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Select Publications
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Note the dates of these publications. Most of them were published before 1996,
the time since which bioinformatics became a hot subject.
Capacities of computers and PCs during the early 1990s were not as high as now.
Thus the compression algorithms, distributed and massively parallel algorithms.
Database integration was attempted on GenBank and PIR in homolog compilation.
Unlike now, there were no specific journals dedicated to bioinformatics.
The journal, Computer Applications in Biosciences (CABIOS), is now the Bioinformatics journal.
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Bioinformatics
Database Search & Analysis
Simulation & Modeling pen.jpg Separation & Sequencing
Software
Miscellaneous
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Publications on PubMed
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Bioinformatics
  1. Hwa A. Lim, "Turbo charging bioinformation for drug discovery", Silicon Valley High Tech, February 2000, Vol. 23, pp. 38-49.
  2. Hwa A. Lim, and Daxi Li, "Biological and Biological-related information as a business commodity and the rise of bioinformatics, Part I", Silicon Valley High Tech, November/December 1999, Vol. 20/21, pp. 40-47.
  3. Hwa A. Lim, and Daxi Li, "Biological and Biological-related information as a business commodity and the rise of bioinformatics, Part II", Silicon Valley High Tech, January 2000, Vol. 22, pp. 51-56.
  4. Hwa A. Lim, and T.V. Venkatesh, "Bioinformatics in pre- and post-genomics eras", Trends in Biotechnology, April 2000, Vol. 18, pp. 133-135.
  5. T.V. Venkatesh, Benjamin Bowen, and Hwa. A. Lim, "Bioinformatics, Pharma and Farmers", Trends in Biotechnology, March 1999, Volume 17 No. 3 (182), pp. 85-88.
  6. Hwa A. Lim and Tauseef R. Butt, "Bioinformatics Takes Charge", Trends in Biotechnology, March 1998, Vol. 16 No. 3 (170), pp. 104-107.
  7. Hwa A. Lim, "Bioinformatics and Cheminformatics in the Drug Discovery Cycle", In: Lecture Notes in Computer Science, Bioinformatics, R. Hofestaedt, T. Lengauer, M. Loffler and D. Schomburg (eds.), (Springer, Heidelberg, 1997), pp. 30--43.
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Database Search and Analysis
  1. Victor B. Strelets and Hwa A. Lim, "Protein k-tuple Preference Analysis: Its Relation to Structure and Structural Prohibitions", International Journal of Mathematical Modelling and Scientific Computing, (1997).
  2. Victor B. Strelets, Igor B. Rogozin, Luciano Milanesi and Hwa A. Lim, "Exon/intron Structure Revealing Based on Protein k-tuple Statistics", International Journal of Mathematical Modelling and Scientific Computing, (1997).
  3. Hwa A. Lim and Victor B. Strelets, "Statistical Analysis of Known Proteins in Sequence Databases and Coding Region Prediction", In: Computational Medicine, Public Health, and Biotechnology (CompMed) Vol. 1, Matthew Witten (ed.), (World Scientific, New Jersey, 1996) 190--210.
  4. Victor B. Strelets and Hwa A. Lim, "Compression of Protein Sequence Databases", Computer Applications in Biosciences (CABIOS), 11(5), 557--561, (1995).
  5. Victor B. Strelets and Hwa A. Lim, "Ancient Splice Junction Shadows with Relation to Blocks in Protein Structure", BioSystems, 36, 37--41, (1995).
  6. V.B. Strelets, I.N. Shindyalov, Hwa A. Lim, "Analysis of Peptides from Known Proteins: Clusterization in Sequence Space", J. Mole. Evolution, 39(6), 625--630, (1994).
  7. V.B. Strelets, A.A. Ptitsyn, L. Milanesi, Hwa A. Lim, "Data Bank Homology Search Algorithm with Linear Computation Complexity", Comput. Appl. Biosci. (CABIOS),10(3), 319--322, (1994).
  8. I.N. Shindyalov, V.B. Streletc, N.A. Kolchanov, Hwa A. Lim, "A Method for Multiple Alignment and Its Application in Homolog Compilation", Protein Seq. Data Anal., 5(5), 219--225, (1993).
  9. V.V. Solovyev, S.V. Korolev, Hwa A. Lim, "A New Approach for the Classification of Functional Regions of DNA Sequences Based on Fractal Representation", Intl J. Genomic Res., 1(1), 109--128, (1993).
  10. Hwa A. Lim, "Classification of Functional Regions of DNA Sequences using Fractal Representation", Mathl. Comput. Modelling, 2, 617--622, (1993).
