Publications

Research articles
    2023
  1. Narumol Jariyasopit, Sakda Khoomrung (2023) Mass Spectrometry-based Analysis of Gut Microbial Metabolites of Aromatic Amino Acids Computational and Structural Biotechnology Journal
  2. Sophida Suta, Apinya Surawit, Pichanun Mongkolsucharitkul, Bonggochpass Pinsawas, Thamonwan Manosan, Suphawan Ophakas, Tanyaporn Pongkunakorn, Sureeporn Pumeiam, Kitti Sranacharoenpong, Sawannee Sutheeworapong, Patcha Poungsombat, Sakda Khoomrung, Pravit Akarasereenont, Iyarit Thaipisuttikul, Bhoom Suktitipat and Korapat Mayurasakorn (2023) Prolonged Egg Supplement Advances Growing Child'as Growth and Gut Microbiota, Nutrients
  3. Mathemaab V. B., Sencd P., Lamichhanec S., Oreљičcd M., Khoomrung S. (2023) Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine, Computational and Structural Biotechnology Journal
  4. Wanichthanarak K. , Nookaew I., Pasookhush P., Wongsurawat T., Jenjaroenpun P., Leeratsuwan N., Wattanachaisaereekul S., Visessanguan W., Sirivatanauksorn Y., Nuntasaen N., Kuhakarn C., Reutrakul V., Ajawatanawong P. and Khoomrung S.(2023) Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae, BMC Plant Biology

    2022
  5. Jariyasopit N., Limjiasahapong S., Kurilung A., Sartyoungkul S., Wisanpitayakorn P., Nuntasaen N., Kuhakarn C., Reutrakul V., Kittakoop p., Sirivatanauksorn Y., and Khoomrung S.(2022) Traveling Wave Ion Mobility-Derived Collision Cross Section Database for Plant Specialized Metabolites: An Application to Ventilago harmandiana Pierre.J. Proteome Res.
  6. Indrati1 N., Phonsatta N., Poungsombat P., Khoomrung S., Sumpavapol1 P. and Panya A. (2022) Metabolic profiles alteration of Southern Thailand traditional sweet pickled mango during the production process.Frontier in Nutrition.
  7. Duangkumpha, K., Jariyasopit, N., Wanichthanarak, k., Dhakal, E., Wisanpitayakorn, P.,Thotsiri S., Sirivatanauksorn Y., Kitiyakara C., Sathirapongsasuti N., Khoomrung S. (2022) GCxGC-TOFMS Metabolomics Analysis Identifies Elevated Levels of Plasma Sugars and Sugar Alcohols in Diabetic Mellitus Patients with Kidney FailureJournal of Biological Chemistry.
  8. Wisanpitayakorn, P., Mickolajczyk, K. J., Hancock, W. O., Vidali, L., Tьzel, E. (2022) Measurement of the persistence length of cytoskeletal filaments using curvature distributions.Biophysical Journal.
  9. Indrati, N., Sumpavapol, P., Samakradhamrongthai, R.S., Phonsatta, N., Poungsombat, P., Khoomrung, S., Panya, A. (2022) Volatile and non-volatile compound profiles of commercial sweet pickled mango and its correlation with consumer preference.International journal of Food Science and Technology.
  10. Mathema, V.B., Duangkumpha, K., Wanichthanarak, K., Jariyasopit, N., Dhakal, E., Sathirapongsasuti, N., Kitiyakara, C., Sirivatanauksorn, Y., Khoomrung, S. (2022) CRISP: a deep learning architecture for GCxGC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics.Briefings in Bioinformatics.

