Publications

2019

  • Siriwat W, Muhardina V, Thammarongtham C, Kalapanulak S, Saithong T (2019) Nitrogen assimilation in cassava: implications for carbon metabolism and biomass synthesis, Journal of Physics: Conference Series, 1232:012002.
  • 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): 47-53.
  • 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, The 10th RMUTs International Conference. 24-26 July 2019, International Convention and Exhibition Center Commemorate the 7th Anniversary of His Majesty the King, Chiang Mai, Thailand. [Proceeding]
  • Chiewchankaset P, Kalapanulak S, Saithong T (2019) Assessment of biomass composition data impact on prediction of low-yield cassava metabolic model (rMeCBM-HN), The 21st National Genetics Conference (NGC2019), 6-22 June 2019, Pattaya, Chonburi, Thailand. [Proceeding]
  • 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. [Poster]
  • 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.
  • 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(04): 605-615.
  • Chiewchankaset P, Kalapanulak S, Saithong T (2019) Extended utilization of constraint-based metabolic model in a long-growing crop. Processes 7(5): 259.
  • Wirojsirasak W, Kalapanulak S, Saithong T (2019) Pan- and core- gene association networks: Integrative approaches to understanding biological regulation, PLoS ONE 14(1): e0210481.
  • 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.


2018

  • 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.
  • 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. [Poster]
  • 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. [Poster]
  • 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]
  • 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]


2017

  • Thanasomboon R, Kalapanulak S, Netrphan S, Saithong T (2017) Prediction of cassava protein interactome based on interolog method, Scientific Reports, 7(1): 17206.
  • 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, Ma Liu Shui, Hong Kong. [Poster]
  • Kalapanulak S, Rangsiwutisak C, Saithong T (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, Ma Liu Shui, Hong Kong. [Poster]
  • 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 Drought-resistant Trait Screening, International Conference on Sustainable Agriculture and Bioeconomy 2017 (AGBIO2017), 22 February - 2 March 2017, Bangkok, Thailand. [Poster]
  • Chiewchankaset P, Dusschoten D, 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 2017 (AGBIO2017), 22 February - 2 March 2017, Bangkok, Thailand. [Poster]
  • Chungloo D, Suksangpanomrung M, Netrphan S, Saithong T, Kalapanulak S (2017) 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 2017 (AGBIO2017), 22 February - 2 March 2017, Bangkok, Thailand. [Poster]


2016

  • 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 (TSB), 28-30 November 2016, Chiangmai, Thailand. [Poster]
  • 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 (TSB), 28-30 November 2016, ‎Chiangmai, Thailand. [Poster]
  • 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 in Medicine and Public Health (SiCMPH), 13-15 June 2016, Bangkok, Thailand. [Poster]
  • 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, The First World Congress on Root and Tuber Crops (WCRTC), 18-23 January 2016, Nanning, China. [Poster]
  • Bumee S, Khampoosa B, Saithong T, Meechai A, Kalapanulak S (2016) Integrative approach for predicting transcription factors controlling starch genes in cassava, The First World Congress on Root and Tuber Crops (WCRTC), 18-23 January 2016, Nanning, China. [Poster]
  • Kalapanulak S, Saithong T, Thammarongtham C (2016) Networking Omic Data to Envisage Systems Biological Regulation. In: Nookaew I. (eds) Network Biology. Advances in Biochemical Engineering/Biotechnology, vol 160. Springer, Cham [Book Chapter]


2015

  • Bumee S, Kalapanulak S, Meechai A, Saithong T (2015) Analysis of reporter metabolites for the compartmentalized genome-scale metabolic model of Arabidopsis leaves, The 6th international conference on Computational Systems-Biology and Bioinformatics 2015 (CSBio), 22-25 November 2015, Bangkok, Thailand. [Proceedings]
  • Vongthaiwan H, Siriwat W, Kalapanulak S, Saithong T (2015) Shape the reconstructed metabolic pathway of cassava carbon assimilation into a cell, The 27th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB2015), 17-22 November 2015, Bangkok, Thailand. [Proceedings]
  • Sriwichai N, Saithong T, Thammarongtham C, Meechai A, Kalapanulak S (2015) A hybrid computational approach for predicting the intergenic microRNA promoters in plants: A case study in cassava, The 27th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB2015), 17-22 November 2015, Bangkok, Thailand. [Proceedings]
  • 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): 531-543.
  • Saithong T Kalapanulak S (2015) Going beyond the current native nutritional food through the integration of the omic data in the post-genomic era: A Study in (Resistant) Starch Systems Biology, Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods 2nd, John Wiley & Sons, Ltd. [Book Chapter]
  • 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.


