Refereed Publications and Technical Reports - mauriceling/mauriceling.github.io GitHub Wiki

My Refereed Publications

[137] Hon, RYH, Ling, MHT. 2024. Science/Education Portraits IX – Reproducibility and Transparency of Systematic Reviews.

[136] Cheng, KW, Aw, C, Lee, LC, Low, MT, Burhanudin, N, Ng, HT, Ong, P, Tan, BKH, Ling, MHT. 2024. A 5-Year Systematic Review (1 November 2019 to 31 October 2023) on the Benefits of the “Miracle Tree” (Moringa oleifera). Acta Scientific Medical Sciences 8{8): 108-119.

[135] Burhanudin, N, Cheng, KW, Aw, C, Lee, LC, Low, MT, Ng, HT, Ong, P, Tan, BKH, Ling, MHT. 2024. A 10-Year Systematic Review (1 January 2014 to 1 January 2024) on the Potential Health Benefits of Quinoa. Medicon Medical Sciences 7(1): 32-49.

[134] Ganesh, VV, Kumaran, V, King, JE, Kiatfuangfung, P, Seah, ZX, Ling, MHT. 2024. Simulation Suggests that Repeated Supplementations from the Wild into Captive Population Reduce but Cannot Eliminate Inbreeding. Acta Scientific Agriculture 8(8): 31-35.

[133] Chen, YT, Ling, MHT, Yang, H, Cai, MH, Koh, RW, Tan, RYH, Xue, X. 2024. Predicting Peroxide Value of Peanut Oil using Machine Learning Models. Acta Scientific Nutritional Health 8(7): 116-122.

[132] Low, KKM, Ling, MHT. 2024. ODE Versus Petri Net Implementation of Identical SEIRS Model. Acta Scientific Medical Sciences 8(6): 100-104.

[131] Teo, W, Kwan ZJ, Lum, AKY, Ng, SMH, Ling, MHT. 2024. Independent Genic-Encoded Enzymatic Reactions May Randomly Link into Multi-Step Biochemical Pathways in the Absence of Large Cell Selective Pressure. EC Microbiology 20(2): 01-07.

[130] Seow, SK, Dave, VS, Ong, RT, Lao, S, Ling, MHT. 2024. A 10-Year Systematic Review (2013 to 2022) on Effects of Diet on Migraine. EC Clinical and Medical Case Reports 7(2): 01-15.

[129] Lum, AKY, Shanmugam, JH, Teo, W, Kwan ZJ, Ng, SMH, Ling, MHT. 2024. Core Genome of Deinococcota Phylum from 72 Strains Across 40 Species Consist of Only One Gene, Beta Subunit of DNA-Directed RNA Polymerase. Medicon Microbiology 3(1): 03-06.

[128] Kwan, ZJ, Teo, W, Lum, AKY, Ng, SMH, Ling, MHT. 2024. Ab Initio Whole Cell Kinetic Model of Stutzerimonas balearica DSM 6083 (pbmKZJ23). Acta Scientific Microbiology 7(2): 28-31.

[127] Ong, RT, Lao, S, Seow, SK, Dave, VS, Ling, MHT. 2024. Systematic Review of PubMed Articles Prior to 2023 on Effects of Breakfast on School Performance. Medicon Medical Sciences 6(1): 11-25.

[126] Yap, SSK, Choy, WJ, Tan, RYH, Ling, MHT. 2024. Assembly of Single Substance Use Epidemiological Models. Acta Scientific Medical Sciences 8(1): 43-50.

[125] Lao, S, Seow, SK, Ong, RT, Dave, VS, Ling, MHT. 2023. Systematic Review on the Effects of Food on Mental Health via Gut Microbiome. SciMedicine Journal 5(2): 81-91.

[124] Işık, EB, Brazas, MD, Schwartz, R, Gaeta, B, Palagi, PM, van Gelder, CWG, Suravajhala, P, Singh, H, Morgan, SL, Zahroh, H, Ling, M, Satagopam, VP, McGrath, A, Nakai, K, Tan, TW, Gao, G, Mulder, N, Schönbach, C, Zheng, Y. De Las Rivas, J, Khan, AM. 2023. Grand Challenges in Bioinformatics Education and Training. Nature Biotechnology 41: 1171–1174.

[123] Dundas, JB, Ling, MHT. 2023. A Computational Approach to Understand the Human Thought Process. 3rd International Conference on Electronic and Electrical Engineering and Intelligent System (ICE3IS).

[122] Chia, VSQ, Ling, MHT. 2023. Potential Information Processing Differences in Male and Hermaphrodite Neural Networks of Caenorhabditis elegans. Medicon Medical Sciences 5(2): 53-59.

[121] Shin, AW, Yan, LZW, Poh, KSH, Ling, MHT. 2023. Science/Education Portraits VIII: Duoethnography of First-Generation Bioscience Undergraduates in a Private Education Institute in Singapore. Acta Scientific Microbiology 6(6): 24-35.

[120] Ling, MHT. 2023. ChatGPT (Feb 13 Version) is a Chinese Room. Novel Research in Sciences 14(2): NRS.000832.

[119] Toh, BCY, Ling, MHT. 2023. Applications Utilizing CRISPR/Cas9. Novel Research in Sciences 14(1): NRS.000826.

[118] Roh, D, Naing, SY, Ling, MHT. 2023. Peptide Properties of Saccharomyces arboricola H-6 Suggest Randomness in Chromosomal Organization. EC Microbiology 19(3): 01-08.

