People

Principle Investigator

   Dr. Artem Cherkasov
   Email: artc@interchange.ubc.ca
   Phone: (604) 875-5555 ext. 68541

Research Assistant

   Dr. Osvaldo Santos-Filho
   Email: osvaldo@interchange.ubc.ca
   Phone: (604) 875-5555 ext. 61518

   Research Interests:
   Structural characterization of genomes by large scale sequence-structure threading
   Quantitative structure-activity relationship (QSAR)
   Chemoinformatics

   Selected Publications:

1. O. A. Santos-Filho, with A. J. Hopfinger; “Structure-based QSAR analysis of a set of 4-hydroxy-5,6-dihydropyrone as inhibitors of HIV-1 protease: an application of receptor-dependent (RD) 4D-QSARformalism”, Journal of Chemical Information and Modeling, 2006, 46(1), 345-354.
2. O. A. Santos-Filho, with T. Zheng, and A. J. Hopfinger; "Characterization of skin penetration processes of organic molecules using molecular similarity and QSAR analysis", Molecular Pharmaceutical, 2004, 1(6), 466-476.
3. O. A. Santos-Filho, with K. F. M. Pasqualoto, E. I. Ferreira, and A. J. Hopfinger, "Rational design of new antituberculosis agents: applications of the (RI) 4D-QSAR formalism to a set of isoniazid derivatives", Journal of Medicinal Chemistry, 2004,47 (15), 3755-3764.
4. O. A. Santos-Filho, with R. T. Delfino, and J. D. Figueroa-Villar; "Molecular modeling of wild-type and antifolate resistant mutant Plasmodium falciparum DHFR". Biophysical Chemistry, 2002, 98 (3),287-300.
5. O. A. Santos-Filho, with R. K. Mishra, and A. J. Hopfinger; "Free Energy force Field (FEFF) 3D-QSAR analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors". Journal of Computer-Aided Molecular Design, 2001, 15 (9),787-810.
6. O. A. Santos-Filho, with M. T. Araujo, and J. D. Figueroa-Villar; "Molecular modeling of the interaction of trypanocide guanyl hydrazones with B-DNA" .Bioorganic & Medicinal Chemistry Letters,1997, 7(13), 1797-1802.

   Background:

   PhD in Chemistry
   Msc in Chemistry
   Specialist in Economic Engineering and Industrial Management
   Industrial Chemist

Post Doctoral Fellows

   Dr. Fuqiang Ban
   Email: fuqiangban@gmail.com
   Phone: (604) 875-5555 ext. 68541

   Research Interests:
   Structure-based drug design, Structure-based virtual database screening, QSAR, and docking,
   Bioinformatics, Theoretical and Computational Chemistry.

Selected Publications:

1. The Effect of Electron-withdrawing Groups on 15N and 13C Chemical Shifts: A Density Functional Study on a Series of Pyrroles. Mothana, B.; Ban, F.; Boyd, R. J.; Thompson, A.; Hadden C.E. Molec. Phys. 2005, 103, 1113.
2. Density Functional Theory Investigations on the Chemical Basis of the Selectivity Filter in the K+ Channel Protein. Ban, F.; Kusalik, P.; Weaver D. F. J. Am. Chem. Soc. 2004, 126, 4712.
3. Recent Applications of Density Functional Theory Calculations to Biomolecules. Ban, F; Rankin, K. N.; Gauld, J. W.; Boyd, R. J. Theor Chem Acc 2002, 108,1
4. Modelling the Reactions of an Antitumor Drug: Tirapazamine. Ban, F.; Gauld, J. W.; Boyd, R. J. J. Am. Chem. Soc. 2001, 123, 7320.
5. Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine. Ban, F.; Lundqvist, M.J.; Boyd, R.J.; Eriksson, L.A. J. Am. Chem. Soc. 2001, 124, 2753.

   Dr. Meilan Huang
   Email: meilanh@interchange.ubc.ca
   Phone: (604) 875-5555 ext. 68541

   Research Interests:
   Protein structure prediction and protein- inhibitor interaction by molecular dynamics and docking    study.

