My Refereed Publications Before 2020 - mauriceling/mauriceling.github.io GitHub Wiki

[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).