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Scholarly Interest Report
         
Deepak Nagrath
Assistant Professor
Assistant Professor in Chemical and Biomolecular Engineering
 
e-mail:Deepak.Nagrath@rice.edu
 
  • M.S. Applied Mathematics (2000) Rensselaer Polytechnic Institute, Troy, NY
  • Ph.D. Chemical Engineering (2003) Rensselaer Polytechnic Institute, Troy, NY
  • B.S. Chemical Engineering (1992) IIT Roorkee, Roorkee, India
 
Primary Department
   Department of Chemical and Biomolecular Engineering
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Department Affiliations
 
  • Department of Bioengineering
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    Websites
     lab web page
     
    Research Areas
     Systems Biology of Cancer: Nutrients Regulated Cancer Growth and Metastasis, Metabolic therapies for Targeting Tumor Microenvironment, Role of Nitric oxide in Ovarian Cancer Metabolism and Visceral Obesity, and Metabolic Reprogramming of Lipodystrophies. Tissue Engineering: Three dimensional models for tumors, Human adipose tissue engineering for generation of three dimensional bio-scaffolds and Regenerative Medicine.
     
    Teaching Areas
     CHBE 682

    SYSTEMS BIOLOGY OF HUMAN DISEASES

    Introduction to concepts necessary for application of systems Biology Approaches to Human Diseases. Topics include transcriptional and metabolic design principles, introduction to various regulatory network motifs in diseases and potential treatments using embryonic stem cells. Analysis of complex diseases using engineering concepts such as optimality, nonequilibrium thermodynamics, multiscale analysis and spatiotemporal transport.

    CHBE 470

    PROCESS DYNAMICS AND CONTROL

    Modeling of dynamic processes. Response of uncontrolled systems. Transfer functions. Feedback controllers; response and stability of controlled systems; frequency response. Design of feedback controllers. Cascade, feed forward and multivariable control systems. Introduction to computer control. Use of simulators to design feedback controllers. Required for B.S. majors in chemical engineering.
     
    Selected Publications
     Refereed articles
     

    1.    Lifeng Yang, Tyler Moss, Lingegowda S. Mangala, Juan Marini, Hongyun Zhao, Stephen Wahlig, Guillermo Armaiz-Pena, Dahai Jiang, Abhinav Achreja, Julia Win, Rajesha Roopaimoole, Cristian Rodriguez-Aguayo, Imelda Mercado-Uribe, Gabriel Lopez-Berestein, Jinsong Liu, Takashi Tsukamoto, Anil K. Sood, Prahlad T. Ram,and Deepak Nagrath, “Metabolic shifts toward glutamine regulates tumor growth, invasion and bioenergetics in ovarian cancer ” Molecular Systems Biology, 2014; 10:728.  Featured in Eureka alert, ASCO Post, Science Daily, and many Press and news releases.


    http://msb.embopress.org/content/10/5/728
     
     

    1.    Lifeng Yang, Tyler Moss, Lingegowda S. Mangala, Juan Marini, Hongyun Zhao, Stephen Wahlig, Guillermo Armaiz-Pena, Dahai Jiang, Abhinav Achreja, Julia Win, Rajesha Roopaimoole, Cristian Rodriguez-Aguayo, Imelda Mercado-Uribe, Gabriel Lopez-Berestein, Jinsong Liu, Takashi Tsukamoto, Anil K. Sood, Prahlad T. Ram,and Deepak Nagrath, “Metabolic shifts toward glutamine regulates tumor growth, invasion and bioenergetics in ovarian cancer ” Molecular Systems Biology, 2014; 10:728.  Featured in Eureka alert, ASCO Post, Science Daily, and many Press and news releases.


    http://msb.embopress.org/content/10/5/728
     
     

    Salimian Rizi B, Caneba C, Nowicka A, Nabiyar AW, Liu X, Chen K, Klopp A, Nagrath D, “Nitric oxide mediates metabolic coupling of omentum-derived adipose stroma to ovarian and endometrial cancer cells.”, Cancer Res. 2015 Jan 15;75(2):456-71. Featured in Drug Discovery & Devpt, Medical Xpress, R&D and Health Canal.


