Email: drleiyang at gmail dot com
Web: http://www.drleiyang.com/

Education

Ph.D., Bioinformatics and Computational Biology, Iowa State University, 2008
M.S., Statistics, Iowa State University, 2005
M.Phil., Biochemistry, Chinese University of Hong Kong, 2001
B.S., Biology; B.E., Economics and Managment, University of Science and Technology of China, 1998

Research Experience

Senior Research Associate, Pioneer Hi-Bred International, DuPont, 2010-Present
Statistical Scientist, Monsanto Company, 2008-2010
Research Assistant, Bioinformatics and Computational Biology, Iowa State University, 2002-2008
Research Assistant, Department of Biochemistry, Chinese University of Hong Kong, 1999-2001

Publications

Journal Papers

• Yang L, Song G and Jernigan RL. Protein Elastic Network Models and the Ranges of Cooperativity (2009), Proc. Natl. Acad. Sci. USA, 106:12347-12352. [Abstract] [PDF]
• Feng Y, Yang L, Kloczkowski A and Jernigan RL. The Energy Profiles of Atomic Conformational Transition Intermediates of Adenylate Kinase (2009), Proteins, 77: 551-558. [Abstract] [PDF]
• Yang L, Song G and Jernigan RL. Comparisons of Experimental and Computed Protein Anisotropic Temperature Factors (2009), Proteins, 76:164-175. [Abstract] [PDF]
• Kloczkowski A, Jernigan RL, Wu Z, Song G, Yang L, Kolinski A and Pokarowski P, Distance Matrix-Based Approach to Protein Structure Prediction (2009), J. Struct. Funct. Genomics, 10:67-81. [Abstract] [PDF]
• Yang L, Song G, Carriquiry A and Jernigan RL. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes (2008), Structure, 16: 321-330. [Abstract] [PDF][Report]
• Yang L, Song G and Jernigan RL. How Well Can We Understand Large-Scale Protein Motions Using Normal Modes from Elastic Network Models? (2007), Biophys. J., 93: 920-929. [Abstract] [PDF]
• Avasarala S, Yang L, Sun Y, Leung AWC, Chan WY, Cheung WT and Lee SST. A Temporal Study on the Histopathological, Biochemical and Molecular Responses of CCl₄-Induced Hepatotoxicity in Cyp2e1-Null Mice (2006), Toxicology, 228: 310-322. [Abstract] [PDF]

Conference Papers

• Yang L, Song G and Jernigan RL. Comparison of Experimental and Computed Protein Anisotropic Temperature Factors, in Proceedings of 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops, pp 89-96, November 2007, Fremont, CA, USA. [Abstract][PDF]

Book Chapters

• Jernigan RL, Yang L, Kurkcuoglu O, Song G and Doruker P. Elastic Network Models of Coarse-Grained Proteins are Effective for Studying the Structural Control Exerted over their Dynamics in Coarse-Graining of Condensed Phase and Biomolecular Systems, Ed. Voth G, Taylor and Francis Group, September, 2008. [Link]

Conference Presentations

• Kloczkowski A, Jernigan RL, Wu Z, Song G, Yang L, Kolinski A and Pokarowski P. Distance Matrix-Based Approach to Protein Structure Prediction, 2008 NIGMS Protein Structure Initiative Bottlenecks Workshop, April 2008, National Institutes of Health (NIH), Bethesda, MD, USA.
• Yang L, Song G and Jernigan RL. How Well Can We Understand Large-Scale Protein Motions Using Elastic Network Modes? The Joint Meeting of the Biophysical Society 52^nd Annual Meeting & 16^th International Biophysics Congress, February 2008, Long Beach, CA, USA.
• Yang L, Song G and Jernigan RL. Comparison of Experimental and Computed Protein Anisotropic Temperature Factors, Computational Structural Bioinformatics Workshop (CSBW) on IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007), November 2007, San Jose, CA, USA.
• Yang L, You L, Song G and Jernigan RL. ENM: An R Package for the Computational Modeling and Analysis of Protein Dynamics Using Elastic Network Models, useR! 2007 - The R User Conference, August 2007, Ames, IA, USA.
• Yang L, Song G, Carriquiry A and Jernigan RL. Identification of Essential Protein Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Agreement with Elastic Network Modes, The 20^th Annual Symposium of The Protein Society & 20^th Anniversary Celebration, August 2006, San Diego, CA, USA.
• Yang L, Song G, Carriquiry A and Jernigan RL. Identifying of Essential Protein Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Agreement with Elastic Network Modes, The 32^nd Steenbock Symposium - Dynamics of Proteins and Macromolecular Assemblies, May 2006, Madison, WI, USA.
• Yang L, Song G, Zhao X, Carriquiry A and Jernigan RL. Motion Analysis of HIV-1 Protease by Anisotropic Network Model and Principal Component Analysis, The 14^th Growth Factors and Signal Transduction Symposium - Integration of Structural and Functional Genomics, September 2005, Ames, IA, USA.
• Yang L, Song G, Zhao X, Carriquiry A and Jernigan RL. Motion Analysis of HIV-1 Protease by Anisotropic Network Model and Principal Component Analysis, The 5^th Annual Joint Bioinformatics Workshop between UI and ISU, July 2005, Iowa City, IA, USA.
• Yang L, Tian L and Lee SST. Identification of CYP2E1 Dependent Genes Involved in Carbon Tetrachloride (CCl₄) and Acetaminophen (APAP) Induced Hepatotoxicity, The 13^th International Symposium on Microsomes and Drug Oxidations (MDO2000), July 2000, Stresa, Italy.
• Tian L, Yang L, Chan WY, Cheung WT and Lee SST. Differential Display Analysis of Peroxisome Proliferator-Activated Receptor Alpha (PPARa) Dependent Genes Involved in the Cellular Fasting Response, The 13^th International Symposium on Microsomes and Drug Oxidations (MDO2000), July 2000, Stresa, Italy.

Professional Activities

• Editor of Journal of Bioinformatics and Sequence Analysis
• Editorial Team, Journal of Computational Biology and Bioinformatics Research
• Editorial Team, Journal of Biophysics and Structural Biology (JBSB)
• Frequent reviewer for various scientific journals, conferences and foundations such as Proteins, Cancer Informatics, Bioinformatics and Biological Insights, Polymer and NSF

Teaching Experience

• Invited Talk for Protein Dynamics in Computational Biochemistry (BBMB541), Iowa State University, Fall 2007
• Teaching Assistant, Survey of Biochemistry (BBMB301), Iowa State University, Spring 2006 & Fall 2006
• Instructor for Transgenic Technology Section in Molecular Biotechnology (MBT4031), Chinese University of Hong Kong, Spring 2000 & Spring 2001
• Teaching Assistant, Molecular Biotechnology (MBT4031), Chinese University of Hong Kong, Spring 2000 & Spring 2001
• Teaching Assistant, Environmental Science (ENS4251), Chinese University of Hong Kong, Spring 2000

Awards and Honors

• Professional Advancement Grant (PAG), Iowa State University, 2006 & 2007
• Research Assistantship, Iowa State University, 2002-2008
• Premium for Academic Excellence (PACE) Award, Iowa State University, 2002
• Postgraduate Studentship, Chinese University of Hong Kong, 1999-2001
• China Mathematical Olympiad (CMO), 2^nd Prize (Silver Medal) in Province, 1992
• China Physical Olympiad (CPO), 3^rd Prize (Bronze Medal) in Province, 1992