2014

  • Liamwirat C, Cheevadhanarak S, Netrphan S, Chaijaruwanich J, Bhumiratana S, Meechai A (2014) Rational identification of target enzymes for starch improvement through system-level analysis of a potato tuber model, Australian Journal of Crop Science, 8(5): 760.
  • Khampoosa B, Bumee S, Saithong T, Suksangpanomrung M, Kalapanulak S (2014) Construction of transcriptional regulatory network proposes bZIP transcription factor controlling rubisco genes in cassava, The 26th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB), 26-29 November 2014, Chiang Rai, Thailand. [Proceedings]
  • Yawichai A, Srisuk T, Kalapanulak S, Thammarongtham C, Saithong T (2014) An exhaustive search for intronic microRNAs in the cassava genome, The 26th Annual Meeting of the Thai Society for Biotechnology and International Conference (TSB), 26-29 November 2014, Chiang Rai, Thailand. [Proceedings]
  • Wirojsirasak W, Saithong T, Sojikul P, Hirunsirisawat P, Kalapanulak S (2014) The Effect of Microarray Data Resolution on the Inferred Transcriptional Regulatory Network Topology, The 2nd ASEAN Plus Three Graduate Research Congress (AGRC), 5-7 February 2014, Bangkok, Thailand. [Proceedings]
  • Khampoosa B, Kalapanulak S, Bumee S, Saithong T (2014) Construction of transcriptional regulatory network of starch metabolism in cassava via Bioinformatics approach, EMBO Conference Series: From Functional Genomics to Systems Biology, 8-11 November 2014, Heidelberg, Germany. [Poster]
  • Yawichai A, Suksamran R, Kalapanulak S, Saithong T, Thammarongtham C (2014) Computational Screening for Intronic microRNAs in Cassava (Manihot esculenta Crantz) Genome, Next Generation Sequencing for Genetic and Genomic Studies (NGS2014), 29-30 July 2014, Bangkok, Thailand. [Poster]
  • Wirojsirasak W, Saithong T, Kalapanulak S (2014) Discovering the prominent processes during cassava root development through gene expression profile analysis, Genome, Next Generation Sequencing for Genetic and Genomic Studies (NGS2014), 29-30 July 2014, Bangkok, Thailand. [Poster]


2013

  • Saithong T, Rongsirikul O, Kalapanulak S, Chiewchankaset P, Siriwat W, Netrphan S, Suksangpanomrung M, Meechai A, Cheevadhanarak S (2013) Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration, BMC Systems Biology, 7(1): 75.
  • Bumee S, Ingkasuwan P, Kalapanulak S, Meechai A, Cheevadhanarak S, Saithong T (2013) Transcriptional regulatory network of Arabidopsis starch metabolism under extensive light conditions: A potential model of transcription-modulated starch metabolism in roots of starchy crops, The 4th international conference on Computational Systems-Biology and Bioinformatics (CSBio), 7-9 November 2013, Seoul, Korea. [Proceedings]
  • Khampoosa B, Kalapanulak S, Saithong T, Suksangpanomrung M (2013) Performing bioinformatics study discloses bZip transcription factor family protein controlling starch metabolism in cassava, Plant Genome Evolution 2013 (PGEV2013), 8-10 September 2013, Amsterdam, Netherlands. [Poster]


2012

  • Saithong T, Bumee S, Liamwirat C, Meechai A (2012) Analysis and practical guideline of constraint-based Boolean method in genetic network inference, PLoS ONE, 7(1): e30232.
  • Saithong T, Meechai A, Chevathanarak S, and Bhumirattana S (2012) A formal path inference of starch biosynthesis via mathematical modelling of metabolic changes in excess CO2, Journal of Computer Science and Systems Biology, 5: 024-038.
  • Ingkasuwan P, Netrphan S, Prasitwattanaseree S, Tanticharoen M, Bhumiratana S, Meechai A, Chaijaruwanich J, Takahashi H, Cheevadhanarak S (2012) Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thalianaleaves using graphical Gaussian model, BMC Systems Biology, 6(1): 100-121.
  • Chiewchankaset P, Srimarut Y, Klanchui A, Kurdi P, Plengvidhya V, Meechai (2012) Systematic identification of Lactobacillus plantarumauxotrophs for fermented Nham using genome-scale metabolic model, Journal of Biotechnology, 162(2-3): 327-335.
  • Siriwat W, Kalapanulak S, Suksangpanomrung M, Netrphan S, Meechai, Saithong T (2012) Transcriptomic data integration inferring the dominance of starch biosynthesis in carbon utilization of developing cassava roots, The 3rdInternational Conference on Computational Systems-Biology and Bioinformatics (CSBio), 3-5 October 2012, Bangkok, Thailand. [Proceedings]
  • Bumee S, Ingkasuwan P, Kalapanulak S, Meechai A, Cheevadhanarak S, Saithong T (2012) Transcriptional regulatory network inference of starch metabolism in root from Arabidopsis gene expression data, The 11th International Conference on Bioinformatics (InCoB2012), 3-5 October 2012, Bangkok, Thailand. [Proceedings]
  • Saithong T, Rongsirikula O, Kalapanulaka S, Netrphan S, Suksangpanomrung M (2012) High-quality pathway of cassava starch biosynthesis in non-photosynthetic tissues inferred by multiple plant templates, The 23rdAnnual Meeting of the Thai Society for Biotechnology “Systems Biotechnology: Quality & Success” (TSB), 1-2 February 2012, Bangkok, Thailand. [Proceedings]
  • Saithong T, Saerue S, Kalapanulak S, Sojikul P, Narangajavana J (2012) Analysis of gene expression during root development implies the distinct gene regulation between root tissues, The 23rdAnnual Meeting of the Thai Society for Biotechnology “Systems Biotechnology: Quality & Success” (TSB), 1-2 February 2012, Bangkok, Thailand. [Proceedings]


2010

  • Saithong T, Painter KJ, Millar AJ (2010) Consistent robustness analysis (CRA) identifies biologically relevant properties of regulatory network models, PLoS ONE, 5(12): e15589.
  • Saithong T, Painter KJ, Millar AJ (2010) The contributions of interlocking loops and extensive nonlinearity to the properties of circadian clock model, PLoS ONE, 5(11): e13867.
  • Bumee S, Liamwirat C, Saithong T, Meechai A (2010) Extended constraint-based Boolean analysis: A computational method in genetic network inference, The 1st International Conference on Computational Systems-Biology and Bioinformatics (CSBio), 3-5 November 2010, Bangkok, Thailand. [Proceedings]
  • Rongsirikul O, Saithong T, Kalapanulak S, Meechai A, Cheevadhanarak S, Netrphan S, Suksangpanomrung M (2010) Reconstruction of starch biosynthesis pathway in cassava using comparative genomic approach, The 1st International Conference on Computational Systems-Biology and Bioinformatics (CSBio), 3-5 November 2010, Bangkok, Thailand. [Proceedings]


2009

  • Bumee S, Liamwirat C, Meechai A (2009) Comprehensive bioinformatics platform for Thailand plant research, The 21th of the Annual Meeting and International Conference of Thai Society for Biotechnology (TSB), 24-25 September 2009, Bangkok, Thailand. [Proceedings]
  • Liamwirat C, Cheevadthanarak S, Meechai A, Bhumiratana S (2009) Enzyme relational network reveals target enzymes within metabolic submodules, The 9th IEEE International Conference on BioInformatics and BioEngineering (BIBE 2009), 22-24 June 2009, Taichung, Taiwan. [Proceedings]
  • Liamwirat C, Meechai A, Cheevadhanarak S, Chaijaruwanich J, Netrphan S, Bhumiratana S (2009) Analysis of simulated metabolite profiling of starch producing cultivars: A rational way to increase yield of energy crop, The 4th Cycle Celebration of KMUTT Sustainable Development to Save the Earth: Technologies and Strategies Vision 2050 (SDSE), 7-9 April 2009, Thailand. [Proceedings]
  • Munkong W, Liamwirat C, Bumee S, Meechai A (2009) A constraint-based Boolean approach to inferring genetic circuits, The 13th International Annual Symposium on Computational Science and Engineering (ANSCSE 13), 25-27 March 2009, Bangkok, Thailand. [Proceedings]


