Nagrath:Publications

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               <h2> Please visit our new website at <a href="http://nagrathlab.rice.edu/">http://nagrathlab.rice.edu/</a></h2></div>

<h1> <span style="text-transform: uppercase">Systems Biology of Human Diseases</span> Laboratory</h1>


<div id="menu"> <ul id="main"> <li><a href="http://openwetware.org/wiki/Nagrath_Lab">Home</a></li> <li><a href="http://openwetware.org/wiki/Nagrath:People">Lab Members</a></li> <li><a href="http://openwetware.org/wiki/Nagrath:Publications">Publications</a></li> <li><a href="http://openwetware.org/wiki/Nagrath:Research">Research Interests</a></li>

                       <li><a href="http://openwetware.org/wiki/Nagrath:Patents">Patents</a></li>
                       <li><a href="http://openwetware.org/wiki/Nagrath:Courses">Courses</a></li>
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Recent Lab News

December 2010 Dr. Nagrath's article in the journal "Tissue Engineering Part A" entitled "Three dimensional primary hepatocyte culture in synthetic self-assembling peptide hydrogel" is among the list of 20 of the most cited articles from 2008-2009.

http://www.liebertpub.com/whatsnew.aspx?id=53


December 2010 Dr. Nagrath has joined to the editorial board of journal "Journal of Biosensor and Bioelectronics".

http://www.omicsonline.org/EditorialboardJBSBE.php


November 2010 Congratulations to our newest lab members: Aaron Damm, Lifeng Yang, Bahar Salimian, first year chemical engineering graduate students!


November 2010 Congratulations to Christine Caneba for receiving 2010 Edgar O'Rear Travel Grant.


July 2010 Congratulations to Professor Nagrath's lab and Professor Grande-Allen's lab (BIOE, RICE) for receiving the Hamill Innovations Award


July 2010 Dr. Nagrath and Dr. Wong (BME, CUNY) publish book chapter entitled Liver Tissue Engineering in Biomaterials for Tissue Engineering Applications: A Review of the Past and Future Trends


May 2010 Congratulations to new group member Christine Caneba (Bioengineering, II year) on joining the group.


May 2010 Professor Deepak Nagrath's paper Soft Constraints-Based Multiobjective Framework for Flux Balance Analysis. is accepted for publication in THE Metabolic Engineering JOURNAL.


March 2010 Professor Deepak Nagrath's research in adipocytes and discovery of natural extracellular matrix has been featured in several science-related websites.

http://www.media.rice.edu/media/NewsBot.asp?MODE=VIEW&ID=13927&SnID=2

http://www.usnews.com/science/articles/2010/03/29/your-fat-may-help-you-heal.html

http://futurity.org/health-medicine/all-natural-healing-power-of-fat/

http://www.sciencedaily.com/releases/2010/03/100325143059.htm

http://www.physorg.com/news188745463.html

http://www.rdmag.com/News/2010/04/Life-Sciences-Biology-Body-Fat-May-Help-Us-Heal/

http://www.hcnonline.com/articles/2010/05/26/river_oaks_examiner/lifestyles/ro_med_fat_healing.txt


February 2010 Professor Deepak Nagrath's paper Adipocyte Derived Basement Membrane Extract With Biological Activity: Applications in Hepatocyte Functional Augmentation In vitro. is accepted for publication in THE FASEB JOURNAL.


Met eng.jpg September 2009 Professor Deepak Nagrath's research in tissue engineering and metabolic engineering is highlighted as cover article. An article entitled "Metabolic Preconditioning of Donor Organs: Defatting Fatty Livers by Normothermic Perfusion Ex Vivo" appears on the cover of the August/September 2009 issue of Metabolic Engineering.

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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) PDF


Nagrath Fig Adipocytes.jpg

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). 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 PDF

Nagrath Fig1.jpg

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 PDF

Nagrath Fig3.jpg

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 PDF

Nagrath Fig4.jpg

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 PDF

Nagrath Fig5.jpg

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 PDF


Effect of Ph fig.jpg

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 PDF

Nagrath Evolution of intrahepatic carbon fig.jpg

7. Nagrath D, Bequette BW, Cramer SM, Messac A. Multiobjective optimization strategies for linear gradient chromatography. AICHE Journal 2005 Feb; 51(2) 511-525 PDF

Nagrath Multiobjective Optimization fig.jpg

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 PDF

Nagrath Evaluation of Selectivity Changes fig.jpg

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 PDF

Nagrath Use and optimization of a dual-flowrate fig.jpg

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 PDF

Nagrath A hybrid model framework fig.jpg

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 PDF

Nagrath Modeling of adsorption Fig.jpg

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

Nagrath Fig13.jpg

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. PDF

A model fig.jpg

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