[117] Wong, KM, Sim, BJH, Ling, MHT. 2023. Consistency Between Saccharomyces cerevisiae S288C Genome Scale Models (iND750 and iMM904). Acta Scientific Microbiology 6(3): 63-68.

[116] Ling, MHT, Musttakim, S, Lau, PN. 2023. Development of a Basic Chemistry Conversational Corpus. Acta Scientific Nutritional Health 7(2): 48-54.

[115] Azan, NK, Ng, ASY, Samsudi, F, Mazlan, MR, Loh, YK, Ling, MHT. 2023. A 5-Year Systematic Review (2018 to 2022) on The Effectiveness of Mediterranean Diet in Preventing Alzheimer’s Disease. Acta Scientific Nutritional Health 7(2): 79-90.

[114] Ng, ASY, Azan, NK, Samsudi, F, Mazlan, MR, Loh, YK, Ling, MHT. 2023. A 5-Year Systematic Review (01 April 2017 to 31 March 2022) on the Causes of Abdominal Obesity. EC Clinical and Medical Case Reports 6(1): 90-110.

[113] Naing, SY, Thia, EWJ, Roh, D, Chew, C, Tun, SK, Wai, MK, Ling, MHT. 2023. Novel Populations from Simulated Admixed Populations. Medicon Medical Sciences 4(1): 9-15.

[112] Tan, JZH, Tan, NTF Tan, Ling, MHT. 2022. Brainopy: A Biologically Relevant SQLite-Based Artificial Neural Network Library. Acta Scientific Computer Sciences 4(12): 13-22.

[111] Loh, BJK, Kannan, KSS, Patil, T, Vij, R, Ling, MHT. 2022. Inconsistent Phylogenetic Trees from Nucleotide or Amino Acid Sequences from Mammalian Mitochondrial Genomes. EC Clinical and Medical Case Reports 5(7): 03-09.

[110] Sim, BJH, Wong, KM, Ling, MHT. 2022. Metabolite Overproduction Potential of Saccharomyces cerevisiae S288C Explored Using Its Genome-Scale Metabolic Model, iMM904. EC Microbiology 18(7): 46-51.

[109] Maitra, A, Ling, MHT. 2022. DOSSIER: A Toolkit to Extract Data from Digital Life Simulations Using Dose. Acta Scientific Computer Sciences 4(7): 37-40.

[108] Kannan, KSS, Patil, T, Vij, R, Loh, BJK, Ling, MHT. 2022. Nutrient Availability Impacts Intracellular Metabolic Profiles in Digital Organisms. Acta Scientific Microbiology 5(6): 18-25.

[107] Tang, AY, Ling, MHT. 2022. Relapse Processes are Important in Modelling Drug Epidemic. Acta Scientific Medical Sciences 6(6): 177-182.

[106] Wee, YY, Kng, X, Sor, SX, Ling, MHT. 2022. Genome-Scale Metabolic Model-Based Reactome-Phenome Map of Synechocystis sp. PCC 6803, A Potential Biofuel Producer. Medicon Microbiology 1 (4): 02-08.

[105] Sor, SX, Wee, YY, Kng, X, Ling, MHT. 2022. A Systematic Scoping Review on the Current Applications of Environmental DNA (eDNA). EC Clinical and Medical Case Reports 5(4): 46-64.

[104] Chua, MTE, Dumanglas, ABG, Ling, MHT. 2022. Gene Co-Expressions Cannot Predict Protein-Protein Interactions in Escherichia coli. EC Microbiology 18(3): 102-109.

[103] Tan, FL, Kuan, ZJ, Amir-Hamzah, N, Kng, X, Wee, YY, Sor, SX, Ling, MHT. 2022. Significant Differences in Media Components and Predicted Growth Rates of 58 Escherichia coli Genome-scale Models. Acta Scientific Microbiology 5(2): 56-68.

[102] Amir-Hamzah, N, Kuan, ZJ, Ling, MHT. 2022. Kinetic Models with Default Enzyme Kinetics from Genome-scale Models. Acta Scientific Computer Sciences 4(1): 59-63.

[101] Ling, MHT. 2021. ZeroOne: Building and Enhancing Executing Simulation by Incremental Patches. Acta Scientific Computer Sciences 3(10): 50-52.

[100] Sim, KS, Ling, MHT. 2021. Installation and Documentation Evaluation of Recent (01 January 2020 to 15 February 2021) Chatbot Engines from Python Package Index (PyPI). Acta Scientific Computer Sciences 3(8): 38-43.

[99] Ang, DGY, Ling, MHT. 2021. Sudden and Steep Harsh Environment Results in Over-Compensation in Digital Organisms. EC Microbiology 17(7): 104-113.

[98] Johny, A, Sumedha, PR, Ling, MHT. 2021. Simulation Suggests that One-Off Simple Supplementation from the Wild into Captive Population May Not Increase Captive Genetic Diversity. EC Veterinary Science 6(7): 107-111.

[97] Lim, GZK, Azmi, HH, Dolmatova, M, Ling, MHT. 2021. Significant Differences in Nucleotide and Peptide Features Between Chromosomes Suggesting Sequence Non-Randomness Across Chromosomes. Acta Scientific Microbiology 4(4): 23-28.

[96] Kuan, ZJ, Amir-Hamzah, N, Ling, MHT. 2021. Coffee as a Potential Nutraceutical. EC Nutrition 16(3): 57-65.