    http://cancerres.aacrjournals.org/content/early/2014/11/25/0008-5472.CAN-14-1337.abstract
     
     

    Christine A. Caneba, Lifeng Yang,  Joelle Baddour, Rebecca Curtis, Sean Hartig,  Juan Marini,  and Deepak Nagrath, “Nitric Oxide is a Positive Regulator of the Warburg Effect in Ovarian Cancer Cells”, Cell Death and Disease. 2014; Jun 26; 5: e1302.


    http://www.nature.com/cddis/journal/v5/n6/full/cddis2014264a.html
     
     

    Deepak Nagrath & Alejandro Soto-Gutierrez, Reply to: "Is the pathway of energy metabolism modified in advanced cirrhosis?" Journal of Hepatology 2014 Aug; 61(2):453.

     
     

    K.C. Nicolaou, C. Nilewski, C.R.H. Hale, C.F. Ahles, C.A. Chiu, C. Ebner, A. ElMarrouni, L. Yang, K. Stiles, D. Nagrath, Synthesis and Biological Evaluation of Dimeric Furanoid Macroheterocycles: Discovery of New Anticancer Agents, JACS, 2014, 53, submitted

     
     

    M. Köhring, S. Huang, M. Jahjah, W. Jiang, W. Ren, U. Willer, C. Caneba, L. Yang, D. Nagrath, W. Schade, F.K. Tittel, QCL based TDLAS sensor for detection of NO towards emission measurements from ovarian cancer cellsApplied Physics B: Lasers and Optics, 2014.

     
     

    Taichiro Nishikawa, Nadège Bellance, Aaron Damm, Han Bing, Zhen Zhu, Iraklis I. Pipinos, Alejandro Soto-Gutierrez, Ira J. Fox, Deepak Nagrath, “A switch in the source of ATP production and a loss in capacity to perform glycolysis are hallmarks of hepatocyte failure in advance liver disease”, Journal of Hepatology, 2014 Jun;60(6):1203-11.

    Featured new articles: Newsroom AmericaScience DailyBioscience TechonologyRedOrbitMedical XpressBionews Texas and MedIndia


    http://www.ncbi.nlm.nih.gov/pubmed/24583248
     
     

    Aleksandra Nowicka, Frank C. Marini, Travis Solley, Paula P.B. Elizondo, Yan Zhang Hadley J. Sharp, Russell Broaddus, Mikhail Kolonin, Samuel C. Mok, Melissa S. Thompson, Wendy A. Woodward, Karen Lu, Bahar Salimian, Deepak Nagrath, Ann H. Klopp, "Human Omental-Derived Adipose Stem Cells Increase Ovarian Cancer Proliferation, Migration and Chemoresistance" PLoS One. 2013 Dec 2; 8 (12):e81859.

     
     

    Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay   Nakhleh, “Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks”, PLoS Comput Biol. 2013 Nov;9(11):e1003306.

     
     

    C. Caneba, N. Bellance, Deepak Nagrath, “Increased Pyruvate Uptake In Highly Invasive Ovarian Cancer Cells During Anoikis” American Journal of Physiology: Endocrinology and Metabolism, 2012 Oct; 303(8):E1036-52.

     
     

    Kakajan Komurov, Jen-Te Tseng, Melissa Muller, Elena G. Seviour, Tyler J. Moss, Lifeng Yang, Deepak Nagrath, Prahlad T. Ram, “The glucose-deprivation response network counteracts EGFR signaling in lapatinib resistant cells”, Molecular Systems Biology (Nature), 2012; 8:596.

     
     

    Marco Avila*, Deepak Nagrath*,#, and Martin L. Yarmush, “Global Thermodynamics Control the Evolution of Transcriptional Regulatory Networks,” Molecular Biosystems 2012 Feb;8(2):511-30. (*Equal Contribution). # Corresponding Author.

     
     

    N. Bellance, L. Pabst, Deepak Nagrath, “Oncosecretomics coupled to bioenergetics identifies a-amino adipic acid, isoleucine and GABA as potential biomarkers of cancer:  Differential expression of c-Myc, Oct1 and KLF4 coordinates metabolic changes” Biochim Biophys Acta. 2012 Nov; 1817(11):2060-71.

