Publications

Bumee S., Ingkasuwan P., Kalapanulak S., Meechai A., Cheevadhanarak,S., and Saithong T. (2013) Transcriptional Regulatory Network of Arabidopsis Starch Metabolism under Extensive Light Condition: A Potential Model of Transcription-Modulated Starch Metabolism in Roots of Starchy Crops,Proceedings of the 4th International Conference on Computational Systems-Biology and Bioinformatics (CSBio 2013), 7-9 November 2013, Korea.[Supplementary Data]

Vorapreeda, T., Thammarongtham, C., Cheevadhanarak, S., and Laoteng, K. (2013) The repertoire of malic enzymes in yeast and fungi: Insight into their evolutionarily functional and structural significance, Microbiology, Vol. 159 no. Pt 12, 2548-2557.

Subpaiboonkit S, Thammarongtham C, Cutler RW, Chaijaruwanich J. (2013) RNA secondary structure prediction using conditional random fields model. Int J Data Min Bioinform. 2013;7(2):118-34.

Oguz C, Laomettachit T, Chen KC, Watson LT, Baumann WT, Tyson JJ. (2013) Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. BMC Systems Biology,7:53, doi: 10.1186/1752-0509-7-53.

Saithong T., Rongsirikul O., Kalapanulak S., Chiewchankaset P., Siriwat W., Netrphan S., Suksangpanomrung M., Meechai A., and Cheevadhanarak S. (2013) Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration, BMC Systems Biology, 7:75 doi:10.1186/1752-0509-7-75

Huang Y, Kittichotirat W, Mayer MP, Hall R, Bumgarner R, Chen C. Mol Oral Microbiol. (2013) Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitan, Molecular Oral Microbiology, 28(1):1-17. doi: 10.1111/omi.12005.

Phuangrat, B., Phironrit, N., Son-Ong, A., Puangchon, P., Meechai, A., Wasee, S., Kositratana, W., Burns, P. (2013) Histological and morphological studies of pollen grains from Elongata, reduced Elongata, staminate flowers in Carica papaya L., Tropical Plant Biology, DOI 10.1007/s12042-013-9118-0.

Zhu F, Patumcharoenpol P, Zhang C, Yang Y, Chan J, Meechai A, Vongsangnak W, Shen B. (2013) Biomedical text mining and its applications in cancer research, Journal of Biomedical Informatics, Vol. 46, p. 200-211.

Lertampaiporn S, Thammarongtham C, Nukoolkit C, Kaewkamnerdpong B, Ruengjitchatchawalya M. (2013) Heterogeneous Ensemble Approach with Discriminative Features and Modified-SMOTEbagging for Pre-miRNA Classification, Nucleic Acids Research, Jan 1;41(1):e21

Klanchui A, Vorapreeda T, Vongsangnak W, Kannapho C, Meechai A, Cheevadhanarak S. (2012) Systems biology and metabolic engineering of Arthrospira cell factories. Computational and Structural Biotechnology Journal. Vol. 3(4)

