Treenut Saithong

Academic Position : Associate Professor

Tel. : (+66)2-470-7714

Email : treenut.sai@kmutt.ac.th

Lab Website : Biological Modeling Laboratory

Research Interests

  • Systems biology and bioinformatics in plant metabolism
  • Biological network construction from high-throughput data
  • Mathematical modelling & omics data integration
    • Genome-scale metabolic model & genetic networks
    • Multi-level regulation in plants
    • Genotype-phenotype relationship
  • System regulation:
    • plant-microbe interaction,
    • plant growth with resource-used efficiency
  • Principle of biological modelling:
    • Model analysis and toy model simulation,
    • Optimisation methods for biological modelling

Education

PhD in Systems Biology

Recent Publications

International Journals

  1. Srinak N, Chiewchankaset P, Kalapanulak S, Panichnumsin P, Saithong T* (2024) Metabolic cross-feeding interactions modulate the dynamic community structure in Microbial Fuel Cell under variable organic loading wastewaters, submitted to PLoS Computational Biology (under revision).
  2. Nguyen NXB, Saithong T, Boonyaritthongchai P, Buanong M, Kalapanulak S, Wongs-Aree C (2024) Methyl salicylate induces endogenous jasmonic acid and salicylic acid in ‘Nam Dok Mai’ mango to maintain postharvest ripening and quality, submitted to Scientia Horticulturae (under review).
  3. Punyasu N, Thaiprsit J, Kalapanulak S, Saithong T*, JA Postma (2024) Modeling cassava root system architecture and the underlying dynamics in shoot-root carbon allocation, https://doi.org/10.1007/s11104-024-06771-y (T1: 90th percentile: Plant science; IF4.6; H-index 225).
  4. Sriwichai N, Sangcharoen R, Saithong T, Simpson D, Goryanin I, Boonapatcharoen N, Kalapanulak S, Panichnumsin P (2024) Optimization of microbial fuel cell performance application to high sulfide industrial wastewater treatment by modulating microbial function, https://doi.org/10.1371/journal.pone.0305673 (Q1: 87th percentile: Agricultural science/Multidisciplinary; IF 3.752; H-index 404).
  5. Soommat P, Raethong N, Ruengsang R, Thananusak R, Laomettachit T, Laoteng K, Saithong T*, Vongsangnak W* (2024) Light-Exposed Metabolic Responses of Cordyceps militaris through Transcriptome-Integrated Genome-Scale Modeling. Biology 13 (3):139 (Q1: Agricultural and Biological Sciences; IF 4.2; H-index 75).
  6. Sukko N, Kalapanulak S, Saithong T* (2023) Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation, Sci. Rep. 13: 19973. (T1: 92th percentile: Natural science/Multidisciplinary; IF 4.9; H-index 282).
  7. Thaiprasit J, Chiewchankaset P, Kalapanulak S, Saithong T* (2023) Cluster-based photography and modeling integrated method for an efficient measurement of cassava leaf area. PLOS ONE 18(10): e0287293. (Q1: 87th percentile: Agricultural science/Multidisciplinary; IF 3.752; H-index 404).
  8. Punyasu N, Kalapanulak S, Saithong T* (2023) CO2 recycling by phosphoenolpyruvate carboxylase enables cassava leaf metabolism to tolerate low water availability, Front. Plant Sci. 14: 1159247. (T1: 93th percentile: Plant science; IF 6.627; H-index 155).
  9. Permana BH, Krobthong S, Yingchutrakul Y, Saithong T, Thiravetyan P, Treesubsuntorn C (2023)  Evidence of brassinosteroid signalling and alternate carbon metabolism pathway in the particulate matter and volatile organic compound stress response of Sansevieria trifasciata, Environ. and Exp. Bot. 205: 105116 (T1: 94th percentile: Plant science; IF 6.028; H-index 154).
  10. Ruengsrichaiya B, Nukoolkit C, Kalapanulak S, Saithong T* (2022) Plant-DTI: Extending the landscape of TF protein and DNA interaction in plants by a machine learning-based approach, Front. Plant Sci. 13:970018. (T1: 93th percentile: Plant science; IF 6.627; H-index 155).