    2021
  11. Anekthanakul, K., Manocheewa, S., Chienwichai, K., Poungsombat, P., Limjiasahapong, S., Wanichthanarak, K., Jariyasopit, N., Mathema,V.B. , Kuhakarn, C., Reutrakul, V.,Phetcharaburanin, J., Panya, A., Phonsatta , N., Visessanguan, W., Pomyen, Y., Sirivatanauksorn, Y., Worawichawong, S., Sathirapongsasuti, N., Kitiyakara, C., and Khoomrung, S. (2021) Predicting Lupus Membranous Nephritis using Reduced Picolinic Acid to Tryptophan Ratio as a Urinary Biomarker.iScience.
  12. Halappanavara, S., Wu, D., Boyadzhieva, A., Solorio-Rodriguez, A., Williams, A., Jariyasopit, N., Saini, A., and Harner, T. (2021) Toxicity screening of air extracts representing different source sectors in the Greater Toronto and Hamilton areas: In vitro oxidative stress, pro-inflammatory response, and toxicogenomic analysis.Mutation Research/Genetic Toxicology and Environmental Mutagenesis.
  13. Kaewnarin, K., Limjiasahapong, N., Jariyasopit, N., Anekthanakul, K., Kurilung, A.,, Choong Chee Wong, S., Sirivatanauksorn, Y., Visessanguan, W., and Khoomrung, S.* (2021) High-Resolution QTOF-MRM for Highly Accurate Identification and Quantification of Trace Levels of Triterpenoids in Ganoderma lucidum Mycelium.American Society for Mass Spectrometry.
  14. Vasiljevic, T., Jariyasopit, N., Schuster, J.K., and Harner, T. (2021) Insights into sources and occurrence of oxy- and nitro-PAHs in the alberta oil sands region using a network of passive air samplers. Environmental Pollution.
  15. Jariyasopit, N., Harner, T., Shin, C., and Park, R. (2021) The Effects of Plume Episodes on PAC Profiles in the Athabasca Oil Sands Region. Environmental Pollution.
  16. Thitisaksakul,M., Sangwongchai, W., Mungmonsin, U., Promrit, P., Krusong, K., Wanichthanarak, K. ,and Tananuwong, K. (2021) Granule morphological and structural variability of Thai certified glutinous rice starches in relation to thermal, pasting, and digestible properties. Cereal Chemistry.
  17. Limjiasahapong, S., Kaewnarin, K., Jariyasopit, N., Hongthong, S., Nuntasaene, N., Robinson, J.L., Nookaew, I., Sirivatanauksorn, Y., Kuhakarn, C., Reutrakul, V., and Khoomrung, S.* (2021) UPLC-ESI-MRM for absolute quantification and MS/MS structural elucidation of six specialized pyranonaphthoquinone metabolites from Ventilago harmandiana. Frontiers in Plant Science. 11:2038.
    18.
  18. Jariyasopit, N., Khamsaeng,S., Panya, A., Vinaisuratern, P., Metem, P., Asawalertpanich, W., Visessanguan, W., Sirivatanauksorn, V., and Khoomrung, S.*(2021) Quantitative Analysis of Nutrient Metabolite Compositions of Retail Cow’s Milk and Milk Alternatives in Thailand Using GC-MS. Journal of Food Composition and Analysis
    19.

    2020
  19. Wanichthanarak, K., and Thitisaksakul, M. (2020) ThRSDB: a database of Thai rice starch composition, molecular structure and functionality. Database: The Journal of Biological Databases and Curation
    20.
  20. Wanichthanarak, K.,Boonchai, C., Kojonna, T., Chadchawan, S., Sangwongchai, W., and Thitisaksakul, M. (2020) Deciphering rice metabolic flux reprograming under salinity stress via in silico metabolic modeling. Computational and Structural Biotechnology Journal
    21.
  21. Winayanuwattikun, W., Varothai, S., Tuchinda, P., Kulthanan, K., Prasertworonun, N., Dasri, P., Wanichthanarak, K. , and Akarasereenont, P. (2020) A double-blinded, randomized, split-side, vehicle-controlled study of the efficacy of cleanser containing Acanthus ebracteatus Vahl., Suregada multiflora, and Acacia concinna in patients with atopic dermatitis: A pilot study. Asian Pacific Journal of Allergy and Immunology
    22.
  22. Pomyen, Y.,Wanichthanarak, K., Poungsombat, P., Fahrmann, J., Grapov, D., and Khoomrung., S.*(2020) Deep Metabolome: Applications of deep learning in metabolomics. Computational and Structural Biotechnology Journal
    23.
  23. Sen, P., Lamichhane, S., Mathema, V.B., McGlinchey, A., Dickens, A.M., Khoomrung, S. , OreЕЎiДЌ, M.(2020) Deep learning meets metabolomics: a methodological perspective. Briefings in Bioinformatics
    24.
  24. Saini, A., Harner, T., Chinnadhurai, S., Schuster, J.K., Yates, A., Sweetman, A., Aristizabal-Zuluaga, B.H., JimГ©nez, B., Manzano, C.A., Gaga, E.O., Stevenson, G., Falandysz, J., Ma, J., Miglioranza, Karina, S.B.M., Kannan, K., Tominaga, M., Jariyasopit, N., Rojas, N.Y., Amador-MuГ±oz, O., Sinha, R., Alani, R., Suresh, R., Nishino, T., and Shoeibs, T.(2020) GAPS-Megacities: A new global platform for investigating persistent organic pollutants and chemicals of emerging concern in urban air. Environmental Pollution, p.115416
    25.
  25. Hodge, K., Makjaroen, J., Robinson, J., Khoomrung, S. and Pisitkun, T. (2020) Deep Proteomic Deconvolution of Interferons and HBV Transfection Effects on a Hepatoblastoma Cell Line. ACS Omega.
    26.
  26. Liu, Y., Liu, Q., Krivoruchko, A., Khoomrung, S., Nielsen, J. (2020) Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production Nature Chemical Biology, 16:197–205
    27.

