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Page 1: Department of Chemical & Biological Engineering Iowa State ... fileJacqueline Vanni Shanks Department of Chemical & Biological Engineering Iowa State University January, 2012

Jacqueline Vanni Shanks

Department of Chemical & Biological Engineering

Iowa State University

January, 2012

Page 2: Department of Chemical & Biological Engineering Iowa State ... fileJacqueline Vanni Shanks Department of Chemical & Biological Engineering Iowa State University January, 2012

Table of Contents

Education: .................................................................................................................................................................... 1

Professional Experience: ............................................................................................................................................. 1

Honorary and Professional Societies: ........................................................................................................................ 1

Special Appointments or Awards:.............................................................................................................................. 2

Research Activities: ..................................................................................................................................................... 2 Research Interests .......................................................................................................................................................... 2 Current Funding ............................................................................................................................................................. 2 Past Funding .................................................................................................................................................................. 3 Thesis Research Directed .............................................................................................................................................. 6

Teaching Experience: .................................................................................................................................................. 7 Iowa State University .................................................................................................................................................... 7 Rice University .............................................................................................................................................................. 7 Caltech ........................................................................................................................................................................... 8

University Service: ....................................................................................................................................................... 8 Iowa State University .................................................................................................................................................... 8 Rice University .............................................................................................................................................................. 8

Professional Service: .................................................................................................................................................... 9 Editorial and Advisory Board Memberships ................................................................................................................. 9 National Committees, Workshops ................................................................................................................................. 9 Workshops ................................................................................................................................................................... 10 Offices ......................................................................................................................................................................... 10 Organizer of Symposia ................................................................................................................................................ 10 Chair of Sessions ......................................................................................................................................................... 10 Reviewer ...................................................................................................................................................................... 10

Community Service: .................................................................................................................................................. 11

Research Publications: .............................................................................................................................................. 11

Books: ......................................................................................................................................................................... 18

Book Chapters: .......................................................................................................................................................... 18

Technical Reports: ..................................................................................................................................................... 19

Technical Software: ................................................................................................................................................... 19

Educational Publications: ......................................................................................................................................... 19

Textbooks: .................................................................................................................................................................. 19

Textbook Web Site: ................................................................................................................................................... 19

Educational Software: ............................................................................................................................................... 19

Lecturer of Continuing-Education Courses: ........................................................................................................... 19

Technical Presentations at Conferences-Abstracts: ............................................................................................... 20

Invited Lectures at Universities, Companies, and Conferences: ........................................................................... 31

Postdoctoral Research Fellows Supervised: ............................................................................................................ 33

Graduate Students Supervised: ................................................................................................................................ 33

Undergrad Research Students Supervised: ............................................................................................................. 33

Undergrad “Labbie” Students Supervised, Iowa State University: ...................................................................... 38

Undergrad Education (Computation) Students Supervised (with S.H. Davis), Rice University: ....................... 38

High School Research Students Supervised: ........................................................................................................... 38

Page 3: Department of Chemical & Biological Engineering Iowa State ... fileJacqueline Vanni Shanks Department of Chemical & Biological Engineering Iowa State University January, 2012

1

JACQUELINE VANNI SHANKS

Curriculum Vitae

Date of Birth: May 10, 1961

Citizenship: United States

Place of Birth: Des Moines, IA

Position: Manley R. Hoppe Professor in Chemical and Biological Engineering

Education:

B.S., Iowa State University, Chemical Engineering 1983

Ph.D., California Institute of Technology, Chemical Engineering 1989

Ph.D. Advisor: James E. Bailey

Professional Experience:

1981-1982 Teaching Assistant, Iowa State University

1982 Process Engineer, Pillsbury, Minneapolis, MN

1982-1983 Undergraduate Research, Iowa State University

1983 Process Engineer, General Electric Corporation, Mount Vernon, IN

1985 SURF Student Advisor, California Institute of Technology

1985 Teaching Assistant, California Institute of Technology

1984-1988 Research Assistant, California Institute of Technology

1988-1993 Assistant Professor in Chemical Engineering, Rice University

1993-1999 Associate Professor in Chemical Engineering, Rice University

1997-1999 Associate Professor in Bioengineering, Rice University

1999 Professor in Bioengineering, Rice University

July 1, 1999-2005 Professor in Chemical Engineering, Iowa State University

July 1, 2001- Adjunct Professor in Bioengineering, Rice University

July 1, 2005-2009 Professor in Chemical & Biological Engineering, Iowa State University

Sept. 1, 2008- 2010 Thrust 2 Co-Leader, NSF Center for Biorenewable Chemicals (CBiRC),

Iowa State University

July 1, 2009- Manley R. Hoppe Professor in Chemical & Biological Engineering, Iowa

State University

Sept. 1, 2010- Thrust 2 Leader, NSF Center for Biorenewable Chemicals (CBiRC), Iowa

State University

Honorary and Professional Societies:

American Chemical Society (ACS)

American Institute of Chemical Engineers (AIChE)

American Institute of Medical and Biological Engineering, Fellow

Houston Society for Engineering in Medicine and Biology (HSEMB)

Steering Committee 1991-1995

Omega Chi Epsilon

Sigma Xi

Society for In Vitro Biology (SIVB)

Society of Women Engineers (SWE)

Tau Beta Pi

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Special Appointments or Awards:

