Yinghao Wu Ph.D.

Center for Computational Biology and Bioinformatics

Depart of Biochemistry and Molecular Biology

Columbia University, New York 

Howard Hughes Medical Institute

Advisor: Prof. Barry Honig  

Phone: 347-688-9519

Email: yw2286@columbia.edu 

Please click here to get a pdf version of my CV  

My most recent paper has been published on Nature in July 2011!  

Home | Research | Publications | Simulation Results | Other Links |  

Education

• Ph.D in Applied Physics and Bioengineering, Rice University , 2007

  Advisor: Dr. Jianpeng Ma

• M.S. in Condensed Matter Physics, Fudan University, 2002

  Advisor: Dr. Jian Zi

• B.S. in Physics, Fudan University, 1999

Selected Awards

• CBSB Outstanding Young Researcher Award (Juelich Research Center) , 2011

• Outstanding Poster Award (13th NY Structural Biology Discussion Group) , 2010

• Government Award for Outstanding Students Abroad (Chinese Government) , 2007

• Best Presentation Award (Rice Quantum Institute Annual Research Colloquium) , 2006

Research Interest

I have initiated and accomplished numerous projects in computational biophysics. My most recent work projects include the innovation of an integrated modeling technique to study cell adhesion. The simulations I have developed in molecular, sub-cellular and multi-cellular levels actualize the possibility of linking molecular affinity to cellular specificity. In the future, I plan to focus on the construction of a general framework of a multi-scale modeling strategy to bridge cellular behaviors to their molecular basis; the scope of this framework will be extended to the application to specific problems such as mechano-chemical coupling between integrin and cytoskeleton, as well as death-domain-regulated complex assembly in intracellular signaling pathways.

Please click here to see the full version.

Selected Publications

Y. Wu, J. Vendome, L. Shapiro, A. Ben-Shaul and B. Honig "Transforming Binding Affinities from Three Dimension to Two With Application to Cadherin Clustering". Nature (2011) 475 510-513. [link]

Y. Wu, X. Jin, O. Harrison, L. Shapiro, H. Honig and A. Ben-Shaul, "Cooperativity between trans and cis interactions in cadherin-mediated junction formation". P.N.A.S. (2010) 107 (41) 17592-17597.

Y. Wu, AD. Dousis, M. Chen, J. Li, and J. Ma, "OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries". J. Mol. Biol. (2009) 385, 1314-1329.

Y. Wu, M. Lu, M. Chen, J. Li, and J. Ma, "OPUS-Ca: A knowledge-based potential function requiring only C-alpha Positions". Protein Science (2007) 16, 1449-1463.

Y. Wu, X. Tian, M. Lu, M. Chen, Q. Wang and J. Ma, "Folding of Small Helical Proteins Assisted by Small-Angle X-Ray Scattering Profiles". Structure (2005) 13, 1587-1597.

Y. Wu, M. Chen, M. Lu, Q. Wang and J. Ma, "Determining Protein Topology from Skeletons of Secondary Structures". J. Mol. Biol. (2005) 350, 571-586.

Y. Wu and J. Ma, "Refinement of F-actin Model against Fiber Diffraction Data by Long-Range Normal Modes". Biophysical J. (2004) 86, 116-124.

Y. Wu and J. Ma, "Normal-mode-based Refinement of an F-actin Model Against Fiber Diffraction Data". Fiber Diffraction Review, (2004) 12, 25-28.

Y. Wu and J. Zi, "Universal Behavior of Localization of Residue Fluctuations in Globular Proteins". Physical Reviews E. (2003) 67, 041909-041912.

Please click here to see the full list.