Selected Publications:

1. Meilan Huang, W. Graham Richards, and Guy H. Grant Diketo acid HIV-1 integrase inhibitors: an ab initio study.J. Phys. Chem. A. 109, (2005), 5198-5202
2. Meilan Huang, Arvi Rauk Reactions of Oxidized Methionine with Oxygen: An ab Initio Study. J. Phys. Chem. A 108 (29) (2004)6222-6230
3. Meilan Huang and Arvi Rauk Structure and reactions of the peroxy radicals of glycine and alanine in peptides: an ab initio study. J. Phys. Org. Chem. 17 (2004) 777-786
4. Meilan Huang, Ding-Yah Yang, Zhicai Shang, Jianwei Zou, Qingsen Yu. 3D-QSAR Studies on 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors by Comparative Molecular Field Analysis (CoMFA). Bioorganic and Medicinal Chemistry Letters. 12/17 (2002) pp. 2271-2275
5. Meilan Huang, Jian-wei Zou, Ding-yah Yang, Bao-Zhu Ning, Zhi-Cai Shang, Qing-Sen Yu. Theoretical Studies on Tautomerism of Benzoylcyclohexane-1, 3-dione and its Derivatives. Journal of Molecular Structure (THEOCHEM). 589-590C (2002) pp. 321-328

PhD Students

   Chris Fjell
   Email: cfjell@interchange.ubc.ca
   Phone: (604) 875-5555 ext. 68541

   Research Interests:
   Bioinformatics of antimicrobial peptides and mechanisms of immune regulation;
   binding of peptide to MHC

   Selected Publications:

1. Robertson G,... Fjell C.,...(2006) cisRED: a database system for genome- scale computational discovery of regulatory elements. Nucleic Acids Res. 2006 Jan 1; 34(Database issue): D68-D73
2. Krzywinski M, ..., Fjell C, ... et al (2004) Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 14 (4):766-79.
3. Gibbs, RA, ..., Fjell. C., ... et al (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428(6982):493-521. 4. Flibotte S, Chiu R, Fjell C, Krzywinski M, Schein JE, Shin H, Marra MA, (2004) Automated ordering of fingerprinted clones.Bioinformatics. 20(8):1264-71 5. Fjell, C., Bosdet, I., Schein, J.E., Jones, S.J.M., and Marra, M.A. (2003) Internet Contig Explorer (iCE) - A Tool for Visualizing Clone Fingerprint Maps, Genome Res. 13(6a): 1244-1249.
6. Gregory, S.G., ..., Fjell. C., ... et al (2002) A physical map of the mouse genome, Nature 418, 743 - 750

   Background:

   BASc (Engineering) UBC 1990
   MSc (Physics) UBC 1995

   Mike Hsing
   Email: mhsing@interchange.ubc.ca
   Phone: (604) 875-5555 ext. 68541

   Research Interests:
   indel analysis, protein interaction networks, protein structure
   modeling, in silico drug development, pathway modeling and
   simulation, semantic networks

Selected Publications:

1. Hsing M, Cherkasov A. Integration of biological data with semantic networks. Current Bioinformatics. 2006 (accepted).
2. Hsing M, Cherkasov A. Bioinformatics tools for researching protein interaction networks, In: Progress in Genome Research. Nova Science Publishers. 2005 (submitted).
3. Hsing M, Modeling of cell signaling pathways in macrophages by semantic networks. M.Sc. Thesis, University of British Columbia, Fancouver, BC 2005.
4. Hsing M, Bellenson JL, Shankey C, Cherkasov A. Modeling of cell signaling pathways in macrophages by semantic networks. BMC Bioinformatics 2004; 5: 156.
5. Lett D, Hsing M, Pio F. Interaction profile-based protein classification of death domain. BMC Bioinformatics. 2004; 5:75.

Rotation Student

   Simon Chan
   Email: skchan@sfu.ca
   Phone: (604) 875-5555 ext. 68541

   Research Interests:
   Protein essentiality, Indel-based drug targeting, network biology, cancer gene expression profiling

Selected Publications:

1. Hokamp, K., F.M. Roche, M. Langille, M. Acab, D.L. Fulton, M. Laird, Y. Li, R. Lo, S.K. Chan, L.A. Babiuk, R.E.W. Hancock and F.S.L. Brinkman (2006). Bioinformatics Tools for Cross-species Comparisons of Microarray Data. World Microarray Congress 2006, March 24-25, 2006, Vancouver, B.C., Canada.
2. Chan SK, Doho G, Mookherjee N, Brown K, Roche F, Brinkman FSL and Hancock REW. Computational Analysis of Transcription Factor Binding Sites in the Promoters of Co-regulated Genes that contribute to the Anti-Endotoxin Effect of LL-37 (2006). 2006 Life Sciences Society Computational Systems Bioinformatics Conference. August 14-18th, 2006. Stanford University, California.

System Administrator

   Evgeny Maksakov
   Email: maerd@ngs.ru
   Phone: (604) 875-5555 ext. 68541

Former Group Memebers

Dr. Zheng Shi (currently @ NRC Canada)

Vadim Astakhov (currently @ UCSD)