Publications

Baek, S., Kim, B., Pathiraja, D. and Choi, I.G. Development of a Transposon-Based Genome Engineering Toolkit for Efficient and Adaptable Genetic Modifications in Wolfiporia cocos. ACS Synth Biol, 2025, 14(4), pp.1152-1160.

Pathiraja, D., 2025. Blue Chassis—Advances in Biochemical Synthesis in Engineered Marine Bacteria. In Transformative Applied Research in Computing, Engineering, Science and Technology (pp. 147-151). CRC Press.

Anjanee, H. I., Pathiraja, D., 2025. Comparative genome analysis of colanic acid biosynthesis.  Proceedings of the 81st Annual Sessions of Sri Lanka Association for the Advancement of Science.

Weerawansa, O. E., Pathiraja, D., 2025. Global secretome analysis of agar-degrading bacteria.   Proceedings of the 81st Annual Sessions of Sri Lanka Association for the Advancement of Science.

Dinisha, M., Pathiraja, D., 2025. Prevalence of antibiotic resistance in culturable microbiome of curd in Sri Lankan market. Proceedings of the 81st Annual Sessions of Sri Lanka Association for the Advancement of Science.

Kim, B.; Xu, X.; Lee, H.; Pathiraja, D.; Jae-Young, K.; Choi, Y. H.; Choi, I.-G.; Kim, S. H. Complete Genome Sequence of Candidate Probiotic Limosilactobacillus Fermentuum KUFM407. J Anim Sci Technol 2024, 66 (4), 859.

Pathiraja, D., 2024. Bioactive sugars from red macroalgae: structure, preparation, and applications. Chemistry in Sri Lanka, vol 41 (2), pp 52-61. Institute of Chemistry Ceylon.

Lakseya, S. A. L., Pathiraja, D. and Hettiarachchi, C. H., 2024. Transcriptome analysis of Ophiorrhiza pumila to identify Camptothecin biosynthetic pathway. 4th International conference on Frontiers in Molecular Life Sciences, Institute of Biochemistry, Molecular Biology and Biotechnology.

Malalasekera, W. S., Hettiarachchi, C., Pathiraja, D., Bathige, S. D. N. K., Zurita F., 2024. Determination of camptothecin levels in stress induced Ophiorrhiza pumila plant. 4th International conference on Frontiers in Molecular Life Sciences, Institute of Biochemistry, Molecular Biology and Biotechnology.

Malalsekara, W. S., Bathige, S. D. N. K., Pathiraja, D. and Hettiarachchi, C. H., 2024. Determination of antibacterial activity in stress induced Ophiorrhiza pumila plant. Frontiers in Chemical Technology, Institute of Chemistry Ceylon.

Kim, J.-Y., Kang, B., Kweon, J., Min, J., Park, H., Oh, S., Lee, J., Kim, B., Pathiraja, D., Choi, I.G. and Chang, I. S., 2024. ASM Microbe, American Society for Microbiology.

Malalsekara, W. S., Bathige, S. D. N. K., Pathiraja, D. and Hettiarachchi, C. H., 2024. Determination of antifungal activity in stress induced Ophiorrhiza pumila plant and qualitative analysis of secondary metabolites. Proceedings of the 80th Annual Sessions of Sri Lanka Association for the Advancement of Science.

Pathiraja, D.; Park, B.; Kim, B.; Stougaard, P.; Choi, I.-G. Constructing Marine Bacterial Metabolic Chassis for Potential Biorefinery of Red Algal Biomass and Agaropectin Wastes. ACS Synth Biol 2023, 12 (6), 1782–1793.

Pathiraja, D.; Cho, J.; Kim, J.; Choi, I.-G. Metabarcoding of eDNA for Tracking the Floral and Geographical Origins of Bee Honey. Food Research International 2023, 164, 112413.

Eor, J. Y.; Lee, C. S.; Moon, S. H.; Cheon, J. Y.; Pathiraja, D.; Park, B.; Shin, M. J.; Kim, J.-Y.; Kim, S.; Noh, Y. Effect of Probiotic-Fortified Infant Formula on Infant Gut Health and Microbiota Modulation. Food Sci Anim Resour 2023, 43 (4), 659.