    2019
  27. Khoomrung, S., Nookaew, I. , Sen ,P., Olafsdottir, T.A., Persson, J., Moritz, T., Andersen, P., Harandi, A.M., Nielsen, J. (2019) Metabolic profiling and compound-class identification reveal alterations in serum triglyceride levels in mice immunized with human vaccine adjuvant Alum Journal of Proteome Research, 19(1):269–278
  28. Gaga, E.E., Harner, T., Dabek-Zlotorzynska, E., Celo, V., Evans, G.J., Jeong, C.H., Halappanavar, S., Jariyasopit, N. Su, Y. (2019) Polyurethane Foam (PUF) Disk Samplers for Measuring Trace Metals in Ambient Air Environmental Science & Technology Letters. 6(9):545-550
  29. Nyunt T, Britton M, Wanichthanarak K , Budamagunta M, Voss JC, Wilson DW, Rutledge JC, Aung HH.(2019) Mitochondrial oxidative stress-induced transcript variants of ATF3 mediate lipotoxic brain microvascular injury Free Radical Biology and Medicine. 143:25-46
  30. Jariyasopit N, Tung P, Su K,Halappanavar S,Evans G. J, Su Y, Khoomrung S, Harner M.(2019) Polycyclic aromatic compounds in urban air and associated inhalation cancer risks: A case study targeting distinct source sectors Environmental Pollution. 252:1882-1891
    31.
  31. Jeennor S, Anantayanon J, Panchanawaporn S, Khoomrung S, Chutrakula C, Laoteng K.(2019) Reengineering lipid biosynthetic pathways of Aspergillus oryzae for enhanced production of γ-linolenic acid and dihomo-γ-linolenic acid. Gene. 706:106-114.
    32.
  32. Wanichthanarakab K, Jeamsripongc S, Pornputtapongde N, Khoomrung S*. (2019) Accounting for biological variation with linear mixed-effects modelling improves the quality of clinical metabolomics data. Computational and Structural Biotechnology Journal. 17:611-618.
    33.

    2018
  33. Guo Z, Khoomrung S, Nielsen J, Olsson L. (2018) Changes in lipid metabolism convey acid tolerance in Saccharomyces cerevisiae. Biotechnol Biofuels. 11 (1):297.
    34.

    2017
  34. Rodriguez A, Chen Y, Khoomrung S, Г–zdemir E, Borodina I, Nielsen J. (2017) Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains. Metab. Eng. 44: 265-272.
    35.

    2016
  35. Fletcher E, Feizi A, Bisschops MMM, Hallström BM, Khoomrung S, Siewers V, Nielsen J. (2016) Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments. Metab. Eng. 39: 19-28.
    36.
  36. Olafsdottir TA, Lindqvist M, Nookaew I , Andersen PL, Maertzdorf J, Persson J, Weiner J, Zhang Y, Anderson J, Khoomrung S, Sen P, Agger EM, Coler R, Carter D, Meinke A, Kaufmann SHE, Reed SG, Harandi AM. (2016) Comparative Systems Biology Analysis Reveals Molecular Signature of Three Clinically Tested Vaccine Adjuvants. Sci. Rep. 6:39097.
    37.
  37. Tippmann S, Nielsen J, Khoomrung S*. (2016) Improved quantification of farnesene during microbial production from S. cerevisiae in two-liquid-phase fermentations. Talanta. 146: 100-106.
    38.