[95] Kim, KD, Chua, SCH, Ling, MHT. 2021. Science/Education Portraits VII Statistical Methods Used in 1081 Papers Published in Year 2020 Across 12 Life Science Journals Under BioMed Central. Acta Scientific Nutritional Health 5(3): 06-12.

[94] Cho, JL, Ling, MHT. 2021. Adaptation of Whole Cell Kinetic Model Template, UniKin1, to Escherichia coli Whole Cell Kinetic Model, ecoJC20. EC Microbiology 17(2): 254-260.

[93] Chua, SCH, Ling, MHT. 2021. Stop Codon Usage Varies on CDS Length, Nucleotide Compositions, and Peptide Instability in Six Escherichia coli Strains. EC Clinical and Medical Case Reports 4(2): 39-46.

[92] Kuan, ZJ, Ling, MHT. 2021. Core Genome of Poales, An Economically Important Order of Monocotyledons. EC Agriculture 7(2): 24-29.

[91] Ling, MHT. 2020. Low Classification Accuracy by Logistic Regression, Support Vector Classifier, and Multi-Layer Perceptron, but Not Decision Tree, on Random Attributes from Hadamard Matrix. EC Clinical and Medical Case Reports 3(12): 07-10.

[90] Teo, YH, Ling, MHT. 2020. A Systematic Review on the Sufficiency of PubMed and Google Scholar for Biosciences. Acta Scientific Medical Sciences 4(12): 03-08.

[89] Wang, VCC, Ling, MHT. 2020. Science/Education Portraits VI: Anecdotes of Life in Singapore During COVID-19 (February 2020 to September 2020). EC Clinical and Medical Case Reports 3(11): 98-111.

[88] Chew, SSM, Murthy, MV, Kamarudin, NJ, Wang, VCC, Tan, XT, Ramesh, A, Yablochkin, NV, Mathivanan, K, Ling, MHT. 2020. Rapid Genetic Diversity with Variability between Replicated Digital Organism Simulations and its Implications on Cambrian Explosion. EC Clinical and Medical Case Reports 3(11): 64-68.

[87] Liu, TT, Ling, MHT. 2020. BactClass: Simplifying the Use of Machine Learning in Biology and Medicine. Acta Scientific Medical Sciences 4(11): 43-47.

[86] Ling, MHT. 2020. AdvanceSyn Toolkit: An Open-Source Suite for Model Development and Analysis in Biological Engineering. MOJ Proteomics & Bioinformatics 9(4):83‒86.

[85] Murthy, MV, Balan, D, Kamarudin, NJ, Wang, VCC, Tan, XT, Ramesh, A, Chew, SSM, Yablochkin, NV, Mathivanan, K, Ling, MHT. 2020. UniKin1: A Universal, Non-Species-Specific Whole Cell Kinetic Model. Acta Scientific Microbiology 3(10): 04-08.

[84] Wang, VCC, Kamarudin, NJ, Tan, XT, Ramesh, A, Chew, SSM, Murthy, MV, Yablochkin, NV, Mathivanan, K, Ling, MHT. 2020. A Case Study using Mitochondrial Genomes of the Order Diprotodontia (Australasian Marsupials) Suggests that Single Ortholog is Not Sufficient for Phylogeny. EC Clinical and Medical Case Reports 3(9): 93-114.

[83] Kamarudin, NJ, Wang, VCC, Tan, XT, Ramesh, A, Chew, SSM, Murthy, MV, Yablochkin, NV, Mathivanan, K, Ling, MHT. 2020. A Simulation Study on the Effects of Founding Population Size and Number of Alleles Per Locus on the Observed Population Genetic Profile: Implications to Broodstock Management. EC Veterinary Science 5(8): 176-180.

[82] Tan, XT, Ramesh, A, Wang, VCC, Kamarudin, NJ, Chew, SSM, Murthy, MV, Yablochkin, NV, Mathivanan, K, Ling, MHT. 2020. Core Pseudomonas Genome From 10 Pseudomonas Species. MOJ Proteomics & Bioinformatics 9(3): 68‒71.

[81] Gunalan, K, Wong, CQL, Neo, MPY, Ling, MHT. 2020. One Percent of Escherichia coli O157:H7 Peptides May Contain Putative Beta-Lactamase Activity. EC Microbiology 16(8): 73-79.

[80] Cheong, KC, Hon, RYH, Sander, CJ, Ang, IZL, Foong, JH, Ling, MHT. 2020. A Simulation Study on the Effects of Media Composition on the Growth Rate of Escherichia coli MG1655 using iAF1260 Model. Acta Scientific Microbiology 3(8): 40-44.

[79] Neo, CY, Ling, MHT. 2020. Prevalence and Length of Open Reading Frames Vary Across Randomly Generated Sequences of Different Nucleotide Compositions. EC Microbiology 16(7): 72-78.

[78] Sim, BKY, Ling, MHT. 2020. Possibility of Abiotic Genesis of Biochemistry. EC Microbiology 16(6): 104-109.

[77] Teng, RSY, Kwang, JCY, Chin, ASQ, Sander, CJ, Ang, IZL, Foong, JH, Cheong, KC, Hon, RYH, Ling, MHT. 2020. Correlation Analysis on Transcriptomes from Published Human Skin Studies Show Variations between Control Samples. EC Clinical and Medical Case Reports 3(6): 143-146.

[76] Ling, MHT. 2020. SeqProperties: A Python Command-Line Tool for Basic Sequence Analysis. Acta Scientific Microbiology 3(6): 103-106.

