Nagrath:Publications

Publications
22. S. Wong and Deepak Nagrath, Liver Tissue Engineering in Biomaterials for Tissue Engineering Applications: A Review of the Past and Future Trends. Edited by Jason Burdick and Rob Mauck. Springer Publisher. (In Press) 2011.

21. Deepak Nagrath*, Fang Xia* and Steven Cramer, "Characterization and Modeling of Nonlinear Hydrophobic Interaction Chromatographic Systems", Journal of Chromatography A (In Press). (* Equal Contribution) 2011.

20. N. Sharma*, D, Nagrath* and M. Yarmush. Adipocyte Derived Basement Membrane Extract With Biological Activity: Applications in Hepatocyte Functional Augmentation In vitro. THE FASEB JOURNAL, 2010 Jul;24(7):2364-74 (* Equal Contribution) [[Media:Adipocyte Derived Basement Membrane Extract With Biological Activity- Applications in Hepatocyte Functional Augmentation In vitro.pdf|PDF]]



19. Marco Avila*, Deepak Nagrath*, and Martin L. Yarmush, Global Thermodynamics Control the Evolution of Transcriptional Regulatory Networks, Plos Computational Biology (In Review). (* Equal Contribution).

18. Deepak Nagrath*, Marco Avila*, Francois Berthiaume, A. Tilles, A. Messac, Martin L. Yarmush, Soft Constraints Based Multiobjective Framework for Metabolic Flux Analysis, Metabolic Engineering Sep;12(5):429-45. (* Equal Contribution). [[Media:soft constraints-based.pdf|PDF]]

17. Deepak Nagrath,* Marco Avila,* and Martin L. Yarmush, Energetic Cost Network Architecture Analysis for Pluripotency in Embryonic Stem Cells Reveals Cofactor Occupancy and Network Hierarchy, (submitted). (* Equal Contribution).

16. Eric Park*, Deepak Nagrath*, Marco Avila*, Cheul Cho, Rongjun Zuo, Arno Tilles, Martin L. Yarmush, “Metabolic Profiling Based Systematic Differentiation of Embryonic Cells Into Hepatocyte Like Cells”, (submitted). (* Equal Contribution).

15. N Sharma*, Deepak Nagrath*, and Martin Yarmush, Metabolic Profiling Based Quantitative Evaluation of Hepatocellular Metabolism in presence of Adipocyte derived Extracellular Matrix, Metabolic Engineering (submitted). (* Equal Contribution).

14. Nagrath D*, Xu H*, Tanimura Y, Zuo R, Berthiaume F, Avila M, Yarmush R, and Yarmush ML. Metabolic preconditioning of donor organs: defatting fatty livers by normothermic perfusion ex vivo. Metab Eng 2009 Jul-Sep; 11(4-5) 274-83. doi:10.1016/j.ymben.2009.05.005 pmid:19508897. (* Equal Contribution). (Selected as Cover Issue). PubMed [[Media:Defatting fatty livers.pdf|PDF]]



13.  Wang S*, Nagrath D*, Chen PC, Berthiaume F, and Yarmush ML. Three-dimensional primary hepatocyte culture in synthetic self-assembling peptide hydrogel. Tissue Eng Part A 2008 Feb; 14(2) 227-36. doi:10.1089/tea.2007.0143 pmid:18333775. (* Equal Contribution) PubMed

12. Wang S*, Nagrath D*, Chen PC, Berthiaume F, and Yarmush ML. Three-Dimensional Primary Hepatocyte Culture in Synthetic Self-Assembling Peptide Hydrogel. Tissue Eng 2008 Jan 3. doi:10.1089/ten.2007.0143 pmid:18173370 (* Equal Contribution) PubMed [[Media:Three-Dimensional Primary Hepatocyte Culture.pdf|PDF]]



11.   Nagrath D, Avila-Elchiver M, Berthiaume F, Tilles AW, Messac A, and Yarmush ML. Integrated energy and flux balance based multiobjective framework for large-scale metabolic networks. Ann Biomed Eng 2007 Jun; 35(6) 863-85. doi:10.1007/s10439-007-9283-0 pmid:17393337 PubMed [[Media:Integrated Energy and Flux Balance Based Multiobjective Framework for Large-Scale Metabolic Networks.pdf|PDF]]



10.   Cho CH, Park J, Nagrath D, Tilles AW, Berthiaume F, Toner M, and Yarmush ML. Oxygen uptake rates and liver-specific functions of hepatocyte and 3T3 fibroblast co-cultures. Biotechnol Bioeng 2007 May 1; 97(1) 188-99. doi:10.1002/bit.21225 pmid:17054120 PubMed [[Media:Oxygen Uptake Rates and Liver-Specific Functions of Hepatocyte and 3T3 Fibroblast Co-Cultures.pdf|PDF]]



9.   Xia F, Nagrath D, and Cramer SM. Effect of pH changes on water release values in hydrophobic interaction chromatographic systems. J Chromatogr A 2005 Jun 24; 1079(1-2) 229-35. pmid:16038309 PubMed [[Media:Effect of pH changes on water release values in hydrophobic interaction chromatographic systems.pdf|PDF]]



8.'   Yokoyama T, Banta S, Berthiaume F, Nagrath D, Tompkins RG, and Yarmush ML. Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a D-galactosamine-induced rat liver failure model. Metab Eng 2005 Mar; 7(2) 88-103. doi:10.1016/j.ymben.2004.09.003 pmid:15781418 PubMed [[Media:Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a D-galactosamine-induced rat liver failure model.pdf|PDF]]



7.   Nagrath D, Bequette BW, Cramer SM, Messac A. Multiobjective optimization strategies for linear gradient chromatography. AICHE Journal 2005 Feb; 51(2) 511-525 [[Media:Multiobjective Optimization Strategies for Linear Gradient Chromatography.pdf|PDF]]



6.   Xia F, Nagrath D, Garde S, and Cramer SM. Evaluation of selectivity changes in HIC systems using a preferential interaction based analysis. Biotechnol Bioeng 2004 Aug 5; 87(3) 354-63. doi:10.1002/bit.20120 pmid:15281110 PubMed [[Media:Evaluation of selectivity changes in HIC systems using a preferential interaction based analysis.pdf|PDF]]



5.  Ghose S, Nagrath D, Hubbard B, Brooks C, and Cramer SM. Use and optimization of a dual-flowrate loading strategy to maximize throughput in protein-a affinity chromatography. Biotechnol Prog 2004 May-Jun; 20(3) 830-40. doi:10.1021/bp0342654 pmid:15176889 PubMed [[Media:Use and optimization of a dual-flowrate loading strategy to maximize throughput in protein-a affinity chromatography.pdf|PDF]]



4.  Nagrath D, Messac A, Bequette BW, and Cramer SM. A hybrid model framework for the optimization of preparative chromatographic processes. Biotechnol Prog 2004 Jan-Feb; 20(1) 162-78. doi:10.1021/bp034026g pmid:14763840 PubMed [[Media:A hybrid model framework for the optimization of preparative chromatographic processes.pdf|PDF]]

3.  Xia F*, Nagrath D*, and Cramer SM. Modeling of adsorption in hydrophobic interaction chromatography systems using a preferential interaction quadratic isotherm. J Chromatogr A 2003 Mar 7; 989(1) 47-54. pmid:12641281 (* Equal Contribution) PubMed [[Media:Modeling of adsorption in hydrophobic interaction chromatography systems using a preferential interaction quadratic isotherm.pdf|PDF]]



2. Nagrath D, Bequette BW, Cramer SM. Evolutionary operation and control of chromatographic processes. AICHE Journal 2003 Jan; 49(1) 82-95 [[Media:Evolutionary operation and control of chromatographic processes.pdf|PDF]]



1.  Nagrath D, Prasad V, Bequette BW. A model predictive formulation for control of open-loop unstable cascade systems. Chemical Engineering Science 2002 Feb; 57(3) 365-378. [[Media:A model predictive formulation for control of open-loop unstable cascade systems.pdf|PDF]]