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