[75] Usman, S, Chua, JW, Ardhanari-Shanmugam, KD, Thong-Ek C, B, V, Shahrukh, K, Woo, JH, Kwek, BZN, Ling, MHT. 2019. Pseudomonas balearica DSM 6083T promoters can potentially originate from random sequences. MOJ Proteomics & Bioinformatics 8(2): 66‒70.

[74] Ling, MHT. 2019. Island: A Simple Forward Simulation Tool for Population Genetics. Acta Scientific Computer Sciences 1(2): 20-22.

[73] Ling, MHT. 2019. Draft Implementation of a Method to Secure Data by File Fragmentation. Acta Scientific Computer Sciences 1(2): 10-13.

[72] Ardhanari-Shanmugam, KD, Shahrukh, K, B, V, Woo, JH, Thong-Ek, C, Usman, S, Kwek, BZN, Chua, JW, Ling, MHT. 2019. De Novo Origination of Bacillus subtilis 168 Promoters from Random Sequences. Acta Scientific Microbiology 2(11): 07-10.

[71] Chang, ED, Ling, MHT. 2019. Explaining Monod in Terms of Escherichia coli Metabolism. Acta Scientific Microbiology 2(9): 66-71.

[70] Ling, MHT. 2019. Science/Education Portraits V: The Scientific Tertiary Education that I had Envisioned. Acta Scientific Medical Sciences 2(8): 75-79.

[69] Kwek, BZN, Ardhanari-Shanmugam, KD, Woo, JH, Usman, S, Chua, JW, B, V, Shahrukh, K, Thong-Ek, C, Ling, MHT. 2019. Random Sequences May Have Putative Beta-Lactamase Properties. Acta Scientific Medical Sciences 3(7): 113-117.

[68] Thong-Ek, C, Usman, S, Woo, JH, Chua, JW, Kwek, BZN, Ardhanari-Shanmugam, KD, B, V, Shahrukh, K, Ling, MHT. 2019. Potential De Novo Origins of Archaebacterial Glycerol-1-Phosphate Dehydrogenase (G1PDH). Acta Scientific Microbiology 2(6): 106-110.

[67] Maitra, A, Ling, MHT. 2019. Codon Usage Bias and Peptide Properties of Pseudomonas balearica DSM 6083T. MOJ Proteomics & Bioinformatics 8(2):27‒39.

[66] Kim, JH, Ling, MHT. 2019. Proteome Diversities Among 19 Archaebacterial Species. Acta Scientific Microbiology 2(5): 20-27.

[65] Ling, MHT. 2019. De Novo Putative Protein Domains from Random Peptides. Acta Scientific Microbiology 2(4): 109-112.

[64] Ling, MHT. 2019. Science/Education Portraits IV: Experiences from a Decade as Informal Career Counsellor can be Summarized as Personopreneurship. Acta Scientific Medical Sciences 3(3): 151-156.

[63] Suwinski, P, Ong, CK, Ling, MH, Poh, YM, Khan, AM, Ong, HS. 2019. Advancing Personalized Medicine through the Application of Whole Exome Sequencing and Big Data Analytics. Frontiers in Genetics 10: 49.

[62] Ling, MHT. 2018. SEcured REcorder BOx (SEREBO) Based on Blockchain Technology for Immutable Data Management and Notarization. MOJ Proteomics & Bioinformatics 7(6):169‒174.

[61] Ling, MHT. 2018. Science/Education Portraits III: Perceived Prevalence of Data Fabrication and/or Falsification in Research. Advances in Biotechnology and Microbiology 11(5):555824.

[60] Lim, JX, Ling, MHT. 2019. Gene Ontology and KEGG Orthology Mappings for 10 Strains of Pseudomonas stutzeri. EC Proteomics and Bioinformatics 3(1): 12-18.

[59] Ling MHT. 2018. RANDOMSEQ: Python Command‒line Random Sequence Generator. MOJ Proteomics & Bioinformatics 7(4):206‒208.

[58] Ling, MHT. 2018. Science/Education Portraits II: Pre-Tertiary and Undergraduate Research Mentors Should Consider Publication as Project Endpoint. MOJ Proteomics & Bioinformatics 7(2):127‒129.

[57] Chan, OYW, Keng, BMH, Ling, MHT. 2018. Science/Education Portraits I: Identifying Success Factors of Pre-Tertiary Bioinformatics Research Experience from Students’ Perspective. Advances in Biotechnology and Microbiology 8(2): 555734.

[56] Ling, MHT. 2018. Back-of-the-Envelope Guide (A Tutorial) to 10 Intracellular Landscapes. MOJ Proteomics & Bioinformatics 7(1): 00209.

[55] Ling, MHT. 2017. Towards Portrait [(Auto) Ethnography, Narrative, and Action Research] of Bioinformatics. EC Proteomics and Bioinformatics 2(1): 29-35.

[54] Ling, MHT. 2017. A Personal Narrative of 6 Pre-University Research Projects Over 7 Years (2009-2015) Yielding 19 Manuscripts. MOJ Proteomics & Bioinformatics 6(3): 00193.

[53] Wang, HJ, Ling, MHT, Chua, TK, Poh, CL. 2017. Two Cellular Resource Based Models Linking Growth and Parts Characteristics Aids the Study and Optimization of Synthetic Gene Circuits. Engineering Biology 1(1): 30 –39.

[52] Chay, ZE, Goh, BF, Ling, MHT. 2016. PNet: A Python Library for Petri Net Modeling and Simulation. Advances in Computer Science: an international journal 5(4): 24-30.