State of Iowa Scholarship 1979-1980

Atlantic Richfield Scholarship 1980-1981

3M Scholarship 1981-1982

Senior Design Award 1983

Senior Research Fellowship 1982-1983

Farmland Industries Scholarship 1982-1983

Graduation with Distinction, Iowa State University 1983

Weyerhauser Company Foundation Predoctoral Fellowship 1983-1984

Amoco Outstanding Young Faculty in Engineering Award 1991

Rice Nomination Presidential Faculty Fellow 1991

Outstanding Faculty Associate, Rice University 1991 and 1992

Rice Nomination Camille-Dreyfus Teacher Scholar 1992

Outstanding Faculty Associate, Wiess College 1992

Herschel Rich Invention Award 1992

NSF Young Investigator Award 1992-1997

Professional Progress in Engineering Award, Iowa State University 1994

American Institute of Medical and Biological Engineering, Fellow 2000

Associate Editor, Biotechnology Progress 2002-2003

Van Lanen Award, Division of Biochemical Technology, ACS 2004

ISU University Foundation Award for Outstanding Achievement in Research 2005

Women of Innovation Award for Research Innovation and Leadership,

by the Technology Association of Iowa 2008

AIChE Food, Pharmaceutical and Bioengineering Division, Area 15c Plenary Award 2010

Research Activities:

Research Interests

Metabolic engineering of biorenewable chemicals.

Metabolic engineering of plant secondary metabolites.

NMR spectroscopic techniques for characterization of cellular metabolism.

Analytical methods for analysis of metabolic pathways.

Enhancement of bioprocess productivity from manipulation of cellular metabolism via changes in

genetic composition or environment.

Current Funding

Principal Investigator, “Evaluate and Identify Metabolic Control Points Determining Assimilate

Partitioning in Developing Seed,” Pioneer Hi-Bred International, $300,000 (11/01/07–10/31/12).

Thrust 2 Leader [Shanks, B, P.I.,] “ERC: Center for Biorenewable Chemicals,” National Science

Foundation, $16,250,000 (08/01/08–07/31/13).

Principal Investigator [with Nikolau, B. (Co-P.I.) and Bobik, T. from ISU; Wolfe, G. (Co-P.I.) from

California State University, Chico; Nadathur, G. (co-PI) from University of Puerto Rico], “ EFRI-

HyBi: Bioengineering a System for the Direct Production of Biological Hydrocarbons for

Biofuels,” NSF, $2,059,528,” (9/1/09 – 8/31/13).

Co-Principal Investigator, [with Vigil, D. (PI)]. “Energy Efficient Cultivation of Microalgae and

Simultaneous Separation of Products using a Novel Taylor Vortex Reactor-Separator” Conoco

Phillips Company. $131,601 (1/1/2011 – 12/31/2012).

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Past Funding

Principal Investigator [with Gibson, S. (Co-P.I.) from Univ. of Minnesota and San, K. Y. (Co-P.I.)

from Rice University], “Collaborative Research: Molecular Genetic and Metabolic Analyses to

Characterize Terpenoid Indole Alkaloid Pathways,” NSF, $174,624 (ISU portion) (9/1/07-8/31/09).

Principal Investigator, “Metabolic Flux Analysis in Plants,” Pioneer Hi-Bred International,

$349,188 (05/01/06-04/31/10).

Principal Investigator [with Dickerson, J. (Co-P.I)], "Understanding oil/protein partitioning in

developing soybean embryos: Linking transcript data and metabolic fluxes," Plant Sciences

Institute, $50,000 (7/1/06-6/31/09).

Participant [with Narashimhan, P.I.], “REU Site in Biological Materials and Processes (BioMaP),”

National Science Foundation, $370,639, (02/01/2006-01/31/2009).

Co-Principal Investigator [Andreotti, P.I., with nine others] “Graduate Research Training Program

in the area of Molecular Biophysics,” Roy J. Carver Charitable Trust, $494,436 (11/06 – 10/09).

Co-Principal Investigator [with Gonzalez, R. (P.I.) and San, K. Y. (Co-P.I.) from Rice University],

“Collaborative Research: Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems

for the Consumption of Plant Biomass Sugars,” Interagency Program in Metabolic Engineering

[NSF (Rice-ISU), U.S. Dept. of Agriculture (ISU), U.S. Dept. of Energy (ISU), Environmental

Protection Agency (Rice)] $569,872 (ISU Portion) (8/15/03-8/31/07).

Co-Principal Investigator [Hong, P.I., with Andreotti, Pruski, Schmidt-Rohr] “Acquisition of a 600

MHz Spectrometer for Biomolecular and Materials Research,” NSF, DBI-0421374, $957,600

(07/04-06/07)

Principal Investigator [with Oliver, D. (Co-P.I)], “Genetic and Biochemical Basis for the

Transformation of Energetic Materials (RDX, TNT, DNTs) by Plants,” SERDP, $828,419

(09/01/02-09/26/06).

Principal Investigator “Integrating molecular, physiological, and agronomic approaches to meet IP

soybean markets of the near future,” ISU Agronomy Foundation, $52,250 (4/1/04-08/31/06). [Part

of larger project with Westgate, M., Batchelor, W., and Nikolau, B.]

Principal Investigator [with Gibson, S. (Co-P.I.) and San, K. Y. (Co-P.I.) from Rice University],

“Collaborative Research: Metabolic Engineering of Hairy Roots for Alkaloid Production,” NSF,

$241,947 (ISU portion) for the period August 15, 2002-July 31, 2006.

