Bioinformatician's den
Arli Aditya Parikesit, Bioinformatics PhD Student at University of Leipzig

Full Papers and Conference Proccedings:

  1. Tambunan, U.S.F., Noval Amri and A.A. Parikesit , 2012. In silico design of cyclic peptides as influenza virus, a subtype H1N1 neuraminidase inhibitor. African Journal of Biotechnology. Vol. 11(52), pp. 11474-11491. [available online]

  2. Tambunan, U.S.F., Danang Febrianto and A.A. Parikesit , 2012. In silico Genetic Variation Pathogenicity Analysis of Hemagglutinin, Matrix 1, and Non Structural 1 Protein of Human H5N1 Indonesian Strain. IIOABJ. Vol.3 (3):5-14. [available online]

  3. Tambunan, U.S.F., R.Harganingtyas and A.A. Parikesit , 2012. In silico Modification of (1R, 2R, 3R, 5S)-(-)- Isopinocampheylamine as Inhibitors of M2 Proton Channel in Influenza A Virus Subtype H1N1, using the Molecular Docking Approach. Trends in Bioinformatics . [available online]

  4. Usman Sumo Friend Tambunan and Arli Aditya Parikesit (2012). HPV Bioinformatics: In Silico Detection, Drug Design and Prevention Agent Development, Topics on Cervical Cancer With an Advocacy for Prevention, Rajamanickam Rajkumar (Ed.), ISBN: 978-953-51-0183-3, InTech [available online]

  5. A.A. Parikesit , P. Stadler, and S. Prohaska. 26th German Conference on Bioinformatics 2011. 7-9 September 2011. Weihenstephan. Evolution of domain co-occurrences: some striking results. PT-141 [available here]

  6. Tambunan, U.S.F., N Bramantya and A.A. Parikesit , 2011. In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC). BMC Bioinformatics.12(Suppl 13):S23 . [available online]

  7. Parikesit, Arli A. ;Stadler, Peter F.;Prohaska, Sonja J. 2011. "Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions." Genes 2, no. 4: 912-924. [available online]

  8. Usman Sumo Friend Tambunan, Nissia Apriyanti, Arli Aditya Parikesit , William Chua and Katarina Wuryani. 2011. Computational design of disulfide cyclic peptide as potential inhibitor of complex NS2B-NS3 dengue virus protease. African Journal of Biotechnology Vol. 10 (57), pp. 12281-12290,ISSN 1684-5315 . Academic Journals . [available online]

  9. Tambunan, U.S.F., R.S. Noors, A.A. Parikesit , Elyana and W. Ronggo, 2011. Molecular dynamics simulation of DENV RNA-dependent RNA-polymerase with potential inhibitor of disulfide cyclic peptide. OnLine J. Biol. Sci., 11: 48-62.DOI: 10.3844/ojbsci.2011.48.62 [available online]

  10. Arli A. Parikesit , Peter Stadler & Sonja J. Prohaska. 25th German Conference on Bioinformatics 2010. Braunschweig, September 20th-22nd, 2010. Quantitative Comparison of Genomic-Wide Protein Domain Distributions. GCB2010 conference proceeding. Vol P-173: pp 93-102 [available here] [slides available here]

  11. Tambunan, U.S.F., Fadilah and A.A. Parikesit , 2010. Bioactive compounds screening from zingiberaceae family as influenza a/swine flu virus neuraminidase inhibitor through docking approach. OnLine J. Biol. Sci., 10: 151-156. [available online]

  12. Arli Aditya Parikesit :The Role of Bioinformatics in Protein-Protein Interaction Study. 2010. Sigma Journal of Science and Technology Vol: 13. No: 1.p:1-7 . University of Sanata Dharma Press, Yogyakarta, Indonesia. [abstract available online]

  13. Usman Sumo Friend Tambunan, and Arli Aditya Parikesit :Cracking The Genetic Code of Human Virus by using Open Source Bioinformatics tools. Journal of Fundamental Sciences Vol 6, No 1 (2010). 42-50 . [abstract available online]

  14. Usman Sumo Friend Tambunan, Agus Limanto and Arli Aditya Parikesit : In Silico Analysis of Hemagglutinin, Neuraminidase, and Matrix2 of H5N1 Virus Indonesian Strain Related to Its High Pathgenicity. IIOABJ, 2010; Vol.1 (3): 17-24. [available online]