[51] Ling, MHT. 2016. Of (Biological) Models and Simulations. MOJ Proteomics & Bioinformatics 3(4): 00093.

[50] Ling, MHT. 2016. COPADS IV: Fixed Time-Step ODE Solvers for a System of Equations Implemented as a Set of Python Functions. Advances in Computer Science: an international journal 5(3): 5-11.

[49] Chew, JS, Ling, MHT. 2016. TAPPS Release 1 Plugin-Extensible Platform for Technical Analysis and Applied Statistics. Advances in Computer Science: an international journal 5(1): 132-141.

[48] Castillo, CFG, Chay ZE, Ling, MHT. 2015. Resistance Maintained in Digital Organisms Despite Guanine/Cytosine-Based Fitness Cost and Extended De-Selection: Implications to Microbial Antibiotics Resistance. MOJ Proteomics & Bioinformatics 2(2): 00039.

[47] Ling, MHT. 2014. Applications of Artificial Life and Digital Organisms in the Study of Genetic Evolution. Advances in Computer Science: an international journal 3(4): 107-112.

[46] Keng, BMH, Chan, OYW, Ling, MHT. 2014. Codon Usage Bias is Evolutionarily Conserved. Asia Pacific Journal of Life Sciences 7(3): 233-242.

[45] Ling, MHT, Poh, CL. 2014. A Predictor for Predicting Escherichia coli Transcriptome and the Effects of Gene Perturbations. BMC Bioinformatics 15: 140.

[44] Castillo, CFG, Ling, MHT. 2014. Resistant Traits in Digital Organisms Do Not Revert Preselection Status despite Extended Deselection: Implications to Microbial Antibiotics Resistance. BioMed Research International 2014, Article ID 648389.

[43] Chan, OYW, Keng, BMH, Ling, MHT. 2014. Bactome III: OLIgonucleotide Variable Expression Ranker (OLIVER) 1.0, Tool for Identifying Suitable Reference (Invariant) Genes from Large Microarray Datasets. The Python Papers Source Codes 6: 2.

[42] Koh, YZ, Ling, MHT. 2014. Catalog of Biological and Biomedical Databases Published in 2013. iConcept Journal of Computational and Mathematical Biology 3: 3.

[41] Loo, BZL, Low, SXZ, Aw, ZQ, Lee, KC, Oon, JSH, Lee, CH, Ling, MHT. 2014. Escherichia coli ATCC 8739 Adapts Specifically to Sodium Chloride, Monosodium Glutamate, and Benzoic Acid after Prolonged Stress. Asia Pacific Journal of Life Sciences 7(3): 243-258.

[40] Castillo, CFG, Ling, MHT. 2014. Digital Organism Simulation Environment (DOSE): A Library for Ecologically-Based In Silico Experimental Evolution. Advances in Computer Science: an International Journal 3(1): 44-50.

[39] Chan, OYW, Keng, BMH, Ling, MHT. 2014. Correlation and Variation Based Method for Reference Genes Identification from Large Datasets. Electronic Physician 6(1): 719-727.

[38] Ling, MHT. 2014. NotaLogger: Notarization Code Generator and Logging Service. The Python Papers 9: 2.

[37] Chen, KFQ, Ling, MHT. 2013. COPADS III (Compendium of Distributions II): Cauchy, Cosine, Exponential, Hypergeometric, Logarithmic, Semicircular, Triangular, and Weibull. The Python Papers Source Codes 5: 2.

[36] Koh, YZ, Ling, MHT. 2013. On the Liveliness of Artificial Life. iConcept Journal of Human-Level Intelligence 3: 1.

[35] Keng, BMH, Chan, OYW, Heng, SSJ, Ling, MHT. 2013. Transcriptome Analysis of Spermophilus lateralis and Spermophilus tridecemlineatus Liver Does Not Suggest the Presence of Spermophilus-liver-specific Reference Genes. ISRN Bioinformatics 2013, Article ID 361321.

[34] Ling, MHT, Ban, Y, Wen, H, Wang, SM, Ge, SX. 2013. Conserved Expression of Natural Antisense Transcripts in Mammals. BMC Genomics 14(1): 243.

[33] Low, SXZ, Aw, ZQ, Loo, BZL, Lee, KC, Oon, JSH, Lee, CH, Ling, MHT. 2013. Viability of Escherichia coli ATCC 8739 in Nutrient Broth, Luria-Bertani Broth and Brain Heart Infusion over 11 Weeks. Electronic Physician 5:576-581.

[32] Ling, MHT. 2012. Re-creating the Philosopher’s Mind: Artificial Life from Artificial Intelligence. iConcept Journal of Human-Level Intelligence 2: 1.

[31] Ling, MHT. 2012. Ragaraja 1.0: The Genome Interpreter of Digital Organism Simulation Environment (DOSE). The Python Papers Source Codes 4: 2.

[30] Ling, MHT. 2012. An Artificial Life Simulation Library Based on Genetic Algorithm, 3-Character Genetic Code and Biological Hierarchy. The Python Papers 7: 5.

[29] Goh, DJW, How, JA, Lim, JZR, NG, WC, Oon, JSH, Lee, KC, Lee, CH, Ling, MHT. 2012. Gradual and Step-wise Halophilization Enables Escherichia coli ATCC 8739 to Adapt to 11% NaCl. Electronic Physician 4(3): 527-535.

[28] How, JA, Lim, JZR, Goh, DJW, NG, WC, Oon, JSH, Lee, KC, Lee, CH, Ling, MHT. 2013. Adaptation of Escherichia coli ATCC 8739 to 11% NaCl. Dataset Papers in Biology 2013, Article ID 219095.