Kim, B.; Kim, K.; Xu, X.; Lee, H.; Pathiraja, D.; Park, D.-J.; Choi, I.-G.; Oh, S. Complete Genome and Two Plasmids Sequences of Lactiplantibacillus Plantarum L55 for Probiotic Potentials. J Anim Sci Technol 2023, 65 (6), 1341–1344.

Kim, B.; Meng, Z.; Xu, X.; Baek, S.; Pathiraja, D.; Choi, I.-G.; Oh, S. Complete Genome Sequence of Limosilactobacillus Fermentum JNU532 as a Probiotic Candidate for the Functional Food and Feed Supplements. J Anim Sci Technol 2023, 65 (1), 271.

Pathiraja, D., Stougaard, P. and Choi, I.G., 2023. Engineering marine bacterium Pseudoalteromonas atlantica KCTC 22877 as a microbial chassis for red algal biorefinery. Proceedings of the 79th Annual Sessions of Sri Lanka Association for the Advancement of Science.

Yeonsoo, P., Pathiraja, D. and In-Geol, C., 2023. Designing and Building Bioparts and Devices for Constructing Multi-targeting Retron Systems. Fall meeting and International Symposium of the Korean Society for Biotechnology and Bioengineering.

Pathiraja, D., Park, B. and Choi, I., 2023, Engineering Marine Bacteria as a Chassis Platform for Red algal Biorefinery. 50th Annual Meeting and Symposium of the Korean Society for Microbiology and Biotechnology.

Pathiraja, D.; Cho, J.; Stougaard, P.; Choi, I.-G. Enzymatic Process for the Carrageenolytic Bioconversion of Sulfated Polygalactans into β-Neocarrabiose and 3, 6-Anhydro-d-Galactose. J Agric Food Chem 2022, 71 (1), 635–645.

Pathiraja, D.; Wee, J.; Cho, K.; Choi, I.-G. 1. Soil environment reshapes microbiota of laboratory-maintained Collembola during host development. Environ Microbiome 2022, 17 (1), 16.

Kim, C.-H.; Yoo, Y.; Kim, D.; Khim, J. S.; Pathiraja, D.; Kim, B.; Choi, I.-G.; Kim, J.-J. Aurantiacibacter Sediminis Sp. Nov., a Marine Bacterium Isolated from a Tidal Flat. Int J Syst Evol Microbiol 2022, 72 (6), 005406.

Pathiraja, D.; Christiansen, L.; Park, B.; Schultz-Johansen, M.; Bang, G.; Stougaard, P.; Choi, I.-G. A Novel Auxiliary Agarolytic Pathway Expands Metabolic Versatility in the Agar-Degrading Marine Bacterium Colwellia Echini A3T. Appl Environ Microbiol 2021, 87 (12), e00230-21.

Kim, D.; Yoo, Y.; Khim, J. S.; Yang, D.; Pathiraja, D.; Park, B.; Choi, I.-G.; Kim, J.-J. Altererythrobacter Lutimaris Sp. Nov., a Marine Bacterium Isolated from a Tidal Flat and Reclassification of Altererythrobacter Deserti, Altererythrobacter Estronivorus and Altererythrobacter Muriae as Tsuneonella Deserti Comb. Nov., Croceicoccus Estronivorus Comb. Nov. and Alteripontixanthobacter Muriae Comb. Nov. Int J Syst Evol Microbiol 2021, 71 (12), 005134.

Kang, H.; Park, B.; Oh, S.; Pathiraja, D.; Kim, J.-Y.; Jung, S.; Jeong, J.; Cha, M.; Park, Z.-Y.; Choi, I.-G. Metabolism Perturbation Caused by the Overexpression of Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Gene Complex Accelerated Gas to Acetate Conversion Rate of Eubacterium Limosum KIST612. Bioresour Technol 2021, 341, 125879.

Kwak, M.-J.; Park, M.-Y.; Choi, Y.-S.; Cho, J.; Pathiraja, D.; Kim, J.; Lee, H.; Choi, I.-G.; Whang, K.-Y. Dietary Sophorolipid Accelerates Growth by Modulation of Gut Microbiota Population and Intestinal Environments in Broiler Chickens. J Anim Sci Biotechnol 2021, 12, 1–9.

Yoo, Y.; Kim, D.; Lee, H.; Khim, J. S.; Kim, B.; Yang, D.; Pathiraja, D.; Choi, I.-G.; Kim, J.-J. Novosphingobium Aureum Sp. Nov., a Marine Bacterium Isolated from Salt Flat Sediment. Int J Syst Evol Microbiol 2021, 71 (7), 004930.

