Maurice Ling's Website

                    Refereed Publications / Technical Reports


My Refereed Publications


 

[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. [Abstract] [PDF]

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

[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. [Abstract] [PDF]

[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. [Abstract] [PDF]

[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. [PDF]

[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. [Abstract] [PDF]

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

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

[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. [Full Text] [PDF]

[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. [PDF] [Zipped Codes] [Application Download]

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

[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. [Abstract and References]

[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. [Abstract] [PDF] [Release]

[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. [Abstract] [PDF] [Application Download]

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

[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. [Abstract] [PDF] [Zipped Codes]

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

[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. [Full Text] [PDF]

[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. [Abstract] [Full Text] [PDF] [Supplementary Materials] [Microarray Dataset]

[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. [PDF]

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

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

[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. [Abstract] [PDF]

[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. [PDF]

[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. [Full Text] [Dataset]

[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. [Abstract] [Full Text] [Dataset]

[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. [Full Text] [PDF]

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

[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. [Full Text] [PDF]

[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. [Full Text] [PDF]

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

[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. [Abstract] [PDF]

[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. [Full Text] [PDF]

[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. [Abstract] [PDF] [Zipped Codes]

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

[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. [Abstract] [PDF] [Zipped Codes]

[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. [PDF]

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

[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. [Abstract] [PDF]

[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. [Abstract] [PDF] [Zipped Codes]

[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. [Abstract]

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

[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. [Full Text] [PDF]

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

[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. [Abstract] [PDF] [Zipped Codes]

[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. [Abstract] [PDF]

[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 [Abstract] [PDF]

[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. [Abstract] [PDF]

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

[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. [Abstract] [PDF]

[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). [Abstract] [PDF]

My Refereed Book Chapters


[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. James V. Rogers (ed), Microarrays: Principles, Applications and Technologies. Nova Science Publishers, Inc. [Abstract and References]

[B2] Ling, MHT, Lefevre, Christophe, Nicholas, KR. 2010. Mining Protein-Protein Interactions from Published Abstracts with MontyLingua. In Zhongming Zhao(ed). Sequence and Genome Analysis: Methods and Applications. iConcept Press Pty Ltd. [PDF]

[B1] Ling, MHT, Lefevre, Christophe, Nicholas, KR. 2009. Biomedical Literature Analysis: Current State and Challenges. In B.G. Kutais (ed). Internet Policies and Issues, Volume 7. Nova Science Publishers, Inc. [Abstract and References]

My Monographs and Collections


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

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

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

My Technical Reports


[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. [Full Text]

[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. [Full Text]

[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. [Full Text]

[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.