[27] Ling, MHT , Rabara, RC, Tripathi, P, Rushton, PJ, Ge, X. 2013. Extending MapMan Ontology to Tobacco for Visualization of Gene Expression. Dataset Papers in Biology 2013, Article ID 706465.

[26] Lee, CH, Oon, JSH, Lee, KC, Lee, CH, Ling, MHT. 2012. Escherichia coli ATCC 8739 Adapts to the Presence of Sodium Chloride, Monosodium Glutamate, and Benzoic Acid after Extended Culture. ISRN Microbiology 2012, Article ID 965356.

[25] Dundas, JB, Ling, MHT. 2012. Reference Genes for Measuring mRNA Expression. Theory in Biosciences 131: 215-223.

[24] Too, IHK, Ling, MHT. 2012. Signal Peptidase Complex Subunit 1 (SPCS1) and Hydroxyacyl-CoA Dehydrogenase Beta Subunit (HADHB) are Suitable Reference Genes in Human Lungs. ISRN Bioinformatics 2012, Article ID 790452.

[23] Heng, SSJ, Chan, OYW, Keng, BMH, Ling, MHT. 2011. Glucan biosynthesis protein G (mdoG) is a Suitable Reference Gene in Escherichia coli K-12. ISRN Microbiology 2011, Article ID 469053.

[22] Ling, MHT. 2011. Bactome II: Analyzing Gene List for Gene Ontology Over-Representation. The Python Papers Source Codes 3: 3.

[21] Ling, MHT, Jean, A, Liao, D, Tew, BBY, Ho, S, Clancy, K. 2011. Integration of Standardized Cloning Methodologies and Sequence Handling to Support Synthetic Biology Studies. Third International Workshop on Bio-Design Automation (IWBDA). San Diego, California, USA.

[20] Tahat, A, Ling, MHT. 2011. Mapping Relational Operations onto Hypergraph Model. The Python Papers 6(1): 4.

[19] Kuo, CJ, Ling, MHT, Hsu, CN. 2011. Soft Tagging of Overlapping High Confidence Gene Mention Variants for Cross-Species Full-Text Gene Normalization. BMC Bioinformatics 12(Suppl 8):S6

[18] Lim, JZR, Aw, ZQ, Goh, DJW, How, JA, Low, SXZ, Loo, BZL, Ling, MHT. 2010. A Genetic Algorithm Framework Grounded in Biology. The Python Papers Source Codes 2: 6.

[17] Ling, MHT. 2010. Specifying the Behaviour of Python Programs: Language and Basic Examples. The Python Papers 5(2): 4.

[16] Chay, ZE, Ling, MHT. 2010. COPADS, II: Chi-Square test, F-Test and t-Test Routines from Gopal Kanji's 100 Statistical Tests. The Python Papers Source Codes 2:3.

[15] Chay, ZE, Lee, CH, Lee, KC, Oon, JSH, Ling, MHT. 2010. Russel and Rao Coefficient is a Suitable Substitute for Dice Coefficient in Studying Restriction Mapped Genetic Distances of Escherichia coli. iConcept Journal of Computational and Mathematical Biology 1:1.

[14] Ling, MHT. 2010. COPADS, I: Distances Measures between Two Lists or Sets. The Python Papers Source Codes 2:2.

[13] Ng, YY and Ling, MHT. 2010. Electronic Laboratory Notebook on Web2Py Framework. In: Peer-Reviewed Articles from PyCon Asia-Pacific 2010. The Python Papers 5(3): 7.

[12] Lee, CH, Lee, KC, Oon, JSH, Ling, MHT. 2010. Bactome, I: Python in DNA Fingerprinting. In: Peer-Reviewed Articles from PyCon Asia-Pacific 2010. The Python Papers 5(3):6.

[11] Chia, CY, Lim, CWX, Leong, WT, Ling, MHT. 2010. High Expression Stability of Microtubule Affinity Regulating Kinase 3 (MARK3) Makes It a Reliable Reference Gene. IUBMB Life 62(3):200-203.

[10] Ling, MHT. 2009. Understanding Mouse Lactogenesis by Transcriptomics and Literature Analysis. Doctor of Philosophy. Department of Zoology, The University of Melbourne, Australia.

[9] Kuo, CJ, Ling, MHT, Lin, KT, Hsu, CN. 2009. BIOADI: A Machine Learning Approach to Identify Abbreviations and Definitions in Biological Literature. BMC Bioinformatics 10(Suppl 15):S7.

[8] Ling, MHT. 2009. Ten Z-test Routines from Gopal Kanji's 100 Statistical Tests. The Python Papers Source Codes 1:5.

[7] Ling, MHT. 2009. Compendium of Distributions, I: Beta, Binomial, Chi-Square, F, Gamma, Geometric, Poisson, Student's t, and Uniform. The Python Papers Source Codes 1:4.

[6] Ling, MHT, Lefevre, C, Nicholas, KR. 2008. Filtering Microarray Correlations by Statistical Literature Analysis Yields Potential Hypotheses for Lactation Research. The Python Papers 3(3): 4.

[5] Ling, MHT, Lefevre, C, Nicholas, KR. 2008. Parts-of-Speech Tagger Errors Do Not Necessarily Degrade Accuracy in Extracting Information from Biomedical Text. The Python Papers 3 (1): 65-80.