  11. Chiewchankaset P, Thaiprasit J, Kalapanulak S, Wojciechowski T, Boonjing P, Saithong T* (2022) Effective Metabolic Carbon Utilization and Shoot-to-Root Partitioning Modulate Distinctive Yield in High Yielding Cassava Variety, Front. Plant Sci. 13: 832304. (T1: 93th percentile: Plant science; IF 6.627; H-index 155).
  12. Kamsen R, Kalapanulak S, Chiewchankaset P, Saithong T* (2021) Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava, Sci Rep, 11(1): 8758. (T1: 92th percentile: Natural science/Multidisciplinary; IF 4.9; H-index 282).
  13. Jaemthaworn T, Kalapanulak S*, Saithong T* (2021) Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava, Sci Rep, 11(1): 7872. (T1: 92th percentile: Natural science/Multidisciplinary; IF 4.9; H-index 282).
  14. Dechpichai P, Puengpien F, Sittipoonprachaya S, Salikupata C, Saithong T, Kalapanulak S (2021) Clustering and Exploring of Gene Functional Modules from Cassava Root Gene Expression Data, KMUTT Research and Development Journal, 44(3): 485-499.
  15. Thanasomboon R, Kalapanulak S, Netrphan S, Saithong T* (2020) Exploring dynamic protein-protein interaction in cassava through the integrative interactome network, Sci Rep, 10, 6510, https://doi.org/10.1038/s41598-020-63536-0. (T1: 92th percentile: Natural science/Multidisciplinary; IF 4.9; H-index 282).
  16. Suksamran R, Saithong T, Thammarongtham C, Kalapanulak S* (2020) Genomic and transcriptomic analysis identified novel putative cassava lncRNAs involved in cold and drought stress, Genes, 11, 366; doi:10.3390/genes11040366.
  17. Thanasomboon R, Kalapanulak S, Netrphan S, Saithong T* (2019) Difference in defense mechanism of two cassava cultivars to bacterial blight disease inferred by analysis of interspecies protein-protein interaction networks. Genomics and Genetics 12(2): 34-40.
  18. Yawichai A, Kalapanulak S, Thammarongtham C, Saithong T* (2019) Genome-wide identification of putative micrornas in cassava (Manihot esculenta Crantz) and their functional landscape in cellular regulation. BioMed Research International 2019: 2019846.
  19. Punyasu N, Kalapanulak S, Siriwat W, Saithong T* (2019) Development of a compartmentalized model for insight into the structured metabolic pathway of carbon metabolism in cassava leaves. Australian Journal of Crop Science 13(4): 605-615.
  20. Chiewchankaset P, Kalapanulak S*, Saithong T* (2019) Extended utilization of constraint-based metabolic model in a long-growing crop. Processes 7(5): 259.
  21. Chiewchankaset P, Siriwat W, Suksangpanomrung M, Boonseng O, Meechai A, Tanticharoen M, Kalapanulak S, Saithong T* (2019) Understanding carbon utilization routes between high and low starch-producing cultivars of cassava through Flux Balance Analysis, Scientific Reports 9: 2964.
  22. Wirojsirasak W, Kalapanulak S, Saithong T* (2019) Pan- and core- gene association networks: Integrative approaches to understanding biological regulation, PLoS ONE 14(1): e0210481.
  23. Siriwat W, Kalapanulak S, Suksangpanomrung M, Saithong T* (2018) Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach, Scientific Reports, 8(1): 16593.
  24. Thanasomboon R, Kalapanulak S, Netrphan S, Saithong T* (2017) Prediction of cassava protein interactome based on interolog method, Scientific Reports, 7: 17206.
  25. Rangsiwutisak C, Saithong T, Kalapanulak S* (2017) Genome-wide identification of potential transcription factor binding sites of cassava via phylogenetic footprinting approach, Chiang Mai University Journal of Natural Sciences, (in press).
  26. Sojikul P*, Saithong T, Kalapanulak S, Pisuttinusart N, Limsirichaikul S, Tanaka M, Utsumi Y, Sakurai T, Seki M, Narangajavana J (2015) Genome-Wide Analysis Reveals Phytohormone Action During Cassava Storage Root Initiation, Plant Molecular Biology, 88(6), pp. 531-43.
  27. Saithong T*, Saerue S, Kalapanulak S, Sojikul P, Narangajavana J, Bhumiratana S (2015) Gene co-expression analysis inferring the crosstalk of ethylene and gibberellin in modulating the transcriptional acclimation of cassava root growth in different seasons. PLoS ONE, 10(9): e0137602.

