Ph.D. thesis “Exploring new functional photosynthetic genes in photosynthetic prokaryote by gene neighborhood analysis”
Adviser  :  Asst. Prof. Dr. Marasri Ruengjitchatchawalya, and Asst. Prof. Dr. Teeraphan Laomettachit
Short description  :  Photosynthetic proteins, especially auxiliary factors, are difficult to identify in wet lab and by common computational approaches. In this work, I developed a new approach using genome neighborhood feature and machine learning approach for identifying photosynthetic proteins and their functions (bicep.kmutt.ac.th/photomod or https://github.com/asangphukieo/PhotoModGO). Also, a new method to visualize genome neighborhood, called photomodGNN has been developed (https://github.com/asangphukieo/PhotoModGNN).

Internship project 1 (at University of Freiburg) “Identification of small regulatory RNA (sRNA) in Synechocystis sp. PCC 6803”
Adviser  :  Prof. Wolfgang R. Hess
Short description  :  Many regulatory sRNAs were identified using several conditions of RNA-sequencing, but the function of these sRNA remains to be elucidated. In this work, I integrate computational tools e.g. GLASSgo (sRNA homolog prediction tool) and CopraRNA (sRNA function prediction tool) as a pipeline. Then, I applied the pipeline to automatically identify sRNA function by using the input sequence from transcriptome data of Synechocystis sp. PCC 6803. All available scripts in this study are available in https://github.com/asangphukieo/sRNA_requirements.

Internship project 2 (at University of Freiburg) “Bioinformatics analysis of SR1 dual-function RNA from Bacillus subtilis”
Adviser  :  Prof. Wolfgang R. Hess
Short description  : SR1 is a regulatory sRNA from the Bacillus subtilis which the function remains to be elucidated. In this work, I identified the distribution of SR1 sRNA among Bacterial domain, and also analyzed the diversity of protein-coding sequence, the conservation of gene synteny and potential gene target of SR1. I showed that SR1 is conserved in 12 genera and the function is involved in sporulation and reproduction.

Internship project 3 (at MSB group) “Development of automated data processing pipeline for GC-MS and GCxGC-MS-based untargeted metabolomics”
Adviser  :  Dr. Sakda Khoomrung
Short description  :  Gas chromatography-mass spectrometry (GCMS)-based metabolomics and GCxGC-MS are powerful technology to carry out untargeted metabolomics profilling of biological samples such as biofluids, cells and tissues, as well as a tool for biomarker discovery. In the GCMS-based workflow, data preprocessing plays a crucial role in overcoming the discovery phase. However, vendor software generally provides limited adjustable features and lack of capability to modify the analysis pipeline and conduct high-throughput data analysis. To overcome this limitation, we developed an open source pipeline to analyse GCMS and GCxGC-MS data (https://github.com/asangphukieo/App-GC).

Internship project 4 (at MORU) “Interactions between Burkholderia pseudomallei genetic variations and host blood glucose level modulate infection outcomes in melioidosis”
Adviser  :  Dr. Claire Chewapreecha
Short description  :  Burkholderia pseudomallei (Bp) is a Gram-negative environmental bacterium and opportunistic pathogen that causes melioidosis, a rapidly severe tropical infectious disease. Melioidosis was predicted to affect 165,000 people, of which 89,000 were estimated to be fatal (54%) per year worldwide. Individuals with diabetes mellitus are at higher risk of developing melioidosis but intriguingly less likely die from the disease. We employed a collection of B. pseudomallei genomes isolated from northeast Thailand to determine bacterial genetic variations associated with 28-day mortality and test how patient hyperglycemic level interacts with bacterial genetic variation to influence the disease outcome.

Master’s thesis “Computational design of new peptides based on cyclotide scaffold as HIV-1 gp120 competitive inhibitor”
Adviser  :  Asst. Prof. Dr. Marasri Ruengjitchatchawalya
Short description  :  Gp120 is an HIV envelope glycoprotein that use for initiating replication cycle. Current gp120-targeting drug is inefficient due to structural barrier of gp120. Cyclotide is a natural peptide that holds anti-HIV feature. In this work, I constructed a new computational method to automatically modify cyclotide molecule to bind to gp120 protein to increase anti-HIV feature. The method consists of many molecular modelling tools (e.g. 3D modelling, docking and binding scoring) connected as a pipeline which is optimized by genetic algorithm.