2007

  • Liamwirat C, Meechai A, Cheevadhanarak S, Chaijaruwanich J, Netrphan S, Bhumiratana S (2007) Modeling of starch biosynthesis in tuber plants: A sensitivity of enzymatic activities to starch production, The 6th Asian Crop Science Association Conference, 7-9 November 2007, Bangkok, Thailand. [Poster]
  • Ingkasuwan P, Cheevadhanarak S, Netrphan S, Meechai A, Prasitwattanaseree S, Chaijaruwanich J, Tanticharoen M, Bhumiratana S (2007) Discovery of starch gene network characteristics in Arabidopsis thaliana, The 6th Asian Crop Science Association Conference, 7-9 November 2007, Bangkok, Thailand. [Poster]
  • Ingkasuwan P, Meganck S, Cheevadhanarak S, Netrphan S, Meechai A, Prasitwattanaseree S, Chaijaruwanich J, Tanticharoen M, Bhumiratana S (2007) Inferring genes regulation network of starch metabolism of Arabidopsis thalianausing graphical Gaussian model, The 2nd FEBS Advanced Lecture Course on Systems Biology: From Molecules to Life, 10-16 March 2007, Gosau, Austria. [Poster]


2006

  • Liamwirat C, Meechai A, Cheevadhanarak S, Chaijaruwanich J, Bhumiratana S (2006) In silicomodel of starch metabolism in leaves, The 18th Annual Meeting of the Thai Society of Biotechnology “Biotechnology: Benefits & Bioethics” (TSB), 2-3 November 2006, Bangkok, Thailand. [Poster]


2005

  • Ingkasuwan P, Sutheeworapong S, Netrphan S, Chaijaruwanich J, Meechai A, Cheevadhanarak S, Bhumiratana S (2005) Meta-analysis of the transcriptome of Arabidopsis: A challenge in studying starch biosynthesis in higher plants, The 3rdConference on Starch Technology, 4-5 November 2005, Bangkok, Thailand. [Proceedings]
  • Meechai A, Saithong T, Saraboon P, Cheevadhanarak S, Bhumiratana S (2005) Numerical simulation of plant starch biosynthesis, The 3rdConference on Starch Technology, 4-5 November 2005, Bangkok, Thailand. [Proceedings]
  • Saithong T, Saraboon P, Meechai A, Cheevadhanarak S, Bhumiratana S (2005) A structured and multi-cellular model of starch biosynthesis in potato, The 2005 International Joint Conference of InCoB, AASBi and KSBI (Bioinfo 2005), 22-24 September 2005, Busan, Korea. [Proceedings]
  • Kalapanulak S, Tang-amornsuksan N, Meechai A, Cheevadhanarak S, Bhumiratana S (2005) An applied process control concept to gene motif network modeling for predicting the gene expression profiles, The 2005 International Joint Conference of InCoB, AASBi and KSBI (Bioinfo 2005), 22-24 September 2005, Busan, Korea. [Poster]

 

Research Talks

2018

  • Thanasomboon R, Kalapanulak S, Saithong T (2018) Genome-wide prediction of protein-protein interaction network in cassava based on Interolog method, The 13th International Symposium of the Protein Society of Thailand (PST2018), 7-9 August 2018, Bangkok, Thailand. [Abstract]


2017

  • Chiewchankaset P, Siriwat W, Thaiprasit J, Kalapanulak S, Saithong T (2017) A proposed subcellular metabolic network of carbon assimilation in cassava storage roots, The 4th Asian Regional Conference on Systems Biology (ARCSB2017), 20-22 November 2018, Putrajaya, Malaysia. [Abstract]
  • Punyasu N, Kalapanulak S, Siriwat W, Saithong T (2017) Construction of a qualitative metabolic model of carbon assimilation in cassava leaf tissue, The 4th Asian Regional Conference on Systems Biology (ARCSB2017), 20-22 November 2018, Putrajaya, Malaysia. [Abstract]


2016

  • Siriwat W, Rongsirikul O, Kalapanulak S, Chiewchankaset P, Netrphan S, Suksangpanomrung M, Meechai, A, Cheevadhanarak S, Saithong T (2016) Starch biosynthesis metabolic pathway of cassava: a quest for conservation and uniqueness, The First World Congress on Root and Tuber Crops (WCRTC), 18-23 January 2016, Nanning, China. [Abstract]
  • Thanasomboon R, Kalapanulak S, Netrphan S, Saithong T (2016) Genome-wide prediction of protein-protein interaction network in cassava based on Interolog method, The First World Congress on Root and Tuber Crops (WCRTC), 18-23 January 2016, Nanning, China. [Abstract]