     
     

    Deepak Nagrath*, Thasni Karedath and Nadege Bellance, “Metabolomics for Mitochondrial and Cancer Studies”, BBA Bioenergetics 2011 Jun; 1807(6):650-63. *Corresponding Author. Most Downloaded paper, Among 25 Hot papers in BBA.

     
     

    Deepak Nagrath, Xia F, Cramer SM. “Characterization and modeling of nonlinear hydrophobic interaction chromatographic systems.” J Chromatography A, 2011 Mar 4;1218(9):1219-26.

     
     

    Nripen S. Sharma*, Deepak Nagrath*, and Martin L. Yarmush, “Metabolic Profiling Based Quantitative Evaluation of Hepatocellular Metabolism in presence of Adipocyte derived Extracellular Matrix”, Plos One, 2011; 6(5):e20137. (*Equal Contribution).

     
     

    Deepak Nagrath*, Marco Avila*, Francois Berthiaume, A. Tilles, A. Messac, Martin L. Yarmush, “Soft Constraints Based Multiobjective Framework for Metabolic Flux Analysis,” Metabolic Engineering 2010 Sep;12(5):429-45. (* Equal Contribution).

     
     

    Nripen S. Sharma*, Deepak Nagrath*, and Martin L. Yarmush, “Adipocyte Derived Novel Extracellular Matrix With Biological Activity: Applications in Hepatocyte Functional Maintenance In vitro”, FASEB J. 2010 Jul; 24(7):2364-74 (* Equal Contribution). Featured in US News & World Report, Eureka alert, Futurity, Science Daily, NSF and many Press and news releases

     
     

    Deepak Nagrath*, Hongzhi Xu*, Yoko Tanimura, Francois Berthiaume, and Martin L. Yarmush, “Metabolic Preconditioning of Donor Organs: Defatting Fatty Livers by Normothermic Perfusion Ex Vivo,” Metabolic Engineering 11: 274-283 (2009). (Selected as Cover Issue).

     
     Book chapters
     

    S. Wang 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. 2010.

     
    Presentations
     Conference abstracts
     

     Abhinav Achreja, Lifeng Yang, Hongyun Zhao, Juan Marini, Deepak Nagrath, “Constraints-based metabolic flux analysis approach links tumor stage to metabolic adaptations and survival in cancer cells,” AACR Annual Meeting, April 2014.

     
     

    Lifeng Yang, Tyler Moss, Juan Marini, Hongyun Zhao, Abhinav Achreja, Stephen Wahlig, Anil Sood, Prahlad Ram,and Deepak Nagrath, “Glutamine Mediated Aggressiveness and Drug Sensitivity In Ovarian Cancer Cells,” Keystone Symposia, Tumor Metabolism, March 2014.

     
     

    Joelle Baddour, Lifeng Yang, Juan C. Marini, Janusz Franco-Barraza, Edna Cukierman, Chaoxin Hu, Anirban Maitra, Deepak Nagrath, “Metabolic influences of pancreatic tumor microenvironment on pancreatic cancer cell’s metabolism,” AACR Annual Meeting, April 2014.

     
     Invited Talks
     

    Lifeng Yang, Tyler Moss, Juan Marini, Hongyun Zhao, Abhinav Achreja, Stephen Wahlig, Anil Sood, Prahlad Ram,and Deepak Nagrath, “Glutamine Mediated Aggressiveness and Drug Sensitivity In Ovarian Cancer Cells,” Keystone Symposia, Tumor Metabolism, January 2015.

     
     

    Tianjin University, Pharmaceutical Engineering, 05/17/2011

     
     

    Sarcoma Research laboratory, MD Anderson Cancer Center, 05/16/2012

     
     

    STar Center, Baylor College of Medicine, 02/04/11

     
     

    Nutrition Center, Baylor College of Medicine, 03/05/2011

     
     

    Tianjin University, Bioengineering, 05/19/2011

     
     Posters
     

     Christine A. Caneba, Juan Marini, Deepak Nagrath, “Effect of nitric oxide on invasiveness and metabolism of cancer cells” AACR Annual Meeting, April 2013.