Book’s chapters

  1. Kalapanulak S, Saithong T*, Thammarongtham C* (2016) Networking Omic Data to Envisage Systems Biological Regulation, In Advances in Biochemical Engineering/Biotechnology. Springer Berlin Heidelberg, Berlin, Heidelberg: pp. 1-21
  2. Saithong T* and Kalapanulak S (2015) Chapter 17 Going beyond the current native nutritional food through the integration of the omic data in the post-genomic era, In Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods 2nd. John Wiley & Sons, Ltd.

Conference Proceedings

  1. Sukko N, Kalapanulak S*, Saithong T* (2023) Screening for plant regulators modulating the early disease-state transition of cassava brown streak disease (CBSV) using dynamic network biomarker (DNB). The 26th International Annual Symposium on Computational Science and Engineering (ANSCSE26), 20-22 July 2023, The A-ONE Royal Cruise Hotel, Pattaya, Thailand.
  2. Saithong T*, Ruengsrichaiya B, Nukoolkit C, Kalapanulak S (2022) Extension of transcriptional regulator resource in cassava by machine learning based modeling, The 13th Application of Smart Technologies for Achieving Sustainable Agriculture (APFITA 2022), 24-26 November 2022, Hanoi, Vietnam.
  3. Punyasu N, Postma JA, Kalapanulak S, Thaiprasit J, Wojciechowski T, Saithong T* (2022) Modeling the impact of low light intensity on storage root development using cassava-OpenSimRoot model, The 13th Application of Smart Technologies for Achieving Sustainable Agriculture (APFITA 2022), 24-26 November 2022, Hanoi, Vietnam.
  4. Chiewchankaset P, Thaiprasit J, Kalapanulak S, Saithong T* (2022) Modeling carbon metabolism in the developing storage roots of Rayong 9 cassava variety under different water conditions, The 13th Application of Smart Technologies for Achieving Sustainable Agriculture (APFITA 2022), 24-26 November 2022, Hanoi, Vietnam.
  5. Sriwichai N, Saithong T, Kalapanulak S  (2022) MeTRN 1.0: An integrative database for reconstructing transcriptional regulatory network in cassava (Manihot esculenta Crantz), The 13th Application of Smart Technologies for Achieving Sustainable Agriculture (APFITA 2022), 24-26 November 2022, Hanoi, Vietnam.
  6. Apiwat I, Thaiprasit J, Kalapanulak S, Saithong T* (2022) Characterization of cassava stem cutting quality by volume density, The 34th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB2022), 24-26 November 2022, Ambassador Hotel, Bangkok, Thailand.
  7. Thaiprasit J, Chiewchankaset P, Kalapanulak S, Saithong T* (2022) Cluster-based Method for a Practical Leaf Area Measurement in Cassava Field, The 34th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB2022), 24-26 November 2022, Ambassador Hotel, Bangkok, Thailand.
  8. Sutthacharoenthad W, Punyasu N, Kalapanulak S, Chiewchankaset P, Ruengsang R, Saithong T* (2022) Modeling carbon metabolism for leaves growth based on the characterized photon uptake scenario of cassava, Thai Society for Biotechnology International Conference Online, 29 April 2022, Bangkok, Thailand.