Co-Principal Investigator [with Glatz, C. E. (PI), Mallapragada, S. K. (co-PI), Reilly, P. J., Huba,

M. (co-PI)], “Chemicals from Biorenewables,” NSF CRCD Program, $418,000, with ISU match up

to $540,000 (03/01-02/06).

Principal Investigator “Managing Stress Tolerance and Seed Composition of Glyphosate-Resistant

Soybeans,” Iowa Soybean Board, $46,022 (2/1/03-6/31/04). [Part of larger project with

Westgate, M.]

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Participant [with Brown, R. (PI ) et. al.], “Multi-Disciplinary Education and Training in Biobased

Products: Graduate Major in Bioresource Engineering,” DOE, $375,000, 7/01-6/04.

Principal Investigator [with Spalding, M. (Co-P.I.) and Westgate, M. (Co-P.I.)], “Development of

NMR Tools for Metabolic Flux Maps of Soybean Seeds,” Plant Science Institute, $50,000 for the

period July 15, 2001-June 31, 2003.

Principal Investigator [with Gibson, S. (Co-P.I.) and San, K. Y. (Co-P.I.) from Rice University],

“Quantifying and Directing Metabolite Flux: Application in Tryptophan Overproduction and Indole

Alkaloid Accumulation in Plant Tissues,” NSF, $197,000 (ISU portion), $ 280,000 (Rice portion)

for the period August 15, 2000-July 31, 2003.

Co-Principal Investigator [with Westgate, M. E. (PI), Hurburgh, C. (co-PI), Nikolau, B (co-PI),

Wurtele, E. (co-PI)] “An Integrated Research Program to Improve the Composition and Value of

Iowa Soybeans,” Iowa Soybean Promotion Board, $124,592 (9/01-8/02).

Participant [with Nikolau, B (PI), and 16 others], “Metabolomics Research Laboratory,” Keck

Foundation, $1,000,000, (7/31/01). {ISU Match 1.3 million}.

Principal Investigator: “Plant Metabolic Engineering Research,” ISU Biotechnology Council,

$150,000 for the period July 1, 1999-June 30, 2002.

Principal Investigator: “Plant Metabolic Engineering Research,” Iowa State University Center for

Crop Utilization Research, $35,000 for the period July 1, 1999-June 30, 2002.

Co-Principal Investigator [with Oliver, D. (P.I.)], “Genetics of 2,4,6-Trinitrotoluene (TNT)

Metabolism by Plants,” SPRIG, ISU, $15,000, January 1, 2001-December 31, 2001.

Principal Investigator: “Plant Metabolic Engineering Research,” Cargill, $25,000 for the period

July 1, 1999-June 30, 2001.

Co-Principal Investigator [with Hughes, J. (P.I.), Bennett, C. (Co-P.I.), Rudolph, F. (Co-P.I.)],

“A Coupled Evaluation of Biotransformation Pathways and Toxicity Reduction for Explosives in

Remediation Systems or the Natural Environments,” Defense Special Weapons Agency, U.S. Dept.

of Defense, $1,981,480 for the period September 30, 1997-October 1, 1999.

Principal Investigator, “Young Investigator Award,” NSF BCS-9257938, $322,750 (includes

$5,250 from private donors) for the period November 1, 1992-January 31, 1999.

Principal Investigator, “Phytoremediation of TNT,” TX Advanced Technology Program 003604-

045, $148,157 for the period January 1, 1996-August 31, 1998.

Principal Investigator, “Young Investigator Award Matching,” Procter and Gamble Company,

$22,500 for the period March 1, 1993-February 28, 1997.

Principal Investigator, “NMR Studies of Elicitation-Mechanism and Metabolic Effects,” Welch

Foundation C-1197, $94,000 for the period June 1, 1993-May 31, 1996.

Principal Investigator (with San, K. Y.), “HPLC Photodiode Array and System Upgrade,” NSF

BES-9411928, $27,278 for the period August 1, 1994-July 31, 1996.

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Co-Principal Investigator [with Hughes, J. (P.I.)], “In situ Biochemical Remediation of

Trinitrotoluene-Contaminated Soils: Integrated Laboratory and Field Studies: Biochemical

Transformations and Pathways,” EPA Hazardous Substance Research Centers Program, $225,000

for the period February 1, 1994-September 30, 1995.

Principal Investigator, “NMR Studies of Biochemical Mechanism of Elicitation-Metabolic

Responses,” Welch Foundation Grant C-1197, $90,000 for the period June 1, 1990-May 31, 1993.

Principal Investigator, “Probing Cellular Processes for Productivity Enhancement in Hairy Root

Cultures of C. roseus,” NSF Grant BCS-9009992, $72,800 for the period July 1, 1990-February 28,

1993.

Co-Principal Investigator [with Mikos, A. (P.I.), Zygourakis, K. (co-P.I.)], “Gel Permeation

Chromatography,” NSF Grant BCS 9213197, $26,567 for the period August 1992-July 1993.

Principal Investigator (with Gustin, M.), “Refractive Index Detector for the HPLC,” National

Institute of Health (NIH) Small Instrumentation Grant (administered by Rice), $6,415,

September 1, 1992.

Co-Principal Investigator (with McIntire, L. V., et al.), “Ultra Low Temperature Freezer,” NIH

Small Instrumentation Grant (administered by Rice), $5,294, September 1, 1992.