Bachelor’s senior projects “The role of gadd45β in stress response of cholangiocarcinoma cells”
Short description  :  Growth arrest and DNA-damage-inducible, beta, also known as gadd45β is involved in the regulation of growth and apoptosis. Its role in cancer cell line, especially the common cancer in Thailand cholangiocarcinoma, remains unclear. In this study, I observed the expression of gadd45β in the level of transcription (RT-PCR) and translation (Western blot assay) in response to drugs of cholangiocarcinoma cell line.

Research Interests

I am a bioinformatician with experience in many types of research projects, e.g., functional genomic of bacterial genomes, protein structure modelling, data processing pipeline of GC-MS and GCxGC-MS-based untargeted metabolomics, Next-generation sequencing data processing, human variant discovery, genome-wide association analysis, etc. During my studies, I have learned many bioinformatic skills, e.g., data mining, R programming, python programming, linux programming, machine learning, etc. I am highly interested and motivated in cancer research since my bachelor’s senior projects. Therefore, I have plan to develop my own projects focusing on cancer research, especially, cancer early diagnosis based on circulating cell-free DNA profile.

Publications

Proceeding :

1. Sangphukieo, A., Nawae, W., Laomettachit, T., Supasitthimethee, U., & Ruengjitchatchawalya, M. (2015). A new computationally designed cyclotide as a potential HIV-1 gp120 inhibitor. 10^th International Symposium of the Protein Society of Thailand. Chulabhorn Research Institute, Don Muang, Bangkok, Thailand.

2022 – Current :

1. Sasimol Udomruk, Areerak Phanphaisarn, Thanat Kanthawang, Apiwat Sangphukieo, Songphon Sutthitthasakul, Siripong Tongjai, Pimpisa Teeyakasem, Patcharawadee Thongkumkoon, Santhasiri Orrapin, Sutpirat Moonmuang, Jeerawan Klangjorhor, Arnat Pasena, Pathacha Suksakit, Sivamoke Dissook, Pitithat Puranachot, Jongkolnee Settakorn, Tonapha Pusadee, dumnoensun Pruksakorn, and Parunya Chaiyawat (2023). Characterization of Cell-free DNA Size Distribution in Osteosarcoma Patients. Clinical Cancer Research
2. Kamolphiwong R, Kanokwiroon K, Wongrin W, Chaiyawat P, Klangjorhor J, Settakorn J, Teeyakasem P, Sangphukieo A, Pruksakorn D. Potential target identification for osteosarcoma treatment: Gene expression re-analysis and drug repurposing. Gene. 2022 Dec 10;856:147106. doi: 10.1016/j.gene.2022.147106. Epub ahead of print. PMID: 36513192.

Journal :

1. Chewapreecha C, Pensar J, Chattagul S, Pesonen M, Sangphukieo A, Boonklang P, Potisap C, Koosakulnirand S, Feil EJ, Dunachie S, Chantratita N, Limmathurotsakul D, Peacock SJ, Day NPJ, Parkhill J, Thomson NR, Sermswan RW, Corander J. Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. Mol Biol Evol. 2022 Jan 7;39(1):msab306. doi: 10.1093/molbev/msab306. PMID: 34662416; PMCID: PMC8760936.
2. Chomkatekaew C, Boonklang P, Sangphukieo A, Chewapreecha C. An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know? Front Microbiol. 2021 Jan 21;11:612568. doi: 10.3389/fmicb.2020.612568. PMID: 33552023; PMCID: PMC7858667.
3. Sangphukieo A, Laomettachit T, Ruengjitchatchawalya M. PhotoModPlus: A web server for photosynthetic protein prediction from genome neighborhood features. PLoS One. 2021 Mar 17;16(3):e0248682. doi: 10.1371/journal.pone.0248682. PMID: 33730083.
4. Sangphukieo A, Laomettachit T, Ruengjitchatchawalya M. Photosynthetic protein classification using genome neighborhood-based machine learning feature. Sci Rep. 2020 Apr 28;10(1):7108. doi: 10.1038/s41598-020-64053-w. PMID: 32346070; PMCID: PMC7189237.
5. Sangphukieo, A., Nawae, W., Laomettachit, T., Supasitthimethee, U., & Ruengjitchatchawalya, M. (2015). Computational design of hypothetical new peptides based on a cyclotide scaffold as HIV gp120 inhibitor. PloS one, 10(10), e0139562.

Address  :  9^th floor – The 50^th Anniversary Building, Faculty of Medicine, Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai 50200

Email  :  apiwat.sang@cmu.ac.th

Organizations  :  Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM)