Contact info:

krischan@egr.msu.edu
Phone: 517.432.4530
Fax: 517.555.5555

Cellular & Biomolecular Laboratory
Center for Systems Biology

PUBLICATIONS

Peer-reviewed Articles:

  1. Chan, C., Arai, N., Lior, N., and Churchill, S. W., "Thermally Stabilized Combustion as a Means of Studying the Devolatilization of Coal", (1992) Industrial Engineering and Chemical Research, 31: 681-687.
  2. Churchill, S. W. and Chan, C., "Improved Correlating Equations for the Friction Factor for Fully Turbulent Flow in Round Tubes and between Identical Parallel Plates, both Smooth and Naturally Rough", (1994) Industrial and Chemical Engineering Research, 33: 2016-2019.
  3. Churchill, S. W. and Chan, C., "Theoretically Based Correlating Equations for the Local Characteristics of Fully Turbulent Flow in Round Tubes and between Parallel Plates", (1995) Industrial and Chemical Engineering Research, 34: 1332-1341.
  4. Churchill, S. W. and Chan, C., "Turbulent Flow in Channels in Terms of Local Turbulent Shear Stress and Normal Stresses", (1995) AIChE Journal, 41: 2513-2521.
  5. Brown, M., Chan, C., Targett, M., Holtzmuller, M. and Churchill, S. W., "Combustion of Ethane with Small Concentrations of Methyl Chloride in a Refractory Tube Burner", (1996) Combustion Science and Technology, 115: 207-227.
  6. Heng, L., Chan, C. and Churchill, S. W., "Essentially Exact Characteristics of Turbulent Convection in a Round Tube", (1998) Chemical Engineering Journal, 71: 163-173.
  7. Washizu, J., Chan, C., Berthiaume, F., Tompkins, R. G., Toner, M., and Yarmush, M. L., "Amino Acid Supplementation Improves Cell-Specific Functions of the Rat Hepatocytes Exposed to Human Plasma", (2000) Tissue Engineering, 6: 497-504.
  8. Washizu, J., Berthiaume, F., Chan, C., Tompkins, R. G., Toner, M., and Yarmush, M. L., "Optimization of Rat Hepatocyte Culture in Citrated Human Plasma", (2000) Journal of Surgical Research, 93: 237-246.
  9. Chan, C., Berthiaume, F., Washuzu, J., Toner, M., and Yarmush, M. L., "Metabolic Pre-Conditioning of Cultured Cells in Physiological Levels of Insulin: Generating Resistance to the Lipid Accumulating Effects of Plasma in Hepatocytes", (2002) Biotechnology and Bioengineering, 78: 753-760.
  10. Chan, C., F., Berthiaume, F., Lee, K., and Yarmush, M. L., "Metabolic Flux Analysis of Cultured Hepatocytes Exposed to Plasma", (2003) Biotechnology and Bioengineering, 81: 33-49.
  11. Chan, C., Hwang, D. H., Stephanopoulos, G. N., Yarmush, M. L., and Stephanopoulos, G., "Application of Multivariate Analysis to Optimize Function of Cultured Hepatocytes?, (2003) Biotechnology Progress, 19: 580-598.
  12. Chan, C., Berthiaume, F., Lee, K., and Yarmush, M. L., "Metabolic flux analysis of hepatocyte function in hormone- and amino acid-supplemented plasma", (2003) Metabolic Engineering, 5: 1-15.
  13. Hwang, D. H., Stephanopoulos, G., and Chan, C., "Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function", (2004) Bioinformatics, 20:487-99.
  14. Li, Z., and Chan, C., "Inferring pathways and networks with a Bayesian framework", (2004) FASEB J 18(6): 746-8 (published on-line Feb 6, 2004, doi:10.1096/fj.03-0475fje).
  15. Kidambi, S., Chan, C., and Lee, I., "Selective Depositions on Polyelectrolyte Multilayers: Self-Assembled Monolayers of m-dPEG Acid as Molecular Templates", (2004) JACS, 126:4697-4703.
  16. Li, Z., and Chan, C., "Integrating gene expression and metabolic profiles", (2004) Journal Biological Chemistry 279: 27124-27137.
  17. Li, Z., Yarmush, M. L., and Chan, C., "Insulin concentration during pre-conditioning mediates the regulation of urea synthesis in primary rat hepatocytes during exposure to amino acid supplemented plasma", (2004) Tissue Engineering 10(11):1737-1746.
  18. Chan, C., Berthiaume, F., Dwarakanath, B., Tilles, A. W., Toner, M., Yarmush, M. L., "Hepatic tissue engineering for adjunct and temporary liver support: Critical technologies", (2004) Liver Transplantation 10(11):1331-1342.
  19. Kidambi, S., Lee, I., and Chan, C., "Controlling Primary Hepatocyte Adhesion and Spreading on Protein Free Polyelectrolyte Multilayer Films", (2004) JACS Communications 126(50):16286-7.
  20. Patil, S. and Chan, C., "Palmitic and stearic fatty acids induce Alzheimer-like hyperphosphorylation of tau in primary rat cortical neurons", (2005) Neuroscience Lett. 384(3):288-293.
  21. Li, Z., Shaw, S. M., Yedwabnick, M. J., and Chan, C., "Using a state-space model with hidden variables to infer transcription factor activities", (2006) Bioinformatics 22(6): 747?754.
  22. Patil, S., Sheng, L., Masserang, A., and Chan, C., "Palmitic acid-induced BACE1 upregulation and accumulation of C-terminal fragment of APP in primary cortical neurons", (2006) Neuroscience Lett. 406: 55?59.
  23. Srivastava, S., and Chan, C., "Hydrogen peroxide and hydroxyl radicals mediate palmitate-induced cytotoxicity to hepatoma cells: relation to MPT", (2007) Free Radical Research, 41(1):38-49.
  24. Kidambi, S., Sheng, L., Toner, M., Yarmush, M., Lee, I., and Chan, C., "Patterned Co-culture of Primary Hepatocytes and Fibroblasts using Polyelectrolyte Multilayer Templates", (2007) Macromolecular Bioscience, 7(3): 344 - 353.
  25. Kidambi, S., Udpa, N., Schroeder, SA, Findlan, R, Lee, I, and Chan, C., "Cell Adhesion on Polyelectrolyte Multilayer Coated Poly(dimethylsiloxane) Surfaces with Varying Topographies", (2007) Tissue Engineering Mar 8; [Epub ahead of print].
  26. Li, Z., Srivastava, S., Yang, S., Mittal, S., Norton, P., Resau, J., and Chan, C., "A Hierarchical Approach to Identify Pathways that Confer Cytotoxicity in HepG2 Cells from Metabolic and Gene Expression Profiles", (2007) BMC Systems Biology May 11;1(21):1-15.
  27. Li, Z., Srivastava, S., Mittal, S., Yang, X., Sheng, L., and Chan, C., "A Three Stage Integrative Pathway Search (TIPS©) framework to identify toxicity relevant genes and pathways", (2007) BMC Bioinformatics June 14 8(101):1-17.
  28. Patil, S., Melrose, J., and Chan, C., "Involvement of astroglial ceramide in palmitic acid-induced Alzheimer-like changes in primary neurons", (2007) European Journal of Neuroscience, 26(8):2131-2141.
  29. Srivastava, S., Li, Z., Yang, X., Yedwabnick, M., Shaw, S., and Chan, C., "Identification of genes that regulate multiple cellular processes/ responses in the context of lipotoxicity in hepatoma cells" (2007) BMC Genomics 8:364.
  30. Srivastava, S. and Chan, C., "Application of Metabolic Flux Analysis to Identify the Mechanisms of Free Fatty Acid Toxicity to Human Hepatoma Cell Line, HepG2", (2008) Biotechnology and Bioengineering, 99: 399?410.
  31. Kidambi, S., Lee, I, and Chan, C., "Directed deposition of cells and macromolecules using salt tunable m-dPEG acid patterns on polyelectrolyte multilayers", (2008) Langmiur, 24(1), 224 -230.
  32. Jin, R., Si, L., and Chan, C., "A Bayesian Framework for Knowledge Driven Regression Model In Micro-array Data Analysis", (2008) International Journal of Data Mining and Bioinformatics (IJDMB) (in press).
  33. Kidambi, S., Lee, I, and Chan, C., "Patterned Co-culture of Neurons and Astrocytes on Polyelectrolyte Multilayer Films for Studying Astrocyte Mediated Oxidative Stress in Neurons", (2008) Advanced Functional Materials(in press).
  34. Li, Z., Srivastava, S., Findlan, R., and Chan, C., "Using dynamic gene module map analysis to identify targets that modulate free fatty acid and tumor necrosis factor (TNF)-α induced cytotoxicity", (2008) Biotechnology Progress, Dec 4 [Epub ahead of print].
  35. Leekumjorn, S., Wu, Y., Sum, A.K., and Chan, C., "Experimental and Computational Studies Investigating Trehalose Protection of HepG2 Cells from Palmitate Induced Cytotoxicity", (2008) Biophysical Journal (in press).
  36. Srivastava, S., Zhang, L., Jin, R., and Chan, C., "A novel unsupervised classification and feature selection method which incorporates ontology information", (in review).
  37. Yang, X. and Chan, C., "Signal Transduction Pathways from PKR to Bcl-2 Mediates the Apoptosis induced by Palmitic Acid and TNF-α in HepG2 Cells", (in review).
  38. Yang, X., Zhou Y., Li, Z., Srivastava, S., Jin, R., and Chan, C., "Learning Phenotype Specific Gene Network by Knowledge Driven Matrix Factorization", (in review).
  39. Patil, S., Balu, D., Melrose, J. and Chan, C., "Brain region specificity of palmitic acid-induced Alzheimer-like changes in primary neurons", (in review).

Invited Reviews:

  1. Berthiaume, F., Chan, C., Yarmush, M. L., "Liver, Bio-artificial", in Encyclopedia of Biomaterials and Biomedical Engineering, eds. Gary Wnek and Gary Bowlin, Marcel Dekker Inc., New York, NY, 2004, Vol. 1, 899-909.
  2. Li, Z., and Chan, C., "Extracting novel information from gene expression data", (2004) Trends in Biotechnology, 22: 381-383.
  3. Patil, S., Li, Z., and Chan, C., "Cellular to Tissue Informatics: Approaches to Optimizing Cellular Function of Engineered Tissue", in Advances in Biochemical Engineering/Biotechnology, eds. K. Lee and D. Kaplan, Springer, 2006, volume 102, p. 139-159.
  4. Walton, SP, Li, Z, and Chan, C, "Biological network analyses: computational genomics and systems approaches", (2006) Molecular Simulation, 32 (Issue is 3-4, 15 March-April): 203-209.
  5. Berthiaume, F., Tilles, A. W., Toner, M., Yarmush, M. L., and Chan, C.,  "Hepatic Tissue Engineering for Adjunct and Temporary Liver Support", in Tissue Engineering and Artificial Organs, ed. Joseph D. Bronzino, Taylor and Francis, Boca Raton, FL, 2006, Chapter 59, p. 1-19.
  6. Chan, C., Li, Z., and Srivastava, S., "Integration of Micro-Array and Metabolic Data", in Mathematical Modeling in Experimental Nutriton, 2007, Chapter 5, p. 82-96.
  7. Srivastava, S., Li, Z.,and Chan, C., "Identification of gene-networks associated with cell-death in lipotoxicity", 2008 (accepted).

Manuscripts submitted:

  1. Srivatsan, K., Lee, I., and Chan, C., "Aptamer Incorporated Polyelectrolyte Multilayer Films Targeting Influenza Virus?s Hemagglutinin Binding Region", (submitted)

Others:

  1. Chan, C. and Tannenbaum, P., "1997 Inter-Society Color Council Annual Meeting and the Color & Appearance Division of the Society of Plastics Engineers", (1998) Color Research and Application, 23:.
  2. Huebner, M., Kroos, L., Chan, C., Sun, F., and Cheng, T., "Biological Networks: Design and Dynamics at Different Levels", Department of Statistics and Probability, Technical Report MSU, RM639.
  3. Jin, R., Si, L., Chan, C., "Improve the Linear Regression Model in Bioinformatics Using Text Mining", Technical Report (MSU-CSE-06-9) of Computer Science and Engineering Dept. of MichiganStateUniversity. It is available at http://www.cse.msu.edu/~rongjin/publications/sigir.textming3.pdf.

CONFERENCE PAPERS

Peer-reviewed conference papers:

  1. Jin, R., Si, L., Srivastava, S., Li, Z. and Chan, C., "A Knowledge Driven Regression Model for Gene Expression and Microarray Analysis", In Proceedings of 28th Annual International Conference IEEE Engineering in Medicine and Biology Society, 2006.
  2. Jin, R., Si, L., and Chan, C., "A Bayesian Framework for Knowledge Driven Regression Model in Micro-array Data Analysis", NIPS, 2006.

Non-refereed papers and Extended Abstracts:

  1. Kidambi, S., Lee, I., and Chan, C., "Salt Tunable m-dPEG Acid Patterns on Polyelectrolyte Multilayers - Templates for Directed Deposition of Macromolecules" ACS Polymer Preprints, 2006.
  2. Kidambi, S., Lee, I., and Chan, C., "Polyelectrolyte Multilayer as Bioactive Surface for Cell Adhesion" ACS Polymer Preprints, 2005.
  3. Li, Z., Srivastava, S., and Chan, C., "Integrating Gene Expression and Metabolic Profiles to Infer Pathways and Networks that Confer Palmitate Induced Cytotoxicity in HEPG2 Cells", ASME Summer Bioengineering Conference Proceedings, 2005.
  4. Kidambi, S., Lee, I., and Chan, C. "Selective Primary Hepatocyte Adhesion on Polyelectrolyte Multilayer: Template for Patterned Cell Co-Culture," AIChE Nanotechnology Preprint, 2004.
  5. Kidambi, S., Lee, I., and Chan, C. "Engineering Polyelectrolyte Multilayer (PEM) Surfaces to Create Cell Resistant and Adhesive Surfaces," Polymer Preprints 45(1), 88-89, 2004.
  6. Chan, C. and Li, Z., "Inferring the Hepatic Network from Experimental Measurements using Bayesian Network Analysis", ASME Summer Bioengineering Conference Proceedings, 2003.
  7. Chan, C., Hwang, D. H., Stephanopoulos, G., Stephanopoulos, G., N., and Yarmush, M. L., "Application of Multivariate Analysis for Optimizing & Predicting Hepatic Function", BMES, 2002.
  8. Chan, C., Hwang, D. H., Stephanopoulos, G., Stephanopoulos, G., N., and Yarmush, M. L., "Application of Metabolic Engineering and Multivariate Analyses for Optimizing Hepatic Function", Metabolic Engineering IV: Applied Systems Biology, 2002.
  9. Chan C., Washizu, J., Berthiaume F., Toner, M., and Yarmush, M. L., "Application of Metabolic Engineering to Cellular Processes of the Liver: As Use in the Development of the Bioartificial Liver", ASME Summer Bioengineering Conference Proceedings, 50: 357-8, 2001.
  10. Chan, C., Berthiaume, F., Washuzu, J., Toner, M., and Yarmush, M. L., "The Effect of Conditioning on Lipid Metabolism of Hepatocytes in Plasma", Metabolic Engineering III, 2000.