Principal Investigator, “MAC Computer for Development of the ChE Programs and Modules,” Rice

University Undergraduate Teaching Committee and the Brown Foundation, $7,838, June 1992.

Principal Investigator, “Herschel Rich Invention Award,” Rice Engineering Alumni Association

Award, $1,000, April 23, 1992.

Principal Investigator (with King, G. C.), “NMRi Software for the Rice University 500 MHz NMR

Center,” New Methods Research Inc. Grant, $35,000 for the period October 1, 1990-November 1,

1991.

Co-Principal Investigator [with Mikos, A. (P.I.), Zygourakis, K. (Co-P.I.)], “UV/VIS System,” NIH

Biomedical Research Support Grant (administered by Rice), $3,100, September 1, 1992.

Principal Investigator, “Outstanding Young Faculty in Engineering,” Amoco Foundation Grant,

$1,750, June 27, 1991.

Co-Principal Investigator [with King, G. C. (P.I.), et al.], “Purchase of a 500 MHz NMR System,”

NIH Grant RR05759-01, $400,000 for the period May 1990-May 1991.

Co-Principal Investigator (with McIntire, L.V., et al.), “Flow Cytometer for Biochemical

Engineering Research,” NSF Grant EET-89-6775, $89,400 for the period July 1989-July 1990.

Principal Investigator, “Microcomputer Grant,” Rice University Grant, $2,500 for the period

August 1988-July 1989.

Principal Investigator, “Faculty Research Grant,” Rice University Grant, $977 for the period

August 1988-July 1989.

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Thesis Research Directed

Doctoral Theses:

Hei-Chan Lee (Principal-Advisor: Glacken, M. W.), “Metabolic Characterization of T Cell

Lymphoblastoid, Jurkat, in the Presence of Respiration Inhibitors in a Continuous Reactor” (1992).

Chih-Huang Ho, “Metabolic Studies of Catharanthus roseus Hairy Root Cultures by 31

P and 13

C

Nuclear Magnetic Resonance Spectroscopy” (1994).

Rajiv Bhadra, “Establishment, Cultivation, and Optimization of Hairy Roots of Catharanthus

roseus for the Synthesis of Indole Alkaloids” (1995).

Sundeep Vani, “Bioreactor Design for Scaleup of Catharanthus roseus Hairy Root Cultures for

Production of Indole Alkaloids” (1996).

Brenda Mann, “In vivo 31

P and 13

C Nuclear Magnetic Resonance Spectroscopy to Study Cellular

Metabolism” (1997).

Sushil Rijhwani, “Stress as a Means to Enhance Secondary Metabolite Productivity and to Probe

Metabolic Pathways” (1997).

John Morgan, “Analysis of Metabolic Flux of Secondary Metabolite Pathways of Catharanthus

roseus Hairy Root Cultures” (1999).

Erik Hughes (Principal-Advisor: San, K.Y.) “Metabolic Engineering of Catharanthus roseus Hairy

Roots Using an Inducible Promoter System” (2003).

Ganesh Sriram, “Flux Analysis in Central Carbon Metabolism in Plants: 13

C NMR Experiments and

Analysis” (2004).

Murali Subramanian. “TNT Phytotransformation in Native and Genetically Modified Species:

Significance of Aromatic Hydroxlamines in the Metabolic Pathway” (2004).

Vidya Iyer. “13

C Metabolic Flux Analysis of Soybean Central Carbon Metabolism: Response to

Temperature and Genotype Effects” (2006).

Guy Sander. “Quantitative Analysis of Metabolic Pathways in Catharanthus roseus Hairy

Roots Metabolically Engineered for Terpenoid Indole Alkaloid Overproduction” (2009).

Master Theses:

Marie Dominique Fernet, “High Resolution NMR Studies of Metabolism in Wild-Type and High

Osmolarity Mutants of S. cerevisiae” (1992).

John Lauritzen, “Catharanthus roseus as a Model System for the Study of the Phytoremediation of

TNT” (1998).

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Vidya Iyer, “Metabolic Fluxes in Developing Soybean Embryos Grown at Varying Temperatures,

Quantified by Biosynthetically Directed Fractional 13-C Labeling Experiments” (2003).

Sarah Rollo, “Phytotransformation of Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX): A Study of

the Biochemical Pathway in Arabidopsis thaliana” (2005).

Madhuresh Choudhury, “Metabolic Engineering of Escherichia coli for the Efficient Utilization of

Plant Sugar Mixtures,” (2008).

Marvin Mercado, “Standard Operating Procedures for Flux Analysis in Escherichia coli,” Oral

Defense (2009) .

Yanfen Fu, “Metabolic Flux Analysis of Escherichia coli MG1655 Under Octanoic Acid

Stress,” (2011).