     
     

    Abhinav Achreja, Lifeng Yang, Hongyun Zhao, Juan C. Marini, Deepak Nagrath, “Integrated energetics and flux analysis reveals differential metabolic reprogramming in highly and less invasive cancer cells”, AACR Annual Meeting, April 2013

     
     

    Bahar Salimian Rizi, Alexandra Nowicka, Ann H. Klopp, Deepak Nagrath, “Metabolic cross talk between omental derived adipose stromal cells from lean and obese patients with ovarian cancer cells, AACR Annual Meeting, April 2013

     
     

     Lifeng Yang, Hongyun Zhao, Juan C. Marini, Collene Jeter, Dean Tang, Deepak Nagrath,Role of NANOG in modulating cancer cell metabolism,” AACR Annual Meeting, April 2013.

     
     

    Bahar Salimian Rizi and Deepak Nagrath,Fatty acids mediated regulation of ovairan cancer metabolism,” AACR Annual Meeting, April 2012.

     
     

    Lifeng Yang and Deepak Nagrath,Role of glutamine in cancer growth, invasion and progression: Therapeutic modulation of glutamine pathway,” AACR Annual Meeting, April 2012

     
    Editorial Positions
     Member of the Editorial Board, Journal of Biosensors and Bioelectronics. (2011 - 2011)

     Member of the Editorial Board, Organogenesis. (2013 - 2017)

     Member of the Editorial Board, Journal of Bioengineering and Biomedical Science. (2013 - 2013)

     Member of the Editorial Board, Organogenesis. Landes Biosciences. (2012 - 2012)

    Supervised Theses & Dissertations
     Aaron Damm, MS A Novel Human Adipocyte-derived Basement Membrane for Tissue Engineering Applications. (2012) (Thesis or Dissertation Director)

     Angela Cintolesi, PhD Kinetic and Stoichiometric Modeling of the Metabolism of Glycerol and Glucose in E. coli for the Synthesis of Biofuels. (2013) (Committee Member)

     Natalie Berestovsky, PhD Toward Integrated Computational Models of Cellular Networks. (2013) (Committee Member)

     Christine Ann Caneba, PhD Ovarian Cancer Metabolism: Effect of Anoikis Condition and Nitric Oxide on Ovarian Cancer Metabolism, and Effect of Metabolites on Ovarian Cancer Migration. (2013) (Thesis or Dissertation Director)

     Satyakam Dash, MS Genome Scale model of Zymomonas mobilis ZM4 with β-oxidation reversal cycle: modifications and product analysis. (2013) (Committee Member)

     kiri Kilpatrick, PhD Reprogramming the proteostasis network to prevent the accumulation of α-synuclein aggregates. (2014) (Committee Member)

     Wenting Zhou, PhD Novel Technologies to Study and Engineer the Proteasomal Degradation. (2015) (Committee Member)

     Ka Wai-Lin, PhD IUnderstanding I Understanding IUnderstanding I Understanding IUnderstanding Insulin nsulin nsulin nsulin Signaling in ignaling in ignaling in ignaling in Glioblastoma lioblastoma lioblastoma lioblastoma lioblastoma lioblastoma Growth and rowth and rowth . (2016) (Committee Member)

     Yimeng Zhang, PhD Expanding the mammalian synthetic biology toolbox: orthogonal regulators and gene circuits for monitoring protein folding and degradation. (2017) (Committee Member)

    Awards, Prizes, & Fellowships
     Invited Talk, Keystone Symposia

     Favorite Professor Award, CHBE Senior Graduating Class (2013)

     IBB Hamill Innovators Award, Hamill Foundation (2013)

     Favorite Professor Award, CHBE Senior Graduating Class (2012)

     John and Ann Doerr Foundation Award, Ken Kennedy institute (2012)

     IBB Hamill Innovation Award, Hamill Foundation (2010)

     IBB Hamill Innovators Award, Hamill Foundation (2010)