[4] Ling, MHT, Lefevre, C, Nicholas, KR, Lin, F. 2007. Re-construction of Protein-Protein Interaction Pathways by Mining Subject-Verb-Objects Intermediates. In J.C. Ragapakse, B. Schmidt, and G. Volkert (Eds.), Proceedings of the Second IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007). Lecture Notes in Bioinformatics 4774. (pp. 286-299) Springer-Verlag.

[3] Ling, MHT. 2007. Firebird Database Backup by Serialized Database Table Dump. The Python Papers 2 (1): 12-16.

[2] Ling, MHT. 2006. An Anthological Review of Research Utilizing MontyLingua, a Python-Based End-to-End Text Processor. The Python Papers 1 (1): 5-12.

[1] Ling, MHT and So, CW. 2003. Architecture of an Open-Sourced, Extensible Data Warehouse Builder: InterBase 6 Data Warehouse Builder (IB-DWB). In Rubinstein, B. I. P., Chan, N. and Kshetrapalapuram, K. K. (Eds.), Proceedings of the First Australian Undergraduate Students' Computing Conference. (pp. 40-45).

My Refereed Book Chapters

[B15] Low, KKM, Ling, MHT. 2024. Cell Modelling and Simulation. [Abstract]

[B14] Maitra, A, Lim, JJH, Ho, CJY, Tang, AY, Teo, W, Alejado, ELC, Ling, MHT. 2024. Experimenting the Unexperimentable with Digital Organisms. [Abstract]

[B13] Sim, BJH, Tan, NTF, Ling, MHT. 2024. Multilevel Metabolic Modelling Using Ordinary Differential Equations. [Abstract]

[B12] Ling, MHT. 2019. SEcured REcorder BOx (SEREBO) Version 1.0. In Current STEM, Volume 2. pp. 67-154. Nova Science Publishers, Inc. ISBN 978-1-53616-042-0.

[B11] Wong, A, Ling, MHT. 2019. Characterization of Transcriptional Activities. In Ranganathan, S., Gribskov, M., Nakai, K., Schönbach, C. (eds.), Encyclopedia of Bioinformatics and Computational Biology, Volume 3, pages 830-841. Oxford: Elsevier. ISBN 978-0-12811-414-8. [Abstract]

[B10] Li, BT, Lim, JX, Ling, MHT. 2019. Analyzing Transcriptome-Phenotype Correlations. In Ranganathan, S., Gribskov, M., Nakai, K., Schönbach, C. (eds.), Encyclopedia of Bioinformatics and Computational Biology, Volume 3, pages 819-824. Oxford: Elsevier. ISBN 978-0-12811-414-8. [Abstract]

[B9] Ling, MHT. 2019. Survey of Antisense Transcription. In Ranganathan, S., Gribskov, M., Nakai, K., Schönbach, C. (eds.), Encyclopedia of Bioinformatics and Computational Biology, Volume 3, pages 842-846. Oxford: Elsevier. ISBN 978-0-12811-414-8. [Abstract]

[B8] Lim, JX, Li, BT, Ling, MHT. 2019. Sequence Composition. In Ranganathan, S., Gribskov, M., Nakai, K., Schönbach, C. (eds.), Encyclopedia of Bioinformatics and Computational Biology, Volume 3, pages 323-326. Oxford: Elsevier. ISBN 978-0-12811-414-8. [Abstract]

[B7] Ling, MHT. 2018. COPADS VI: Fixed Time-Step ODE Solvers with Mixed ODE and non-ODE Function, and Script Generator. In Current STEM, Volume 1, page 173-212. Nova Science Publishers, Inc. ISBN 978-1-53613-416-2.

[B6] Ling, MHT. 2018. COPADS V: Lindenmayer System with Stochastic and Function-Based Rules. In Current STEM, Volume 1, page 143-172. Nova Science Publishers, Inc. ISBN 978-1-53613-416-2.

[B5] Ling, MHT. 2018. A Cryptography Method Inspired by Jigsaw Puzzles. In Current STEM, Volume 1, page 129-142. Nova Science Publishers, Inc. ISBN 978-1-53613-416-2.

[B4] Castillo, CFG, Ling, MHT. 2018. Digital Organism Simulation Environment (DOSE) Version 1.0.4. In Current STEM, Volume 1, page 1-106. Nova Science Publishers, Inc. ISBN 978-1-53613-416-2.

[B3] Too, IHK, Heng, SSJ, Chan, OYW, Keng, BMH, Chia, CY, Lim, CWX, Leong, WT, Chu, QH, Ang, EJG, Lin, YJ, Ling, MHT. 2013. Identification of Reference Genes by Meta-Microarray Analyses. In Microarrays: Principles, Applications and Technologies. Nova Science Publishers, Inc. ISBN 978-1-62948-669-7.

[B2] Ling, MHT, Lefevre, Christophe, Nicholas, KR. 2010. Mining Protein-Protein Interactions from Published Abstracts with MontyLingua. In Sequence and Genome Analysis: Methods and Applications. iConcept Press Pty Ltd. ISBN 978-1-453753-859.

[B1] Ling, MHT, Lefevre, Christophe, Nicholas, KR. 2009. Biomedical Literature Analysis: Current State and Challenges. In Internet Policies and Issues, Volume 7. Nova Science Publishers, Inc. ISBN 978-1-61668-745-8.