Teaching Experience:

Iowa State University

Primary:

ChE 210 (U) “Material and Energy Balances” Fall 1999, 2000, 2002, 2007; Spring 2010

Use of basic mathematical concepts, physical laws, stoichiometry, and thermodynamic

properties of matter to obtain material and energy balances for steady state and

unsteady state systems

ChE 325 (U) “Chemical Engineering Lab I” Spring 2000

Friction factor and viscosity lab modules

ChE 381 (U) “Thermodynamics” Spring 2001, 2003, 2008; Fall 2006; Spring 2008, 2009

ChE 406 (U) “Environmental Chemodynamics” Fall 2004, 2005, 2008, 2009,2011

ChE 415/515 (U/G) “Biochemical Engineering” Spring 2005, 2006, 2007

ChE 525X (U/G,N) “Metabolic Engineering” Spring 2002

ChE 525L (U/G,N) “Metabolic Engineering Laboratory” Spring 2002

Engr 101 (U) “Seminar for Freshmen in Chemical Engineering” Fall 2000-2003

Rice University

Primary:

Bioe 698 (G) “Graduate Seminar” Fall 1998

Ceng 301 (U) “Chemical Engineering Fundamentals” Fall 1988-1994; 1996-1998

Use of basic mathematical concepts, physical laws, stoichiometry, and thermodynamic

properties of matter to obtain material and energy balances for steady state and

unsteady state systems.

Bioe 562; Ceng 562 (G, N) Spring 1989; 1991; 1994; 1997

“NMR Applications in Engineering” (Formerly Ceng 720; 582)

Survey of the basic principles and applications of nuclear magnetic resonance

spectroscopy to bioengineering and chemical engineering problems, using material

from the current literature. Includes in vivo NMR, imaging, NMR microscopy,

2-dimensional methods, solid state.

Ceng 662 (G) “Graduate Seminar” Spring 1990, 1995

Nsci 102 (U) “Natural Science” Spring 1992

Guest Lecturer:

Bioe 551 “Introduction to Bioengineering” Phytocatalysis

Bios 425 “Plant Molecular Biology” Metabolic Engineering in Plants

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Bios 482 “NMR Spectroscopy” In Vivo NMR; Enzyme Kinetics in vivo

Hons 470 “Rice University Scholars Program” Effective Oral Presentations

Caltech

Ch. E. 163 (G) “Biochemical Engineering” (with Prof. James E. Bailey) 1985

U=Undergraduate; G=Graduate; N=New Course not Previously Given

University Service:

Iowa State University

University:

Engineering Curriculum Committee 2002-2005

Engineering Representative, Radiation Safety Committee 2004-2011

Faculty Senate Women and Minorities Committee 2000-2001

College of Engineering Cluster Champion (Bio) 2008-2009

Dean of Engineering Search Committee 2008-2009

University (General):

Engineering Representative, Biotechnology Council 2008-2011

Engineering Representative, Plant Sciences Institute Council 2003-2008

Plant Sciences Institute Graduate Fellowship Committee 2004-2007

Faculty Search Committee, Dept. of Food Science and Nutrition 1999-2002

Chemical Engineering:

Faculty mentor, Dr. Laura Jarboe 2008- present

Promotion and Tenure Committee, Chair 2006-2010

Safety Committee 2005-2008

Chair Search Committee 2004-2005

Post Tenure Review 2003-2006

Faculty mentor, Dr. Ramon Gonzalez 2002-2005

Governance Committee, Chair 2004-2005

Governance Committee 2002-2005

Curriculum Committee, Chair 2001-2004

Scholarship Committee 1999-2003

Faculty Search Committee, Chair 2000-2002

Faculty Search Committee 1999-2000, 2002-2003, 2007-2008, 2011-2012

Undergrad Recruiting & Minority Student Enhancement 1999-2001, 2005-2007

Internet Committee 1999-2001

Rice University

University Standing Committees:

Committee on Affirmative Action 1989-1993

University Council 1990

Faculty Council 1990

Marshalls Committee 1996-1998

Rice Athletic Committee 1996-1999

Chair, Rice Athletic Committee 1998-1999

University (General):

Wiess College Faculty Associate 1989-1995

Academic Blue Chip Recruiter for Admissions 1989-1999

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Faculty Club Board of Directors 1991-1995

Nanotechnology Task Force 1993-1994

Provost Search Committee 1993-1994

Nanotechnology Committee 1994-1996

Sid Rich College Faculty Associate 1998-1999

Rice Women’s Conference Planning Committee 1998-1999

Engineering and Sciences:

Chair of SWE Panel and Open Forum on Women in Engineering, Rice 1990

Dean’s Committee on a new course in Technology 1991

Tau Beta Pi Advisor 1994-1996

Clare Booth Luce Fellowship Committee and Mentor 1994-1996

Co-Chair (w/Joe Hughes) Engineering Ad hoc Committee on Dept. Structure 1997

Natural Science Curriculum Committee 1998-1999

Bioengineering:

Curriculum Development Committee 1993-1998

Undergraduate Committee 1996-1999

Faculty Search Committee 1997-1999

Chair, Undergraduate Committee 1998-1999

Chemical Engineering:

Undergraduate Committee 1988-1999

Library Representative 1989-1991

Graduate Student Symposium 1990 and 1991, 1995

Strategic Plan Committee 1996

Faculty Search Committee 1997-1998

Professional Service:

Editorial and Advisory Board Memberships

Guest Editor, Biochemical Engineering, Current Opinion in Biotechnology 2000

Associate Editor, Biotechnology Progress 2002-2003

Guest Editor, Metabolic Engineering 2002

Editorial Advisory Board, Biotechnology Progress 2000-present

Scientific Advisory Committee, Metabolic Engineering VI Conference 2005-2006

Advisory Board, NSF project: Educational Materials to Enhance CHE Curricula with 2007-2009

Biological Applications, San Jose State University and University of Arkansas

Editorial Advisory Board, Current Opinion in Biotechnology 2010-present

Advisory Board, DOE, The Office of Biological and Environmental Research (BER) 2011-present