Christiansen, L.; Pathiraja, D.; Bech, P. K.; Schultz-Johansen, M.; Hennessy, R.; Teze, D.; Choi, I.-G.; Stougaard, P. A Multifunctional Polysaccharide Utilization Gene Cluster in Colwellia Echini Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan. mSphere 2020, 5 (1), 10–1128.

Pathiraja, D.; Chun, Y.; Cho, J.; Min, B.; Lee, S.; Park, H.; Byun, J.; Choi, I.-G. Novel Monomeric Fungal Subtilisin Inhibitor from a Plant-Pathogenic Fungus, Choanephora Cucurbitarum: Isolation and Molecular Characterization. Appl Environ Microbiol 2020, 86 (22), e01818-20.

Pathiraja, D.; Byun, J.; Lee, S.; Choi, I.-G. Preparation of a Ribosomally Synthesized Fungal Peptide Toxin Precursor and Its In-Vitro Cyclization. J Biotechnol 2020, 308, 124–129.

Kang, H.; Park, B.; Bolo, N. R.; Pathiraja, D.; Park, S.; Cha, M.; Choi, I.; Chang, I. S. Gene‐Centric Metagenome Analysis Reveals Gene Clusters for Carbon Monoxide Conversion and Validates Isolation of a Clostridial Acetogen for C2 Chemical Production. Biotechnol J 2019, 14 (6), 1800471.

Hennessy, R. C.; Park, B.; Pathiraja, D.; Choi, I.-G.; Schultz-Johansen, M.; Stougaard, P. Draft Genome Sequences of Two Glycoalkaloid-Degrading Arthrobacter Strains Isolated from Green Potato Peel. Microbiol Resour Announc 2019, 8 (16), 10–1128.

Pathiraja, D.; Lee, S.; Choi, I.-G. Model-Based Complete Enzymatic Production of 3, 6-Anhydro-L-Galactose from Red Algal Biomass. J Agric Food Chem 2018, 66 (26), 6814–6821.

Dichmann, S. I.; Park, B.; Pathiraja, D.; Choi, I.-G.; Stougaard, P.; Hennessy, R. C. Draft Genome Sequence of a Novel Serratia Sp. Strain with Antifungal Activity. Microbiol Resour Announc 2018, 7 (22), 10–1128.

Jeong, J.-J.; Sang, M. K.; Pathiraja, D.; Park, B.; Choi, I.-G.; Kim, K. D. Draft Genome Sequence of Phosphate-Solubilizing Chryseobacterium Sp. Strain ISE14, a Biocontrol and Plant Growth-Promoting Rhizobacterium Isolated from Cucumber. Genome Announc 2018, 6 (26), 10–1128.

Jeong, J.-J.; Moon, H.-J.; Pathiraja, D.; Park, B.; Choi, I.-G.; Kim, K. D. Draft Genome Sequences of Bacillus Megaterium KU143, Microbacterium Testaceum KU313, and Pseudomonas Protegens AS15, Isolated from Stored Rice Grains. Genome Announc 2018, 6 (22), 10–1128.

Jeong, J.-J.; Lee, Y. J.; Pathiraja, D.; Park, B.; Choi, I.-G.; Kim, K. D. Draft Genome Sequences of Chryseobacterium Lactis NCTC11390T Isolated from Milk, Chryseobacterium Oncorhynchi 701B-08T from Rainbow Trout, and Chryseobacterium Viscerum 687B-08T from Diseased Fish. Genome Announc 2018, 6 (26), 10–1128.

Pathiraja, D.; Kim, K. H.; Choi, I.-G. Rapid and Robust Enzymatic Sensing and Quantitation of 3, 6-Anhydro-L-Galactose in a Heterogeneous Sugar Mixture. Carbohydr Res 2017, 446, 13–18.

Wu, C.; Hwang, S. H.; Jia, Y.; Choi, J.; Kim, Y.-J.; Choi, D.; Pathiraja, D.; Choi, I.-G.; Koo, S.-H.; Lee, S.-J. Olfactory Receptor 544 Reduces Adiposity by Steering Fuel Preference toward Fats. J Clin Invest 2017, 127 (11), 4118–4123.