  15. Parikesit, Arli Aditya . Stadler, Peter., Prohaska, Sonja. 2010. Detection of Protein Domains in Eukaryotic Genome Sequences. Proceedings of 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31--September 3, 2010. Lecture Notes in Bioinformatics, Vol 6268. pp:71-74. [online journal]

  16. Tambunan, Usman Sumo., Parikesit, Arli Aditya . 2010. In silico Design of Drugs and Vaccines for Dengue Disease. Trends in Bioinformatics. Vol 3. [available online]

  17. Tambunan, Usman Sumo., Sugito, Sylvia., Parikesit, Arli Aditya . 2010. Design and Evaluation of Three Pair Primers for Exon 1 Amplification of Hyaluroglucosaminidase-1 Gene. OnLine Journal of Biological Science. 10(2):66-72 [available online]

  18. Parikesit, Arli Aditya . 2009. The role of Bioinformatics as auxilliary tools for Molecular Biology. Proceeding of World-Wide Indonesian Student Association Scientific Writing Olympic. Pp:23-29. [available here]

  19. Tambunan, Usman Sumo., Parikesit, Arli Aditya., Hendra., Ichsan Taufik, Rizky., Amelia, Fitri,. Syamsudin., 2009. In Silico Analysis of E DENV-2 and E DENV-3 Protein as the Backbone of Dengue Virus Tetravalent Vaccine by Using Homology Modeling Method. OnLine Journal of Biological Science. 9(1):6-16 [available online]

  20. Tambunan, Usman Sumo., Parikesit, Arli Aditya . Tochary, Theo., Sugiono, Dedy. 2007. Computational Study of Post Translation Modification in Chimeric Virus Like Particles Vaccine of Human Papilloma Virus with Virion Capsid L1. Makara journal of Science. University of Indonesia. Vol.11(2):56-62. [available online]

My Talks and Poster abstracts

  1. A.A. Parikesit , P. Stadler, and S. Prohaska. 27th German Conference on Bioinformatics 2011. 19-22 September 2012. Jena. Large-Scale Evolutionary Patterns of Protein Domain Distribution in Eukaryotes. P01 [available here]

  2. A.A. Parikesit , P. Stadler, and S. Prohaska. Regional Seminar of Advances in Tropical Genomics: Conservation and Sustainable Utilization of Tropical Biodiversity. 20-21 December 2011. Bogor, West Java, Indonesia. Utilization of Modern Protein Domain Annotation Technique. [available here] [poster available here]

  3. A.A. Parikesit , S. Prohaska and P. Stadler. 4th Berlin Summer meeting: Computational and Experimental Molecular Biologist meet, Berlin, 23-25 June 2011. Quantitative Comparison of Selected Genomic-wide Protein Domain Co-occurrences in 18 Species. [available here] [poster available here]

  4. A.A. Parikesit , S. Prohaska and P. Stadler. Leipzig Research Festival 17 December 2010. Quantitative Measurement of Genome-wide Protein Domain Co-occurrence of Transcription Factors. Pp:345 [available here] [poster available here]

  5. A.A. Parikesit , S. Prohaska and P. Stadler. 4th ESFF Conference 14-17 April 2010. Dresden. Protein domain co-occurrences reveal functional changes of regulatory mechanisms during evolution. New Biotechnology/Elsevier. Vol 27 Pages S44-S45. [available online] [Poster available here]

Bompfünewerer Consortium Seminar

  1. Winterseminar 2012. Bled, Slovenia. Title: Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions. [available online]

  2. Winterseminar 2011. Bled, Slovenia. Title: Quantitative Measurement of Genome-wide Protein Domain Co-occurence of Transcription Factors. [available online]

  3. Winterseminar 2010. Bled, Slovenia. Title: Domain Distribution of Transcription Factor. [available online]

  4. Herbstseminar 2009. Decin, Czech Republic. Title: Domain Cooccurence Distribution of Genetic Regulation Activation from an Evolutionary Perspective. [available online]

Note : Some of the papers/abstracts are only available in Uni Leipzig internal network. When requested, I will sent it.

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