Advisory Committee (BERAC)

National Committees, Workshops

National Research Council Committee on Biobased Industrial Products 1994-1999

National Academy of Engineering Workshop, “Academic Engineering February 1994

Research in a Changing World”

USDA Cooperative State Research, Education, and Extension February 4-8, 2001

Service (CSREES) Review Team, Agricultural and Biological

Engineering Department, Purdue University

Metabolic Engineering, Young investigator award, subcommittee member 2002, 2004

ACS, BIOT Division, various award committees, subcommittee member 2003-present

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AIChE, FP&BE Award Committee, subcommittee member 2007

Search Committee for Editor of Biotechnology Progress 2009-2010

NSF Math and Physical Science (MPS) Energy Workshop (invited speaker) March, 2010

Arlington, VA 22230.

Workshops

Plasma Workshop, National Center for Genome Resources, Santa Fe, NM May 1999

Zia Symposium and Workshop on Computer Modeling of Plant January 2000

Metabolism, Las Cruces, NM

Division Officer Training Conference, ACS, Clearwater Beach, FL January 2000

Malaysian-MIT Biotechnology Partnership Program Workshop, May 2000

Bioreactor Processes for Plant Cell Cultures, Cambridge, MA

“Coaching Strong Women in the Art of Strategic Persuasion” November 2001

Workshop sponsored by the Committee on the Advancement of

Women Chemists, ACS, Reno, NV

“Using Assessment Effectively” workshop sponsored by Fall 2001

Dr. Mary Huba, ISU Center for Teaching Excellence, Ames, IA

Offices

Steering Committee of the HSEMB 1991-1995

ACS Alternate Councilor, BIOT Division 1995-1997

ACS Newsletter Editor, BIOT Division 1998-2000

ACS Chair-Elect, BIOT Division 2000

ACS Chair, BIOT Division 2001

ACS Past-Chair, BIOT Division 2002

Organizer of Symposia

Organizer of Biotechnology Symposia of HSEMB 1991-1995

Chair of Sessions

Chair of Biotechnology Sessions of HSEMB 1990-1992, 1994, 1997

AIChE, Chair of Plant Tissue Culture Sessions 1993, 1994, 2003

ACS, Chair of Plant Tissue Culture Sessions 1996

ACS, Chair of Biocatalysis/Bioremediation Session 1998

ACS, Chair of Plant Transgenic/Engineering Session 1999

Metabolic Engineering Conference, Chair of Plant Met. Engineering 2002

ACS, Chair of Plant Transgenic/Engineering Session 2003

Natural Products Conference, Chair of Cell Environment Optimization 2006

Natural Products Conference, Chair of Plant Cell Culture Session 2008

Metabolic Engineering Conference, Chair of Nutrition and Agriculture Session 2008

Reviewer

Research Proposals and Panels:

Australian Research Council, Large Research Grants Program

Interagency Panel on Metabolic Engineering proposals

NSF

NIH

NSF Panel on Emerging Frontiers in Research and Innovation; Engr.

NSF Panel on Career Awards; Biotech. and Bioeng.

NSF Panel on Quantitative Systems Biology; Biotech. and Bioeng.

NSF Panel on SBIR proposals; Biotech. and Bioeng.

NSF Panel on Engineering Equipment proposals; Biotech. and Bioeng.

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NSF Panel on Research Initiation proposals; Biotech. and Bioeng.

NSF and EPA Panel on Sustainable Technology

U.S. Department of Agriculture

U.S. Department of Energy

U.S. Department of Energy, site-visit reviewer for JBEI center renewal

Manuscripts:

AIChE Journal

Biotechnology and Bioengineering

Biotechnology Progress

Chemosphere Environmental Science and Technology

Enzyme and Microbial Technology

International Journal of Phytoremediation

JACS

Journal of Biological Chemistry

Journal of Biotechnology

Journal of Experimental Botany

Mathematical Biosciences

Metabolic Engineering

Plant Physiology

Phytochemistry

Phytochemistry Reviews

Tissue Engineering

Trends in Biotechnology

Community Service:

Memorial Drive Presbyterian Church Sunday School Teacher, Older 2s 1995-1996

Memorial Drive Presbyterian Church Sunday School Teacher, Older 2s 1998-1999

MDPC Little Yellow School House Science Lecture, Volunteer 1997-1998

Bunker Hill Elementary Volunteer 1998-1999

Westview School for Special Needs, Volunteer 1998-1999

Collegiate Presbyterian Church, Christian Education, early youth 2000-2002

Collegiate Presbyterian Church, Christian Education, youth 2002-2008

Collegiate Presbyterian Church, Design Committee 2003-2004

Collegiate Presbyterian Church, University Ministry Committee 2004-2005, 2008

Sawyer Elementary Volunteer 2000-2007

"A Noble Tale of Plant Chemotherapy Drugs", Talk to Golden K Kiwanis,

Ames, IA August 7, 2008

Research Publications:

h-index: 20

Number of Citations (Thomson ISI) shown in [square brackets] for selected publications as of

January, 2012

1. Galazzo, J. L., Shanks, J. V. and Bailey, J. E., “Comparison of Suspended and Immobilized Yeast

Metabolism Using 31

P Nuclear Magnetic Resonance Spectroscopy,” Biotechnology Techniques, 1, 1-

6 (1987).

