Raquel Mateos, Michael Harvey, Surash Ramanathan, Nazalan Najimudin, Maqsudul Alam, Laura Bravo, and Luis Goya. 2012. Free Radicals and Antioxidants, 2(3):10-19.

Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina
Md. Shahidul Islam, Md. Samiul Haque, Mohammad Moinul Islam, Emdadul Mannan Emdad, Abdul Halim, Quazi Md. Mosaddeque Hossen, Md. Zakir Hossain, Borhan Ahmed, Sifatur Rahim, Md. Sharifur Rahman, Md. Monjurul Alam, Shaobin Hou, Xuehua Wan, Jennifer A. Saito, and Maqsudul Alam. 2012. BMC Genomics, 13,493

 Co-expressed peJK genes of lobster (Jasus edwardsii)

Schadich E., Mason D., Sin F. 2012. Australian Journal of Zoology, 60,10-17