Lee-Wei Yang, PhD
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Program:
Biochemistry and Molecular Genetics
Graduated:
12/2005
Mentor:
Dr. Ivet Bahar
Thesis:
Biomolecular Dynamics Revealed by Computational Models of Hierarchical Complexities and Mechanical Key Sites for Ligand Binding
Previous Institutions Attended:
National Taiwan University, BS in Chemical Engineering
National Tsing Hua University, MS in Chemical Engineering
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After defending my thesis last year, I continued working as a postdoc in my PhD advisor's, Dr. Ivet Bahar's, lab until earlier this month (June of 2006). I am currently heading to Japan for my new position as a research assistant professor (equivalent to research associate here) in Dr. Akio Kitao's lab, Laboratory of Molecular Design in the Center for Bioinformatics at the Institute of Molecular and Cellular Biosciences at the University of Tokyo.
Recent Publications:
Yang, L.-W., Eyal, E., Chennubhotla, C., Jee, J., Gronenborn, AM., Bahar, I. (2007) Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-ray Data with Computational Predictions. Structure (in press).
Eyal, E., Chennubhotla, C., Yang, L.-W., Bahar, I. (2007) Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models. Bioinformatics (2007 ISMB/ECCB issue).
Eyal, E., Yang, L.-W., Bahar, I. (2006) Anisotropic Network Model: systematic evaluation and a new web interface. http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi. Bioinformatics, 22, 2619-2627.
Yang, L.-W., Rader, A.J., Liu, X., Jursa, C.J., Chen S.C., Karimi, H. and Bahar, I. (2006) "oGNM: A protein dynamics online calculation engine using the Gaussian Network Model" http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm Nucleic Acids Res (in press)
Yang, L.-W. and Bahar, I. (2005) Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure, 13, 893-904
Yang, L.-W., Liu, X., Jursa, C.J., Holliman, M., Rader, A.J., Karimi, H.A., Bahar, I. (2005) iGNM: a database of protein functional motions based on Gaussian Network Model. http://ignm.ccbb.pitt.edu/ Bioinformatics, 21, 2978-2987.
Publications while a graduate student at Pitt:
Yang, L.-W. and Bahar, I. (2005) Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure, 13, 893-904.
Yang, L.-W., Liu, X., Jursa, C.J., Holliman, M., Rader, A.J., Karimi, H.A., Bahar, I. (2005) iGNM: a database of protein functional motions based on Gaussian Network Model. http://ignm.ccbb.pitt.edu/ Bioinformatics, 21, 2978-2987.
Seki, M., Masutani, C., Yang, L.-W., Schuffert, A., Iwai, S., Bahar, I. and Wood, R.D. (2004) High efficiency bypass of DNA damage by a single human DNA polymerase. EMBO J. 23, 4484-4494
What did you enjoy most about your research experiences and graduate studies here at Pitt?
What I enjoyed most at Pitt has been the interactions with my PhD advisor, Dr. Ivet Bahar. In computational biology, most of the research results can be quickly obtained (compared with those in the wet lab). It was the design of methodologies and the interpretation of the data that took most of the time. It was common to have tens of email exchanges a day with Ivet till midnight. There wasn’t much greetings and socializing, but rather these emails were the literature forwarders, idea exchangers, theory explorers and manuscript polishers. Most importantly, Ivet has shown me how motivated and respectable research can be done. I had 7 publications and one book chapter during the studentship and completed all the milestones required for a PhD within 4 years. Ivet played a dominant part of it. In what ways did your training at Pitt prepare you for your current position?
Intensive research experience and literature survey. As a graduate of Molecular Genetics and Biochemistry doing computational biology research, my course work has been mostly biology rather than computation or computational biology. Quite often, I have to learn how to do research while doing the research. The discussions with Ivet and other colleagues as well as the review of literature have been helpful in my profession.
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