    2015
  38. Khoomrung S*, Martinez JL, Tippmann, S, Jansa-Ard S, Buffing M, Nicastro R, Nielsen J. (2015) Expanded metabolite coverage of Saccharomyces cerevisiase extract through improved chloroform/methanol extraction and t-BDMS derivatization. Anal. Chem Res. 6:9-16.
    39.
  39. Qin J. G., Zhou Y. J., Krivoruchko A, Huang M, Liu L, Khoomrung S, Siewers S, Jiang B, Nielsen J. (2015) Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine. Nat Commun 6: 8224.
    40.
  40. Nicastro R, Tripodi F, Guzzi C, Reghellin V, Khoomrung S, Airoldi C, Nielsen J, Alberghina L, Coccetti P. (2015) Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK. BBA- Mol Cell Res. 1853: 1615-1625.
    41.

    2014
  41. Khoomrung S*, Raber G, Laoteng K, Francesconi KA. (2014) Identification and characterization of fish oil supplements based on fatty acid analysis combined with a hierarchical clustering algorithm. Eur Lipid Sci Tech. 116:795-804.
    42.
  42. Knuf C, Nookaew I, Remmers I, Khoomrung S, Brown S, Berry A, Nielsen J. (2014) Physiological Characterization of the High Malic Acid-Producing Aspergillus oryzae Strain 2103a-68. Appl Microbiol Biotechnol 98(8): 3517-3527.
    43.

    2013
  43. Hussain A, Olausson H, Nilsson S, Nookaew I, Khoomrung S, Andersson L, Koskela A, Tuukkanen J, Ohlsson C, Holmag A. (2013) Maternal beef and postweaning herring diets increase bone mineral density and strength in mouse offspring. Exp Biol Med (Maywood). 238:1362-1369.
    44.
  44. Hussain A, Nookaew I, Khoomrung S, Andersson L, Larsson I, Hulthen L, Jansson N. Jakubowicz R, Nilsson S, Sandberg AS, Nielsen J, Holmang A. (2013) A maternal diet of fatty fish reduces body fat of offspring compared with a maternal diet of beef and a post-weaning diet of fish improves insulin sensitivity and lipid profile in adult C57BL/6 male mice. Acta Physiol. 209: 220-234.
    45.
  45. Khoomrung S, Chumnanpuen P, Jansa-Ard S, StГҐhlman M, Nookaew I, Boren J, Nielsen J. (2013) Rapid quantification of yeast lipid using microwave-assisted total lipid extraction and HPLC-CAD. Anal Chem. 85: 4912-4919.
    46.

    2012
  46. Khoomrung S, Chumnanpuen P, Jansa-ard S, Nookaew I, Nielsen J. (2012) Fast and accurate preparation fatty acid methyl esters by microwave-assisted derivatization in the yeast Saccharomyces cerevisiae. Appl Microbiol Biotechnol, 94: 1637-1646.
    47.
  47. Shi S, Valle-RodrГ­guez JO, Khoomrung S, Siewers V, Nielsen J. (2012) Functional expression of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production. Biotechnol Biofuels, 5:7.
    48.

    2009
  48. Raber G, Khoomrung S, Taleshi MS, Edmonds JS, Francesconi KA. (2009) Identification of arsenolipids with GC/MS. Talanta. 78: 1215-1218.
    49.

    2008
  49. Khoomrung S, Laoteng K, Jitsue S, Cheevadhanarak S. (2008) Significance of fatty acid supplementation on profile of cell growth, fatty acid and gene expression of three desaturases in Mucor rouxii. Appl Microbiol Biotechnol. 80: 499 -506.
    50.

Review article
  1. Grapov D, Fahrmann F, Wanichthanarak K, Khoomrung S. (2018) Rise of deep learning for genomic, proteomic and metabolomic data integration in precision medicine. OMICS. 10: 630-636.
    2.
  2. Khoomrung S*, Wanichthanarak K, Nookaew I, Thamsermsang O, Seubnooch P, Laohapand T, Akarasereenont P. (2017) Metabolomics and integrative omics for the development of Thai traditional medicine. Front. Pharmacol 8: 474.
    3.

* = Corresponding author