My Monographs and Collections

[M7] Ling, MHT. 2023. Two-Thirds. ISBN 978-1-312-16410-9. [PDF] [Purchase Link]

[M6] Ling, MHT. 2019. Autobiographic Verses, Volume 1. ISBN 978-1-79476-063-9. [PDF] [Purchase Link]

[M5] Ling, MHT. 2018. 100 Pieces of Gobi Jade (金丝玉). ISBN 978-1-387-58931-9. [PDF] [Purchase Link]

[M4] Ling, MHT. 2018. Stones and Seeds. ISBN 978-1-387-57971-6. [PDF] [Purchase Link]

[M3] Ling, MHT. 2014. Hormonal Regulation of Mouse Lactogenesis: Using Transcriptomics and Literature Analysis. Scholars’ Press. ISBN 978-3-639-66810-0. [Amazon Link]

[M2] Ling, MHT. 2013. Six Years of Melbourne: July 2002 to April 2008. ISBN 978-1-304-41694-0. [PDF] [EPUB] [Purchase Link]

[M1] Ling, MHT and Li, MQA (ed). 2010. Proceedings of PyCon Asia-Pacific 2010. The Python Papers Monograph 2.

My Technical Reports

[TR17] Ling, MHT. 2017. Problem-Based Learning (PBL), an Important Paradigm for Bioinformatics Education. MOJ Proteomics and Bioinformatics 5(4): 00166. [PDF]

[TR16] Ling, MHT. 2016. The Bioinformaticist’s/Computational Biologist’s Laboratory. MOJ Proteomics and Bioinformatics 3(1): 00075. [PDF]

[TR15] Castillo, CFG, Ling, MHT. 2015. Improved Implementation of Digital Organism Simulation Environment (DOSE Version 1.0.4). Colossus Technologies LLP Technical Report Number 001.

[TR14] Dundas, J, Ling, MHT. 2011. Higher Level Intelligence in Machines. iConcept Journal of Human-Level Intelligence, 2: 2. (An editorial) [PDF]

[TR13] Heng, SSJ, Chan, OYW, Keng, BMH, Ling, MHT. 2011. Identifying Invariant Genes in Escherichia coli. Proceedings of the 17th Youth Science Conference. Singapore.

[TR12] Chong, WY, Lee, BMJ, Tan, SY, Ling, MHT. 2011. Qualitative Study on the Lifestyle of Working Adults. Specialist Diploma in Nutrition and Health Promotion Project. School of Chemical and Life Sciences, Singapore Polytechnic, Singapore.

[TR11] Keong, BY, Leong, APH, Weng, JY, Ling, MHT. 2011. Qualitative Study on the Dietary, Exercise and Rest Patterns on Mid-Late Teenagers Specialist Diploma in Nutrition and Health Promotion Project. School of Chemical and Life Sciences, Singapore Polytechnic, Singapore.

[TR10] Aw, ZQ, Low, SXZ, Loo, BZL, Ling, MHT. 2011. Adaptive Evolution of Escherichia coli: Fitness and Genetic Changes beyond 100th Passage. Diploma in Biotechnology Final Year Project. School of Chemical and Life Sciences, Singapore Polytechnic, Singapore. [PDF]

[TR9] Lim, JZR, Goh, DJW, How, JA, Ling, MHT. 2011. Adaptive Evolution of Escherichia coli: Growth Kinetics and Genetic Changes from 2 to 10% Halophilzation. Diploma in Biotechnology Final Year Project. School of Chemical and Life Sciences, Singapore Polytechnic, Singapore. [PDF]

[TR8] Chu, QH, Lin, YJ, Ang, EJG, Ling, MHT. 2010. Identification of Transcriptional Invariant Genes in Mouse Endocrine Glands from Microarray Data. Proceedings of the 16th Youth Science Conference. Singapore.

[TR7] Ling, MHT. 2010. Lecturer's Personal Website is a Tool for Improving Lecturer-Students' Rapport. School of Chemical and Life Sciences, Singapore Polytechnic, Singapore.

[TR6] Lee, CH, Lee, KC, Oon, JSH, Ling, MHT. 2010. Evolution Characterization of Escherichia coli using RFLP DNA Fingerprinting. Diploma in Biotechnology Final Year Project. School of Chemical and Life Sciences, Singapore Polytechnic, Singapore. [PDF]

[TR5] Teo, DCT, Lee, NFL, Tham, CCF, Ling, MHT. 2010. Health Benefits of the Sun and Yang Styles of Tai Chi : A Questionnaire Study. Specialist Diploma in Nutrition and Health Promotion Project. School of Chemical and Life Sciences, Singapore Polytechnic, Singapore.

[TR4] Chia, CY, Lim, CWX, Leong, WT, Ling, MHT. 2009. Identification of Transcriptional Invariant Genes in Mouse Liver from Microarray Data. Proceedings of the 15th Youth Science Conference. Singapore.

[TR3] Ng, JPH, Ong, YC, Ling, MHT, Xu WJ. 2009. Properties of Histatin 5. Proceedings of the 15th Youth Science Conference. Singapore.

[TR2] Ling, MHT. 2002. Identifying the Roles of Insulin, Prolactin, and Glucocorticoid in the Initiation of Murine Lactogenesis. Bachelor of Science (Degree with Honours) Thesis. Department of Zoology, The University of Melbourne, Australia.

[TR1] Chia, YC, Ling, MHT, Wong, ECK, Yap, E, Koh, SI. 1999. Development of Rapid Strain Typing of Aedes Mosquito by Random Amplified Polymorphic Typing Adult DNA (RAPD). Diploma in Biotechnology Final Year Project Report. Department of Chemical Process and Biotechnology, Singapore Polytechnic, Singapore.