  9. Sutthacharoenthad W, Punyasu N, Kalapanulak S, Chiewchankaset P, Ruengsang R, Saithong T* (2022) Modeling carbon metabolism for leaves growth based on the characterized photon uptake scenario of cassava, Thai Society for Biotechnology International Conference Online, 29 April 2022, Bangkok, Thailand.
  10. Kamsen R, Kalapanulak S, Saithong T* (2020) Modeling metabolic fluxes underlying cassava storage root growth through E-Fmin analysis, The 11th International Conference on Computational Systems-Biology and Bioinformatics (CSBio2020), 19 November 2020, Thailand.
  11. Suksamran R, Thammarongtham C, Saithong T, Kalapanulak S (2020) Genome-wide investigation of lincRNAs in cassava and their potential roles in specific tissue, The 5th RSU International Research Conference (RSUSSH2020), 1 May 2020 , Pathum Thani, Thailand.
  12. Thanasomboon R, Netrphan S, Kalapanulak S*, Saithong T* (2019) Exploring genome-wide protein-protein interaction network of cassava KU50 toward the understanding in high starch yield cultivar, Proceedings of The 10th RMUTs International Conference, 24-26 July 2019, Chiang Mai International Exhibition and Conventional Center, Chiang Mai, Thailand.
  13. Chiewchankaset P, Kalapanulak S*, Saithong T* (2019) Assessment of biomass composition data impact on prediction of low-yield cassava metabolic model (rMeCBM-HN), Proceedings of The 21st National Genetics Conference (NGC2019), 6-22 June 2019, Pattaya, Chonburi, Thailand.
  14. Jaemthaworn T, Ruengsrichaiya B, Saithong T, Kalapanuluk S* (2018) Clustered Network Topology of Regulatory System Strengthens the Cellular Robustness to Stress: a Case Study in a Resistant Cultivar of Cassava (Manihot esculenta Crantz) to Viral Infection, Proceedings of the 9th International Conference on Computational Systems-Biology and Bioinformatics (CSBio2018), 10-13 December 2018, Bangkok, Thailand.
  15. Bumee S, Kalapanulak S, Meechai A, Saithong T* (2015) Analysis of reporter metabolites for the compartmentalized genome-scale metabolic model of Arabidopsis leaves, Proceedings of 6th international conference on Computational Systems-Biology and Bioinformatics 2015 (CSBio2015), 22-25 November 2015, Thailand.
  16. Vongthaiwan H, Siriwat W, Kalapanulak S, Saithong T* (2015) Shape the reconstructed metabolic pathway of cassava carbon assimilation into a cell, Proceedings of the 27th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB2015), 17-22 November 2015, Thailand.
  17. The first prize in the outstanding proceedings award over hundreds of all presented proceeding
  18. Sriwichai N, Saithong T, Thammarongtham C, Meechai A. and Kalapanulak S*. (2015) A hybrid computational approach for predicting the intergenic microRNA promoters in plants: A case study in cassava, Proceedings of the 27th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB2015), 17-22 November 2015, Bangkok, Thailand.