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2. Bailey, J. E., Axe, D. D., Doran, P. M., Galazzo, J. L., Reardon, K. F., Seressiotis, A. and Shanks, J.

V., “Redirection of Cellular Metabolism: Analysis and Synthesis,” Ann. N. Y. Acad. Sci., 506, 1-23

(1987).

3. Bailey, J. E., Khosla, C., and Shanks, J. V., “Enhancement of Cell Growth Characteristics Using

Genetic Engineering,” Proceedings 8th International Biotechnology Symposium, in Paris, 424-432

(1988).

4. Shanks, J. V. and Bailey, J. E., “Estimation of Intracellular Sugar Phosphate Concentrations in

Saccharomyces cerevisiae Using 31

P Nuclear Magnetic Resonance Spectroscopy,” Biotechnol.

Bioeng., 32, 1138-1152 (1988).

5. Shanks, J. V. and Bailey, J. E., “Elucidation of the Cytoplasmic and Vacuolar Components in the

Intracellular Inorganic Phosphate Region in the 31

P NMR Spectrum of Yeast,” Biotechnol. Bioeng.,

35, 1102-1110 (1990).

6. Bailey, J. E., Birnbaum, S., Galazzo, J. L., Khosla, C. and Shanks, J. V., “Strategies and Challenges

in Metabolic Engineering,” Ann. N. Y. Acad. Sci., 589, 1-15 (1990).

7. Galazzo, J. L., Shanks, J. V. and Bailey, J. E., “Comparison of Intracellular Sugar-Phosphate Levels

from 31

P Nuclear Magnetic Resonance Spectroscopy of Intact Cells and Cell-Free Extracts,”

Biotechnol. Bioeng., 35, 1164-1168 (1990).

8. Shanks, J. V. and Bailey, J .E., “Comparison of Wild-Type and Reg1 Mutant Saccharomyces

cerevisiae Metabolic Levels During Glucose and Galactose Metabolism Using 31

P NMR

Spectroscopy,” Biotechnol. Bioeng., 35, 395-407 (1990).

9. Bhadra, R., Ho, C.-H., Rosi, S. and Shanks, J. V., “Establishment and Cultivation of Hairy Root

Lines of Catharanthus roseus ,” In Vitro Cell. Dev. Biol., 26, 69A (1990).

10. Bailey, J. E. and Shanks, J. V., “31

P and 13

C NMR Studies of Recombinant Saccharomyces

cerevisiae with Altered Glucose Phosphorylation Activities,” Bioprocess Engineering, 6, 273-284

(1991). (Error in order of authors in final print; should be Shanks and Bailey).

11. Bhadra, R., Ho, C.-H., and Shanks, J. V., “Growth Characteristics of Hairy Root Lines of

Catharanthus roseus,” In Vitro Cell. Dev. Biol., 27, 109A (1991).

12. Ho, C.-H. and Shanks, J. V., “Effects of Initial Medium pH on Growth and Metabolism of Hairy

Root Cultures of Catharanthus roseus-A Study with 31

P and 13

C NMR Spectroscopy,” Biotechnol.

Lett., 14, 959-964 (1992).

13. Bhadra, R., Vani, S. and Shanks, J. V., “Production of Indole Alkaloids by Selected Hairy Root

Lines of Catharanthus roseus,” Biotechnol. Bioeng., 41, 581-592 (1993).

14. Fernet, M.-D., Melvin, B., Gustin, M. and Shanks, J. V., “13

C NMR Spectroscopy Studies of

Glucose Metabolism in Osmolarity Mutants of Saccharomyces cerevisiae,” Enzyme and Microbial

Technology, 16, 207-215 (1994).

15. Bhadra, R. and Shanks, J. V., “Statistical Design of the Effect of Inoculum Conditions on Growth of

Hairy Root Cultures of Catharanthus roseus,” Biotechnology Techniques, 9, 681-686 (1995).

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16. Melvin, B. K. and Shanks, J. V., “Influence of Aeration on Cytoplasmic pH of Yeast in an NMR

Airlift Reactor,” Biotechnology Progress, 12, 257-265 (1996).

17. Lauritzen, J., Hughes, J. and Shanks, J. V., “Phytoremediation of TNT: C. roseus Hairy Roots as a

Model System,” Proceedings of the Fifth World Congress of Chemical Engineering, 3, 795-800

(1996).

18. Hughes, J. B., Shanks, J., Vanderford, M., Lauritzen, J. and Bhadra, R., “Transformation of TNT by

Aquatic Plants and Plant Tissue Cultures,” Environmental Sci. and Tech., 31, 266-271 (1997).

19. Vanderford, M., Shanks, J. V. and Hughes, J. B., “Phytotransformation of Trinitrotoluene (TNT) and

Distribution of Metabolic Products in Myriophyllum aquaticum,” Biotechnology Letters, 19, 277-280

(1997).

29. Bhadra, R. and Shanks, J. V., “Transient Studies of Nutrient Uptake, Growth, and Indole Alkaloid

Accumulation in Heterotrophic Cultures of Hairy Roots of Catharanthus roseus” Biotechnology and

Bioengineering, 55, 527-534 (1997).

21. Shanks, J. V., Bhadra, R., Morgan, J., Rijhwani, S. K., and Vani, S., “Quantification of Metabolites

in the Indole Alkaloid Pathways of Catharanthus roseus: Implications for Metabolic Engineering,”

Biotechnology and Bioengineering, 58, 333-338 (1998).

22. Rijhwani, S. K. and Shanks, J. V., “Effect of Subculture Cycle on Growth and Indole Alkaloid

Biosynthesis by Catharanthus roseus Hairy Root Cultures,” Enzyme and Microbial Technology, 22,

606-611 (1998).

23. Rijhwani, S. K. and Shanks, J. V., “Effect of Elicitor Dosage and Exposure Time on Biosynthesis of

Indole Alkaloids by Catharanthus roseus Hairy Root Cultures,” Biotechnology Progress, 14, 442-

449 (1998).

24. Bhadra, R., Morgan, J. and Shanks, J. V., “Transient Studies of Light-adapted Cultures of Hairy

Roots of Catharanthus roseus: Growth and Indole Alkaloid Accumulation,” Biotechnology and

Bioengineering, 60, 670-678 (1998).

25. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Biochemical Pathways of 2,4,6-TNT

Abatement by Phytoremediation,” AIChE Symposium Series, Topical Conference on Pollution

Prevention and Environmental Reduction, Miami Beach, FL, (1998).

26. Morgan, J. and Shanks, J. V., “Inhibitor Studies of Tabersonine Metabolism in Catharanthus roseus

Hairy Roots,” Phytochemistry, 51, 61-68 (1999).

27. Rijhwani, S. K., Ho, C.-H. and Shanks, J. V., “In vivo 31

P and Multilabel 13

C NMR Measurements

for Evaluation of Plant Metabolic Pathways” Metabolic Engineering, 1, 12-25 (1999).

28. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Confirmation of Conjugation Processes

during TNT Metabolism by Axenic Plant Roots,” Environmental Sci. and Tech., 33, 446-452 (1999).

30. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Conjugate Formation During the

Metabolism of 2,4,6-Trinitrotoluene in Plant Roots,” in A. Leeson and B. C. Alleman (Eds.),

Phytoremediation and Innovation Strategies for Specialized Remedial Applications, Vol. 5(6),

pp. 21-125, Batelle Press, Columbus, OH (1999).

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31. Shanks, J. V., Morgan, J., “Plant Hairy Root Culture,” Current Opinion in Biotechnology, 10, 151-

155 (1999).

32. Bhadra, R., Wayment, D., Hughes, J. and Shanks, J. V., “Characterization of Oxidation Products of

TNT Metabolism in Aquatic Phytoremediation Systems of Myriophyllum aquaticum,”

Environmental Sci. and Tech., 33, 3354-3361 (1999).

33. Wayment, D. G., Bhadra, R., Lauritzen, J., Hughes, J. and Shanks, J. V., “A Transient Study of

Formation of Conjugates During TNT Metabolism by Plant Tissues,” International Journal of

Phytoremediation, 1(3), 227-239 (1999).

34. Morgan, J. A., Barney, C. S., Penn, A.H. and Shanks, J. V., “The Effect of Buffered Media on

Growth and Alkaloid Productivity of C. roseus Hairy Root Cultures,” Applied Microbiology and

Biotechnology, 53, 262-265 (2000).

35. Bhadra, R., Spanggord, R. J., Wayment, D., Hughes, J. and Shanks, J. V., “Oxidative Metabolism of

2,4,6- Trinitrotoluene in Aquatic Phytoremediation Systems of Myriophyllum aquaticum,” Wetlands

Remediation Int. Conf., 127-132 (2000).

36. Morgan, J. and Shanks, J. V., “Determination of metabolic rate-limitations by precursor feeding in

Catharanthus roseus hairy root cultures,” Journal of Biotechnology, 79, 137-145 (2000).

37. Shanks, J. V. and Stephanopoulos, G. “Biochemical Engineering: Bridging the Gap between Gene

and Product,” Current Opinion in Biotechnology, 11, 169-170 (2000).

38. Shanks, J. V. “In Situ NMR Systems,” Current Issues in Molecular Biology, 3, 15-26 (2001).

39. Bhadra, R., Wayment, D. G., Williams, R. K., Barman, S. N., Stone, M. B., Hughes, J. B., and

Shanks, J. V., “Studies on plant-mediated fate of the explosives RDX and HMX,” Chemosphere,

44/5, 1259-1264 (2001).

40. Sriram, G. and Shanks, J. V., “A mathematical model for carbon bond labeling NMR experiments:

Analytical solutions and sensitivity analysis for the effect of reaction reversibilities on estimated

fluxes.” Proc. 31st Annual Biochemical Engineering Symposium, Manhattan, KS, September 08,

2001, 45–54.

41. Hughes, E. and Shanks, J. V., “Metabolic Engineering of Plants for Alkaloid Production,” Metabolic

Engineering, 4, 41-48 (2002).

42. Hansen, A. and Shanks, J. V., “Plant Metabolic Engineering-Entering the S Curve,” Metabolic

Engineering, 4, 1-2 (2002).

43. Morgan, J. and Shanks, J. V., “Quantification of Metabolic Flux in Plant Secondary Metabolism by a

Biogenetic Organizational Approach,” Metabolic Engineering, 4, 257-262 (2002).

44. Hughes, E. Hong, S.-B., Shanks, J. V., San K.-Y., and Gibson, S. I. “Characterization of an

Inducible Promoter System in Catharanthus roseus Hairy Roots,” Biotechnology Progress, 18,

1183-1186 (2002).

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45. Iyer, V. V., Sriram, G., