Ilkka Havukkala

Senior Patent Examiner, IPONZ, New Zealand Government Patent Office

Contact details

Phone:+64 4 4990152
Email:ilkka.havukkala@gmail.com

Key Publications

Publications of Ilkka Havukkala

 

Current total ~180 publications, of which over 75 patenting related.  Partial listing below.

 

1. Patents:

 

Inventor in over 75 biotechnology and genomics related patents and patent applications (more than a dozen issued in various countries, several are big patent families progressed past the PCT filing stage in various individual countries). Several new RNAi therapy and autoimmunity related applications pending publication/issuance.

 

Current listing available from USPTO http://www.uspto.gov/patft/index.html and EPO http://ep.espacenet.com/quickSearch?locale=en_EP

A sampling of my patents is below:

  1. US007910326 – 2011-22-11 Materials and methods for the modification of plant lignin content
  2. 20100287672 – 2011-11-11 Plant cell signalling genes
  3. US2009229008 - 2009-09-10 Transcription factors
  4. WO2008026946 - 2008-03-06 Compositions and methods for the treatment and prevention of neoplastic disorders
  5. EP1826265 - 2007-08-29 Materials and methods for the modification of plant lignin content
  6. US20070079401 – 2007-04-05 Control of floral induction
  7. US20070039071 – 2007-02-15 Cell signaling genes and related methods
  8. US2006251635 - 2006-11-09 Lactobacillus rhamnosus polynucleotides, polypeptides and methods for using them
  9. EP1716164 - 2006-11-02 Targeted delivery of RNA interference molecules for the treatment of IGE-mediated disorders
  10. US7125698 – 2006-10-24 Polynucleotides, materials incorporating them, and methods for using them 
  11. EP1711609 - 2006-10-18 Polynucleotides and polypeptides isolated from Lactobacillus rhamnosus HN001, materials incorporating them and methods for using them
  12. WO2006091112 - 2006-08-31 Compositions for the delivery of RNA interference molecules and methods for their use (target gene is CXCR4, SDF-1 and/or HCLCA1)
  13. US2006183895 - 2006-08-17 Materials and methods for the modification of plant lignin content
  14. US7087426 – 2006-08-08 Materials and methods for the modification of plant lignin content
  15. BRPI0411028 - 2006-07-25 Compositions and methods for regulating polysaccharides of a plant cell
  16. US7052896 – 2006-05-30 Lactobacillus rhamnosus polynucleotides, polypeptides and methods for using them
  17. BRPI0411002 - 2006-05-23 polinucleotìdios isolados, fator de transcrição de planta, …
  18. NZ533254 - 2006-04-28 Materials and methods for the modification of plant lignin content
  19. US20050202077 - 2005-09-15 Targeted delivery of RNA interference molecules.
  20. US20050202437 – 2005-09-15 Polynucleotides, and polypeptides … (Lactobacillus rhamnosus)
  21. WO2005080410 - 2005-09-01 Targeted delivery of RNA interference molecules for the treatment of IGE-mediated disorders
  22. NZ534397 - 2005-07-29 Lactobacillus rhamnosus carboxylesterase
  23. US20050130263 - 2005-06-16 Compositions isolated from bovine mammary gland and methods for use
  24. NZ526078 - 2005-01-28 Lactobacillus rhamnosus polynucleotides, polypeptides and methods for using them in the improvement of milk and milk-derived products
  25. CA2528544 A1 - 2005-01-06 Compositions and methods for regulating polysaccharides of a plant cell
  26. WO0036081  Materials and methods for the modification of isoprenoid content, …
  27. WO09967421 Plant microsatellite markers and methods for their use
  28. US6544772 Polynucleotides, materials incorporating them… (Lactobacillus rhamnosus)
  29. US6653528 Pinus radiata nucleic acids encoding O-methyl transferase and methods …
  30. US5850020 Materials and methods for the modification of plant lignin content

 

2. Scientific publications:

 

About 100 publications in several languages and various fields, covering bioinformatics, molecular biology, enzymology, biological control and entomology. A partial listing is below.

Books, book chapters, theses

2010 Havukkala, I. Biodata mining and visualization: novel approaches. 300 pp. World Scientific Press (published July 2010)

2008 Kasabov, N., Song, Q., Benuskova, L., Gottgtroy, P., Jain, V.,  Verma, A., Havukkala, Rush, E., Pears, R., Tjahjana, A., Hu, Y. & MacDonnel, S. – Integrating Local and Personalised Modelling with Global Ontology Knowledge Bases for Biomedical and Bioinformatics Decision Support. Chapter in: “Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems, in the Springer Verlag two-volume book, in book series "Studies in Computational Intelligence",  eds. Tomasz G. Smolinski, Mariofanna M. Milanova & Aboul-Ella Hassanien, vol 151, pp. 93-116.

2008 Pang, S., Havukkala, I., Hu, Y. and Kasabov, N. Bootstrapping Consistency Method for Optimal Gene Selection from Microarray Gene Expression Data for Classification Problems. Chapter 11, pp. 89-110 in: Y.-Q. Zhang and Jagath C Rajapakse (eds.), “Machine Learning in Bioinformatics,” Wiley Book Series on Bioinformatics: Computational Techniques and Engineering, John Wiley & Sons

2007  Deng, X., Deng, X & Havukkala, I. Strong GC and AT Skew Correlation in Chicken Genome. In: Pattern Recognition in Bioinformatics. Lecture Notes in Computer Science LNCS 4774: 51-59. DOI 10.1007/978-3-540-75286-8_6

2006 Havukkala, I., Benuskova, L., Pang, P., Jain, V., Kroon, R. & Kasabov, N.  Image and fractal information processing for large-scale chemoinformatics, genomics analyses and pattern discovery. In: Lecture Notes in Bioinformatics Eds. J.C. Rajapakse, L. Wong & R. Acharya, Spinger Verlag, LNBI 4146: 163-173.

2006 Pang, S., Havukkala, I., Kasabov, N. Two-class SVM trees (2-SVMT) for biomarker data analysis. In: Lecture Notes in Computer Science. Eds. J. Wang, Z. Yi,

 J. M. Zurada, B.-L. Lu & H. Yin, Spinger Verlag, LNCS 3973: 629 - 634.  http://dx.doi.org/10.1007/11760191_92 

1998 Miyao, A., Havukkala, I. et al. Chapter 34: Rice as a model for genome analysis. (pp. 789-815) In: ICR Handbook of Genome Analysis (Vol. 2). Eds. Spurr, N.K., Young, B.D. & Bryant, S.P. - Blackwell Science Ltd.

1980 Havukkala, I. Locomotory manoeuvres of beetles responding to non-directional humidity cues. – PhD thesis, 158 pp. University of London, Imperial College.

 

Other publications: (selection)

 

2008 Chan, S., Havukkala, I, Jain, V, Hu, Y & Kasabov, N. Soft computing methods to predict gene regulatory networks: an integrative approach on time-series gene expression data. Applied and Soft Computing 8(3):1189-1199.

2007 Deng, X, Havukkala, I & Deng, X. Large-scale genomic 2D visualization reveals extensive GC-AT skew correlation in bird genomes. BMC Evolutionary Biology 7:234 doi:10.1186/1471-2148-7-234

2007 Havukkala, I. & Vanderlooy, S. On the Reliable Identification of Plant Sequences Containing a Polyadenylation Site. Journal of Computational Biology 14(9): 1229-1245.

2007 Pang, S., Havukkala, I., Hu, Y. & Kasabov, N. Classification Consistency Analysis for Bootstrapping Gene Selection. Neural Computing and Applications 16(6):527-539.  DOI 10.1007/s00521-007-0110-1

2005 Havukkala, I., Pang, S. N., Jain, V., & Kasabov, N. Classifying MicroRNAs by Gabor Filter Features from 2D Structure Bitmap Images on a Case Study of Human microRNAs.  Journal of Computational and Theoretical Nanotechnology 2(4): 506-513.

2005 Wilson, T., … Havukkala, I. et al. 24K AgR Bovine Array. GEO dataset GPL1854. Retrieved 19.4.2006, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1854

2000 Sleeman M.A., … Havukkala I, et al. 2000. Gene expression in rat dermal papilla cells: analysis of 2529 ESTs. Genomics 69(2):214-224.

1997 Shenk A, ... Havukkala I. et al. Pinus radiata cDNA sequencing as a resource for tree biotechnology. – Forestry Research International Bulletin 203: 70-78.

1996 Havukkala I. Genome research and evolution in rice and other cereals. - Current Opinion in Genetics & Development, 6(6): 711-714.

1996 Miyao A, … Havukkala I, et al. Characterization and genetic mapping of simple sequence repeats in the rice genome. - DNA Research  3(4): 233-238.

1996 Hirayae, K.,.. Havukkala, I., et al. In vitro growth inhibition of plant pathogenic fungi, Botrytis spp., by Escherichia coli transformed with a chitinolytic gene from a marine bacterium, Alteromonas sp. Strain 79401. Annals Phytopath. Soc. Japan, 62: 30-36.

1995 Havukkala, I. et al.. Rice genome analysis by integration of sequencing and mapping data. – Journal of Biotechnology. 41: 139-148.

1994 Sasaki, T.,... Havukkala, I. et al. Toward cataloguing all rice genes: Large scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant Journal 6: 615-624.

1993 Havukkala, I., et al.. Induction and purification of Beauveria bassiana chitinolytic enzymes. - Journal Invertebrate Pathology 61: 97-102.

1993 Usha Rani, P. and Havukkala, I. 1993. Predatory and mating behaviour of Eocanthecona furcellata (Wolff) (Heteroptera: Pentatomidae), a promising natural enemy of lepidopterous larvae. - Journal of Biological Control 7 (1): 9-11.

1992 Havukkala, I. et al. Onion fly egg distribution in soil: a new sampling method and the effect of two granular insecticides. – Entom. experimentalis et applicata. 63: 283-289.

1984 Havukkala, I. & Kennedy, J.S. A programme of self- steered turns as a humidity response in  Tenebrio, and the problem of categorizing spatial manoeuvr es.Physiological Entomology. 9: 157-164.

1980 Havukkala, I. Klinokinetic and klinotactic humidity reactions of the beetles Hylobius abietis and Tenebrio molitor. - Physiological Entomology 5(2):133-140.

1980 Havukkala, I. Arthropod orientation in choice chambers as a Markov chain. Physiological Entomology 5: 121-131.

1979 Havukkala, I. The humidity reactions of the large pine weevil, Hylobius abietis (Coleoptera, Curculionidae), during three stages of its life cycle. Annales Entomologici Fennici. 45:59-64.

1976 Havukkala, I. & Selander, J. Reactions of the large pine weevil, Hylobius abietis L. (Col., Curculionidae), to various light and humidity stimuli during three stages of its life cycle. - Annales Entomologici Fennici 42: 54-62

 

Conferences: (selection of recent ones)

 

2009 Havukkala, I. Ontologies and semantic mining for bio-technology and chemistry data and patents. Proceeding of the 2nd international workshop on Patent information retrieval. Hong Kong, China. Keynote address II. Pages 41-42.

2007 Kuijper, A. & Havukkala, I. Computationally efficient matching of microRNA shapes using mutual symmetry. – The Ninth IASTED International Conference on Signal and Image Processing (SIP 2007), August 20 – 22, 2007, Honolulu, Hawaii, USA. Proceedings, Acta Press, pp. 477-482.

2006 Hu, Y., Pang, S. & Havukkala, I. A Novel Microarray Gene Selection Method Based on Consistency, Proceedings, p. 14,  Sixth International Conference on Hybrid Intelligent Systems (HIS'06) http://doi.ieeecomputersociety.org/10.1109/HIS.2006.7

2006 Liefting, L.W., Havukkala, I., Andersen, M.T., Lough, T.J. & Beever, R.E. The Complete Genome Sequence of “Candidatus Phytoplasma australiense”. The 16th International Congress for the International Organization for Mycoplasmology, 9-14th July 2006, St John's College Cambridge, UK, Proceedings, p. 43.

2006 Havukkala, I. Large-scale macromolecule classification and clustering by 2D structure bitmap image analysis. The 1st Korean-New Zealand Joint Workshop on Advance of Computational Intelligence Methods and Applications, 17 February 2006, Auckland, New Zealand. 17 February 2006, Proceedings, pp. 20-21.

2006 Benuskova, L., Kroon, R. & Havukkala, I. A Compact 2D Representation and Visualization of Large Symbolic Sequences and Applications for Comparative Genome Studies. The 1st Korean-New Zealand Joint Workshop on Advance of Computational Intelligence Methods and Applications, 17 February 2006, Auckland, New Zealand, Proceedings, pp. 26-27.

2005 Verma, A., Gottgtroy, P., Havukkala, I., & Kasabov, N. An Ontological Representation of Nutrigenomics Knowledge about Type-2 Diabetes. Poster presented at the First Internat’l Conf. on Nutrigenomics, Singapore, 9-10 Dec 2005. Proceedings, p. 100.

2005 Verma, A, Gottgtroy, P, Havukkala, I & Kasabov, N. Understanding the molecular basis of Type-2 diabetes by means of “Evolving Ontologies” and intelligent modelling. – Poster presented at Queenstown Molecular Biology Meeting (QMB2005), August 2005, Proceedings, P2.

1999 Havukkala, I., et al. EST sequencing for tree gene discovery. Genome Diversity and Bioinformatics, FAOBMB, November/December 1999, p. 61.

1992. Havukkala, I. Chitinolytic enzymes and plant pests. - Proceedings of the second Asia-Pacific Biotechnology Congress, Los Banos, 22-24 May 1991. 195 pp. Eds. L.L. Ilag & A.K.  Raymundo. pp. 127-140.