Conference Posters

  1. Thaiprasit J, Kalapanulak S, Saithong T* (2019) The variation of shoot-root carbon allocation during storage root initiation in 6 cassava varieties in Thailand, The 21st National Genetics Conference (NGC2019), 6-22 June 2019, Pattaya, Chonburi, Thailand.
  2. Saithong T*, Thanasomboon R, Kalapanulak S, Netrpan S, Suksangpanomrung M (2018) Highlighting the condition-specific protein-protein interaction by integrating expression data into the interactome network: A case of AGPase protein, The 19th International Conference on Systems Biology (ICSB), 28 October – 1 November 2018, Lyon, France.
  3. Kalapanulak S*, Sriwichai N, Saithong T, Suksangpanomrung M, Netrpan S (2018) Unraveling transcriptional regulation of starch metabolic genes in cassava through computational prediction with Yeast-one hybrid validation, The 19th International Conference on Systems Biology (ICSB), 28 October – 1 November 2018, Lyon, France.
  4. Chiewchankaset P, Siriwat W, Kalapanulak S, Saithong T* (2018) Genome-scale metabolic model predicts carbon flux partitioning towards starch biosynthesis in storage root of cassava, The 11th International Multiconference on Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB- 2018), 20-25 August 2018, Novosibrisk, Russia. [Poster]
  5. Kalapanulak S*, Rangsiwutisak C, Saithong T (2018) Genome-wide prediction of transcription factor binding sites in cassava via phylogenetic footprinting between plants in Euphorbiaceae family, The 11th International Multiconference on Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2018), 20-25 August 2018, Novosibrisk, Russia. [Poster]
  6. Siriwat W, Kalapanulak S, Saithong T* (2017) Investigation of canonical metabolic network of plants through topology-based analysis, The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB2017), 3-7 May 2017, University of Hongkong, Hongkong.
  7. Rangsiwutisak C, Saithong T, Kalapanulak S* (2017) Exploring the landscape of regulatory elements on non-coding regions of cassava genome via motif-based screening, The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB2017), 3-7 May 2017, University of Hongkong, Hongkong. Hongkong.
  8. Chungloo D, Netrphan S, Suksangpanomrung M, Kalapanulak S, Saithong T (2107) A study towards understanding of transcriptional regulation of ADP-glucose pyrophosphorylase genes in cassava through bioinformatics and molecular biology techniques, International Conference on Sustainable Agriculture and Bioeconomy (AGBIO2017), 27 February-2 March 2017, BITEC, Bangkok, Thailand.
  9. Dusschoten D, Chiewchankaset P, Saithong T, Kalapanulak S, Wojchiechowski T (2017) Development of fine roots of cassava in soil as observed by 3D MRI, International Conference on Sustainable Agriculture and Bioeconomy (AGBIO2017), 27 February-2 March 2017, BITEC, Bangkok, Thailand
  10. Sriwichai N, Saithong T, Kalapanulak S* (2017) Transcription Factors Controlling the Involvement of MIR164 and MIR167 in Cassava Response to Drought Stress Condition: A Potential Marker for
  11. Drought-resistant Trait Screening, International Conference on Sustainable Agriculture and Bioeconomy (AGBIO2017), 27 February-2 March 2017, BITEC, Bangkok, Thailand.
  12. Punyasu N, Kalapanulak S, Bumee S, Saithong T* (2016) Unravelling the changes in metabolism during storage root development of cassava through reporter metabolite analysis, The 28th Annual Meeting of the Thai Society for Biotechnology and International Conference, 28-30 Novermber 2016, The Empress Hotel, Chiangmai, Thailand.
  13. Suksamran R, Saithong T, Thammarongtham C, Kalapanulak S* (2016) A comparative approach to genome-wide discovery of intragenic non-coding RNAs in cassava, The 28th Annual Meeting of the Thai Society for Biotechnology and International Conference, 28-30 Novermber 2016, The Empress Hotel, Chiangmai, Thailand.
  14. Thanasomboon R, Kalapanulak S, Saithong T* (2016) Protein-Protein Interaction Network of Host and Pathogen inferring the Infection Mechanism of Xanthomonas axonopodis in Cassava, Siriraj International Conference, June 2016, Siriraj Hospital, Thailand.
  15. Chiewchankaset P, Boonseng O, Suksangpanomrung M, Kalapanulak S*, Saithong T* (2016) Investigation of growth behavior inferring the distinct carbon allocation between high and low starch-content traits of cassava, 1st international conference on World Congress on Root and Tuber Crops 2016, 18-23 January 2016, Mingyuan Xindu Hotel, Nanning, Guangxi, China.
  16. Bumee S, Khampoosa B, Saithong T*, Meechai A, Kalapanulak S (2016) Integrative approach for predicting transcription factors controlling starch genes in cassava, Proceedings of 1st international conference on World Congress on Root and Tuber Crops 2016, 18-23 January 2016, Mingyuan Xindu Hotel, Nanning, Guangxi, China.