Contact

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Associate Professor
Department of Biomedical Engineering
803 Shelby Interdisciplinary Biomedical Research Bldg
1825 University Blvd

Birmingham, AL
35294-2182
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(205) 996-6939
(205) 975-4919 (fax)

Miscellaneous Information

ACADEMIC BACKGROUND

Postdoc training, Computational Biology, Washington University in St. Louis, 2002-2005
Postdoc training, Computational Biomechanics, University of Pittsburgh, 2001-2002
Postdoc training, Computational Materials Science & Engineering, Tsinghua University, 1998-2001
Ph.D., Materials Science & Engineering, Harbin Institute of Technology, 1998
M.S., Materials Science & Engineering, Harbin University of Science and Technology, 1996
B.S., Materials Science & Engineering, Jilin University of Technology, 1989

TEACHING

BME 333-Biomechanics of Solids
BME 690:790-Biomolecular Modeling

RESEARCH

My research group is using integrated computational modeling and experimental approaches to investigate the fundamental structural and functional mechanisms of the biomolecular interactions underlying the death receptor-mediated apoptosis and to identify molecular targets to overcome the drug resistance in breast cancer. Multiscale modeling of the protein complexes in regulating cell adhesion and collagen expression in tissue remodeling is another focus of the group. I am also interested in the optimized design of biomaterials and small molecules/drugs for cell-based therapeutics, including the applications in immunoisolation nanotechnology. Methodology development for multiscale modeling of complex biological systems continues to be a focus of my research group. The research outcomes could contribute to multiscale computational bioengineering, biomolecular engineering, cancer, regenerative medicine, biomechanics and orthopedic research fields.

RECENT PUBLICATIONS

1.Lingyun Wang, Joanne E, Murphy-Ullrich, Yuhua Song*. Molecular insight for the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry. 2014, 53(40):6309-22
2. Romone Fancy, Lingyun Wang, Tiara Napier, Jiabei Lin, Gu Jing, Aaron Lucius, Jay M McDonald, Tong Zhou, Yuhua Song*. Characterization of calmodulin and Fas death domain interaction: an integrated experimental and computational study. Biochemistry, 2014, 53 (16), pp 2680–2688
3. Qi Yan, Jay M McDonald, Tong Zhou, Yuhua Song*. Structural Insight for the Roles of Fas Death Domain Binding to FADD and Oligomerization Degree of the Fas - FADD complex in the Death Inducing Signaling Complex Formation: A Computational Study. Proteins: Structure, Function, and Bioinformatics, 2013, 81(3):377-85
4..Di Pan, Yuhua Song*. Effects of altered restraints in β1 integrin on the force-regulated interaction between the glycosylated I-like domain of β1 integrin and fibronectin III9-10: a steered molecular dynamic study. Mol Cell Biomech, 2011, 8(3): 233-52
5. Di Pan,Qi Yan, Yabing Chen, Jay M McDonald, Yuhua Song*. Trifluoperazine Regulation of Calmodulin Binding to Fas: A Computational Study. Proteins: Structure, Function, and Bioinformatics, 2011, 79(8):2543-56.
6..John T. Wilson, Wanxing Cui, Veronika Kozlovskaya, Eugenia Kharlampieva, Di Pan,, Zheng Qu, Venkata R. Krishnamurthy, Joseph Mets1, Vivek Kumar1, Jing Wen, Yuhua Song, Vladimir V. Tsukruk, and Elliot L. Chaikof. Cell Surface Engineering with Polyelectrolyte Multilayer Thin Films. J Am Chem Soc. 2011,133(18):7054-64
7. Qi Yan, Joanne E. Murphy-Ullrich, Yuhua Song*. Molecular and Structural Insight for the Role of Key Residues of Thrombospondin-1 and Calreticulin in Thrombospondin-1- Calreticulin Binding. Biochemistry 2011, 50, 566–573
8. Di Pan, Yuhua Song*, Role of Altered Sialylation of the I-like Domain of β1 Integrin in the Binding of Fibronectin to β1 Integrin: Thermodynamics and Conformational Analyses.Biophys J, 99 (1), 208-217, 2010
9. Qi Yan, Joanne E. Murphy-Ullrich, Yuhua Song*. Structural Insight for the Role of Thrombospondin-1 Binding to Calreticulin in Calreticulin-Induced Focal Adhesion Disassembly. Biochemistry, 2010, 49 (17), pp 3685–3694
10. Yawar J. Qadri, Yuhua Song, Catherine M. Fuller and Dale J. Benos. Amiloride Docking to Acid-sensing Ion Channel-1. J Biol Chem. 2010 Mar 26;285(13):9627-35. Epub 2010 Jan.

RESEARCH FUNDING (2013-Current)

NSF CBET-1159859 (Song, PI) Thrombospondin-1/calreticulin binding in regulating cell intermediate adhesion and collagen expression, NSF, 10/1/2012 - 09/30/2016
NIH 5K25 CA140791 (Song, PI) Protein interactions underlying Fas-mediated DISC in Cholangiocarcinoma, Principal Investigator, NIH/NCI, 08/14/2009 – 06/30/2015
AHA 14GRNT2048002 (Bevensee, PI; role: collaborator) Molecular Physiology of Na/Bicarbonate Cotransporters, AHA, 07/01/14 – 06/30/16
NIH R01GM038953 (Charles N. Falany, PI; role: co-investigator) Human Cytosolic Sulfotransferases, Co-Investigator, NIH/NIGMS, 9/30/2010 - 8/31/2014

SERVICE (current)

Professional Service
Editorial Boards

MCB: Molecular & Cellular Biomechanics
Journal of Bioprocessing & Biotechniques
Journal of Thermodynamics & Catalysis

Manuscript Reviewer
Biophysical Journal
Biomechanics and Modeling in Mechanobiology
Journal of Biological Chemistry
PLoS ONE
ACS Nano
Journal of Biomechanics
Computational Science & Discovery
Journal of Mechanics in Medicine and Biology

University Service
Faculty Advisor for Society of Women Engineers
School’s representative on the UAB commission on the Status of Women
Quality Assessment Committee, School of Engineering
Faculty advisor for Highschool, Undergraduate, Master and PhD students

Community Service
Outreach activities with UAB Center for Community OutReach Development program.