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  11. Hwa A. Lim, V.V. Solovyev, "A New General Approach for Searching Functional Regions Using Fractal Representation of Nucleotide and Amino Acid Sequences ", Harnessing Biotechnology for the 21st Century, Ed. M.R. Ladisch and A. Bose, pp. 387--391 (American Chemical Society, Washington, D.C., 1992).
  12. Hwa A. Lim, "Chaos Games Yield DNA Portraiture in Random Samples" (ed. Constance Holden), Science, 258, 894--895, (1992).
  13. E. Hamori, G. Varga, M.T. Carroll, Hwa A. Lim, "Protein Fragment with Functional Role Viewed as the Sum Total of All DNA Sequences Coding for the Same Function", FASEB J., 5(6), A1536, (1991).
  14. V.V. Solovyev, S.V. Korolev, V.G. Tumanyan, Hwa A. Lim, "A New Approach to the Classification of DNA Sites Based on the Fractal Representation of a Set of Functionally Similar Sequences", Doklady Biochemistry, (Communicated by Academician A.D. Mirzabekov), 319(6), 1496--1500, (1991).
  15. Hwa A. Lim, Ilya N. Shindyalov and Nikolay A. Kolchanov, "Computer Studies of Molecular Evolution of Gene Families Coding for Proteins", In: ISOZYMES: Organization and Roles in Evolution, Genetics and Physiology, Ed. C.L. Markert, J.G. Scandalios, H.A. Lim and O.L. Serov, (World Scientific Pub. Co., New Jersey, 1994), pp. 253--266.
  16. Hwa A. Lim and Ilya N. Shindyalov, "Homologous Gene Family Database Compilation", In: Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. Ed. H.A. Lim, J.W. Fickett, C.R. Cantor and R.J. Robbins, (World Scientific Pub. Co., New Jersey, 1993), pp. 403--411.
  17. Ilya N. Shindyalov, Vcitor B. Streletc, Nikolay A. Kolchanov, Luciano Milanesi, P. Vezzoni, M. Repetto and Hwa A. Lim, "A Method for Joining Contigs in Automatics DNA Sequencing", In: Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. Ed. H.A. Lim, J.W. Fickett, C.R. Cantor and R.J. Robbins, (World Scientific Pub. Co., New Jersey, 1993), pp. 413--418.
  18. Nikolay A. Kolchanov, Alexander E. Kel, M.P. Ponomarenko, A.G. Romachenko, J. Likhachev, Luciano Milanesi and Hwa A. Lim, "Patterns of Oligonucleotide Distribution within DNA and RNA Functional Sites", In: Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. Ed. H.A. Lim, J.W. Fickett, C.R. Cantor and R.J. Robbins, (World Scientific Pub. Co., New Jersey, 1993), pp. 445--463.
  19. Alexander E. Kel, Nikolay A. Kolchanov, V.V. Kapitonov, M.P. Ponomarenko, E.A. Likhachev, Hwa A. Lim and Luciano Milanesi, "Computer Analysis and Recognition of Functional Sites via Oligonucleotide Pattern Distributions", In: Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. Ed. H.A. Lim, J.W. Fickett, C.R. Cantor and R.J. Robbins, (World Scientific Pub. Co., New Jersey, 1993), pp. 521--543.
  20. Victor V. Solovyev, Hwa A. Lim, Luciano Milanesi and Charles Lawrence, "A Fractal Representation Approach for the Classification of Functional Regions of DNA Sequences", In: Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. Ed. H.A. Lim, J.W. Fickett, C.R. Cantor and R.J. Robbins, (World Scientific Pub. Co., New Jersey, 1993), pp. 609--622.
  21. G. Varga, E. Hamori, M.T. Carroll, Hwa A. Lim, "Computer Graphics Algorithm for Abstract Representation of Protein and DNA Sequences Using PHIGS and Motif Program Development Tools", Proceedings of The 2nd International graPHIGS User's Group Conference and Workshop, 11, 1991.
  22. Hwa A. Lim, "Graphical Representation of DNA and Polyamino Acid Sequences", Proceedings of the International Conference on Modelling and Computer Methods in Molecular Biology and Genetics, (NOVA Science, New York, 1991).
  23. S.V. Korolev, V.V. Solovyev, V.G. Tumanyan, Hwa A. Lim, "Interactive Graphics Program of Chaos Game Representation of DNA Sequences", FSU-SCRI-91-02, 1990.
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Software
  1. S.L. DeKorte, Hwa A. Lim, "ADEPT: An Application Development Tool", International Journal of Mathematical Modelling and Scientific Computing, (1997).
  2. Victor B. Strelets and Hwa A. Lim, "SAGITTARIUS-- A Dialog Shell for Compressing Sequence Databases on IBM PC (PIR and GenBank Versions)", International Journal of Mathematical Modelling and Scientific Computing, (1997).
  3. Dimitriy K. Kuznetsov, and Hwa A. Lim, "A Protein Visualization Program", In: Visualizing Biological Information, C.A. Pickover (ed.), (World Scientific Publishing Co., New Jersey, 1995), pp. 61-71.
  4. I.N. Shindyalov, V.B. Streletc, N.A. Kolchanov, Hwa A. Lim, "Homologous Sequence Analysis Toolbox Development: Multiple Alignment and Classification of Evolutionary Modes", Biomedical Modelling and Simulation, Ed. J. Eisenfeld, D.S. Levine and M. Witten, pp. 189--199 (Elsevier Science Publishers B.V., North Holland, 1992).
  5. M.T. Carroll, G. Varga, and Hwa A. Lim, "Parallel And Serial Methods of Graphically Representing Polyamino Acid Sequences with H-Trees", FSU-SCRI-91-157, October 1991.
  6. D.K. Kuznetsov, Hwa A. Lim, "VisiCoor-A Simple Program for Protein Visualization", J. Molecular Graphics, 10, 21--28, (1991).
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Separation & Sequencing
  1. G. Varga, J. Schmutz, B. Hauser, and Hwa A. Lim, "Neural Network Analysis of Sequencing By Hybridization (SBH) Signatures", In: LNCS Proceedings of German Conference on Bioinformatics, '96.
  2. E.J. Buks van Rensburg, Hwa A. Lim, "A Monte Carlo Study of Electrophoresis of Circular Polymer and DNA", Math. Modelling and Sci. Computing, (1997, to appear).
  3. Hwa A. Lim, "Electrophoresis of Topologically Nontrivial Macromolecules: Mathematical and Computational Studies", International Journal Modern Physics C, 7(2), (1996) 217--271.
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Simulation and Modeling
  1. Hwa A. Lim, "Mathematical and Computational Studies of Kinesin Motility".
  2. Hwa A. Lim, E.J. van Rensburg, "A Numerical Simulation of Electrophoresis of Knotted DNA", Math. Modelling and Sci. Computing, 1(1), 153--163, (1993).
  3. V.V. Solovyev, S.K. Salikhova and Hwa A. Lim, "Spatial Structure Calculations of alpha-Helical Domains of Protein Molecules Using Quasispherical Primary Approximations", Biomedical Modelling and Simulation, Ed. J. Eisenfeld, D.S. Levine and M. Witten, pp. 201-211 (Elsevier Science Publishers B.V., North Holland, 1992).
  4. Hwa A. Lim, M.T. Carroll, and E.J. van Rensburg, "Electrophoresis of Knotted DNA in a Regular and a Random Electrophoretic Medium", Biomedical Modelling and Simulation, Ed. J. Eisenfeld, D.S. Levine and M. Witten, pp. 213--223 (Elsevier Science Publishers B.V., North Holland, 1992).
  5. Hwa A. Lim, "Mathematical Formulations and Computer Enumerations of Polymer Models with Loops", Intl. J. Mod. Phys., 3(2), 385--446, (1992).
  6. D.M. Pettus, N.P. Pettus and Hwa A. Lim, "A Computer Simulation of the Life Cycle of the Florida Bald Eagle", Mathl. Comput. Modeling, 16(10), pp. 183--196, (1992).
  7. Hwa A. Lim, E.J. van Rensburg, "Electrophoresis of Circular & Knotted Polymers/DNA", Mathematical Modelling and Scientific Computing, 2, 622--629, (1992).
  8. Hwa A. Lim, G.W. Slater, J. Noolandi, "A Model of the DNA Transient Orientation Overshoot during Gel Electrophoresis", J. Chem. Phys., 92, 709--721, (1990).
  9. D.E. Burnette, Hwa A. Lim, "Mathematical Models and Computer Enumerations of Polymers with Loops", Mathl. Comput. Modelling, 14, 486--493, (1990).
  10. Hwa A. Lim, J. Noolandi, G.W. Slater, "Generalized Tube Model of Biased Reptation for DNA-Gel Electrophoresis", Mathl. Comput. Modelling, 14, 494--499, (1990).
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  11. Hwa A. Lim, D.E. Burnette, "Alternative Way to Locate the Transition Temperatures of Polymeric Models with Loops", Phys. Rev. A, 40, 5342--5350, (1989).
  12. J. Noolandi, G.W. Slater, Hwa A. Lim, J.L. Viovy, "Generalized Tube Model of Biased Reptation for Gel Electrophoresis of DNA", Science, 243, 1456--1458, (1989).
  13. Hwa A. Lim, "Monte Carlo Simulations of the Physical Mechanisms for Separation of Topologically Nontrivial Macromolecules during Electrophoresis", In: Proceedings of the Second International Conference on Computational Physics, Biology Section, Ed. De-Yuan Li, Da-Hsuan Feng, Michael R. Strayer and Tian-Yuan Zhang, (International Press, Cambridge, MA, 1995), 216--227.
  14. Andrew Hasenfeld, Eric Pepke, Hwa A. Lim and Charles R. Cantor, "A New Agarose Model", In: Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. Ed. H.A. Lim, J.W. Fickett, C.R. Cantor and R.J. Robbins, (World Scientific Pub. Co., New Jersey, 1993), pp. 501--504.
  15. Young Park, Hwa A. Lim, "Dynamic Electrophoretic Transport in Separation Process", FSU Technical Report FSU-SCRI-95-12 (1993).
  16. Young Park, Hwa A. Lim, "Electrophoretic Mass Transport of Polyelectrolyte in Composite Membranes: I. Macroscopic Study", FSU Technical Report FSU-SCRI-95-13 (1993).
  17. Young Park, Hwa A. Lim, "Electrophoretic Mass Transport of Polyelectrolyte in Composite Membranes: II. Molecular Study", FSU Technical Report FSU-SCRI-95-14 (1993).
  18. Gotz Schonherr, Hwa A. Lim, Gary W. Slater, Jaan Noolandi, "DNA Gel Electrophoresis: A Monte Carlo Simulation", FSU Technical Report (1991).
  19. A. Hasenfeld, C.R. Cantor, Hwa A. Lim, "Continuous Modulation of the Electric Field in PFG: A Numerical Study", FSU-SCRI-90-169, 1990.
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Miscellaneous
  1. Hwa A. Lim, "Scientific Communication: In search of one-handed scientists", Asia Pacific Biotech, 17(10&11), 2013, pp. 29-35.
  2. Hwa A. Lim, "Genes, Stem Cells and Regenerative Medicine", Asia Pacific Biotech, 17(8), 2013, pp. 25-31.
  3. Hwa A. Lim, "Dance for Life", European Papers on the New Welfare, No.17, 2011.
  4. Hwa A. Lim, "Stem Cells and Regenerative Medicine", Asia Pacific Biotech, 14(3), 2010, pp. 20-27.
  5. Hwa A. Lim, "Creativity 2.0", Symbiosis, September/December 2010.
  6. Hwa A. Lim, "Bioinformatics in Communicable Diseases - The way forward", Asia Pacific Biotech, 14(12), December 2010, pp. 12-21.
  7. Hwa A. Lim, "Eco-fficiency - Green this and green that", Symbiosis, May/August 2010.
  8. Hwa A. Lim, "Eco-friendlily Yours: The way forward", Asia Pacific Biotech, 14(7), July 2010, pp. 17-25.
  9. Hwa A. Lim, "Einformatics - A green-collar career", Malaysia Energy Guide, 2010/2011, July 2010, pp. 31-35.
  10. Hwa A. Lim, "Renewable and alternative energies", Malaysia Energy Guide, 2009/2010, pp. 30-33.
  11. Hwa A. Lim, "Renewable and alternative energies", Symbiosis, June 2008, pp. xx-yy.
  12. Hwa A. Lim, "The business of innovation", Symbiosis, March 2008, pp. 6-9.
  13. Hwa A. Lim, "Technology adoption", Symbiosis, March 2008, pp. 23-26.
  14. Hwa A. Lim, "The Ninth Malaysia Plan: Looking in from outside", Symbiosis, Oct 2006, pp. xx-yy.
  15. Hwa A. Lim, "Biofuels - the fifth utility", Symbiosis, October 2006, pp. 8-13.
  16. Hwa A. Lim, "Incentives in promoting biotechnology", Symbiosis, Nov 2005/Jan 2006, pp. 21-23.
  17. Hwa A. Lim, "Agriculture - nature's gift", Symbiosis, August 2005, pp. 10-12.
  18. Hwa A. Lim, "The Internet - Human-computer symbiosis", Symbiosis, February-April 2005, pp. 22-25.
  19. Hwa A. Lim, "Biotechnology - Past, present and future", Symbiosis, October 2004, pp. 31-34.
  20. Hwa A. Lim, "From human resource to human capital", Symbiosis, May 2004, pp. 5-10.
  21. Hwa A. Lim, "Creativity, culture, and entrepreneurship", Symbiosis, February 2004, pp. 4-10.
  22. Hwa A. Lim, "Bioinformatics, nanotechnology & SARS", Symbiosis, October 2003, pp. 26-29.
  23. Hwa A. Lim, "Change please, please change", Symbiosis, October 2003, pp. 8-12.
  24. Hwa A. Lim, "Education: A life-long process", Symbiosis, December 2002, pp. 13-17.
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