Bioinformatics

Prabhas Chongstitvatana
Department of Computer Engineering, Chulalongkorn University
my office  022186982,  Eng Building 4, floor 18, room 13.
email  prabhas at chula dot ac dot th

2013

General introduction to Bioinformatics   (EMBL-EBI)
http://www.ebi.ac.uk/training/online/

Online lecture on Bioinformatics (a good one)
http://http://www.ebi.ac.uk/training/online/

Bioinformatics Tools  video  (Ohio State U)
http://www.extension.org/pages/32521/bioinformatics-101-video

Portal site for System Biology
http://systems-biology.org/

Synthetic Genome
http://www.aaas.org/news/releases/2010/0520sp_synthetic_genome.shtml
the article:
Daniel G. Gibson, et al., "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome," Science 329, 52 (2010); DOI: 10.1126/science.1190719

System Biology (e-cell),  Asawin Meechai (KMUTT) overview (10 slides)

Machine learning
Introduction to machine learning (three methods with examples), by Boonserm Kijsirikul

Video

intro to bioinformatics  2010  (3 min)
http://www.youtube.com/watch?v=xODTm4a6nsM

ncbi blast search tutorial  2009 (8 min)
http://www.youtube.com/watch?v=rlK-5joOlyU

current issue in bioinformatics  Googgle talk 2008 (1 hour)
http://www.youtube.com/watch?v=bVhOntMCmnQ

Assignment

Write an essay on the topics "Synthetic Genome".  The length of the report should be about 5-10 pages.  You can write any perspective that you are interested in, for examples technical, social impact, future applications.  Plagiarism is considered unethical.  Hand-in deadline Friday 2nd August, 4pm.  Send your report by email to me at prabhas at chula dot ac dot th.

Textbook

System biology
Handbook of System Biology, Walhout and Marian, 2012
http://www.sciencedirect.com/science/book/9780123859440  (full text from Chula)

Recommended reading

Siddhartha Mukherjee, The Emperor of All Maladies: A Biography of Cancer, 2011


Some of my work in Bioinformatic

* Hengpraprohm, S. and Chongstitvatana, P., "Feature Selection by Weighted-SNR for Cancer Microarray Data Classification", International Journal of Innovative Computing, Information and Control (ISSN 1349-4198), vol 5, no. 12(A), December 2009,  pp. 4627–4635. ( preprint)
Chanma, C., Pichyangkura, R., Ratanamahatana, C.A., and Chongstitvatana, P.,"An Algorithm to Compute Protein Homology Based On Hydrophobic Cluster Analysis", Int. Joint. Conf. on Computer Science and Software Engineering, Thailand, 2009. (pdf )
Sumanon, P., Chongstitvatana, P. and Suriyapol, P., "Major SNPs Sequence Assembling Simulation of Dengue Virus Genome from Massively Parallel Sequencing Technique", National Computer Science and Engineering Conf., 20-21 Nov. 2008, Thailand. ( pdf )
Rujeerapaiboon, P., Buratarchanai, A. and Chongstitvatana, P., "An Algorithm for the Shortest Superstring Problem: A Dynamic Programming Approach", Int. Joint. Conf. on Computer Science and Software Engineering, Thailand, 7-9 May, 2008. ( pdf )
Seeluangsawat, P. and Chongstitvatana, P., "Multiple Objectives Evolutionary Algorithms for Multiple Sequence Alignment," Poster paper, Genetic and Evolutionary Computation Conference, USA, June 2005, p.477-478.  ( pdf )

last update 16 July 2013