Zhu F, Patumcharoenpol P, Zhang C, Yang Y, Chan J, Meechai A, Vongsangnak W, Shen B. (2012) Biomedical text mining and its applications in cancer research. Journal of Biomedical Informatics. 
Saithong T, Bumee S, Liamwirat C, and Meechai A. (2012) Analysis and Practical Guideline of Constraint-based Boolean Method in Genetic Network Inference. PLoS ONE. Vol. 7(1): e30232.
Sootanan P, Prom-on S, Meechai A, and Chan JH. (2012) Pathway-based microarray analysis for robust disease classification. Journal of Neural Computing and Applications (Special Issue on ICONIP2011). Vol. 21(4): 649-660.
Vorapreeda T, Thammarongtham C, Cheevadhanarak S, and Laoteng K. (2012) Alternative routes of acetyl-CoA synthesis identified by comparative genomic analysis: Involvement in lipid production of oleaginous yeast and fungi. Microbiology.Vol.158: 217-228.
Cheevadhanarak S, Paithoonrangsarid K, Prommeenate P, Kaewngam W, Musigkain A, Tragoonrung S, Tabata S, Kaneko T, Chaijaruwanich J, Sangsrakru D, Tangphatsornruang S, Chanprasert J, Thongsima S, Kusolmano K, Jeamton W, Dulsawat S, Klanchui A, Vorapreeda T, Chumchua V, Khannapho C, Thammarongtham C, Plengvidhya V, Subudhi S, Hongsthong A, Ruengjitchatchawalya M, Meechai A, Senachak J, and Tanticharoen M. (2012) Draft genome sequence of Arthrospira platensis C1 (PCC9438). Standards in Genomic Sciences. Vol. 6: 43-53. 
Saithong T, Meechai A, Chevathanarak S, 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. Vol.5(1): 24-38.
Klanchui A, Khannapho C, Phodee A, Cheevadhanarak S, and Meechai A. (2012) iAK692: A genome-scale metabolic model of Spirulina platensis C1, BMC Systems Biology, Vol. 6(1): 71.
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 thaliana leaves using graphical Gaussian model. BMC Systems Biology. Vol. 6: 100.
Chiewchankaset P, Srimarut Y, Klanchui A, Kurdi P, Plengvidhya V, Meechai A. (2012) Systematic identification of Lactobacillus plantarum auxotrophs for fermented Nham using genome-scale metabolic model. Journal of Biotechnology. Vol. 162(2-3): 327-35.
Lertampaiporn S, Thammarongtham C, Nukoolkit C, Kaewkamnerdpong B, Ruengjitchatchawalya M. (2012) Heterogeneous Ensemble Approach with Discriminative Features and Modified-SMOTEbagging for Pre-miRNA Classification. Nucleic Acids Research. 1-12.

Subpaiboonkit S, Thammarongtham C, Cutler R, and Chaijaruwanich J. (2011) RNA secondary structure prediction using conditional random fields model. International Journal of Data Mining and Bioinformatics.

Prom-on S, Chanthapan A, Chan JH, and Meechai A. (2011) Enhancing biological relevance of a weighted gene co-expression network for functional module identification. Journal of Bioinformatics and Computational Biology (JBCB). Vol. 9(1): 111-129.

Sritakae A, Praseartkul P, Cheunban W, Miphokasap P, Eiumnoh A, Burns P, Phironrit N, Phuangrat B, Kitsubun P, and Meechai A. (2011) Mapping airborne pollen of papaya (Carica papaya L.) and its distribution related to land use using GIS and remote sensing. Data Mining and Bioinformatics.

Kurdrid P, Senachak J, Sirijuntarut M, Yutthanasirikul R, Phuengcharoen P, Jeamton W, Roytrakul S, Cheevadhanarak S, Hongsthong A. (2011) Comparative analysis of the Spirulina platensis subcellular proteome in response to low- and high-temperature stresses: uncovering cross-talk of signaling components. Proteome Science. Vol. 9(39): 1-16.

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Hongsthong A, Sirijuntarut M, Yutthanasirikul R, Senachak J, Kurdrid P, Cheevadhanarak S, Tanticharoen M. (2009) Subcellular proteomic characterization of the high-temperature stress response of the cyanobacterium Spirulina platensis. Proteome Science. Vol. 7(33): 1-19.

Chumchua V, Pornputtapong N, Thammarongthan C, and Meksuriyen D. (2008) Homology modeling of Mycoplasma pneumoniae enolase and its molecular interaction with humana plasminogen. Journal of Bioinfomation. Vol. 3: 18-23.

Nookaew I, Jewett M, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, and Bhumiratana S. (2008) The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Systems Biology. Vol. 2(71): 1-15.

Nookaew I, Meechai A, Thammarongtham C, Loateng K, Ruanglek V, Cheevadhanarak S, Nielsen J, and Bhumiratana S. (2007) Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks. Journal of Biotechnology and Bioengineering. Vol. 97(6): 1535 -1549.

Saithong T, Meechai A, Cheevadhanarak S, and Bhumiratana S. (2004) Metabolic control analysis of starch biosynthesis pathways in amyloplast organelle. Thai J. Biotechnol. Vol 5(1): 23-33.

Meechai A, Pongakarakun S, Deshnium P, Cheevadhanarak S, and Bhumiratana S. (2004) Metabolic flux distribution for g-linolenic acid synthetic pathways in Spirulina platensis. Biotechnol. Bioprocess Eng. Vol 9(6): 506-513

Homthawornchoo W, Sattithamajit S, Meechai A, Cheevadhanarak S, Thammarongtham C, and Bhumiratana S. (2004) Genome-scale metabolic representation of Mycobacterium tuberculosis. Thai J. Biotech.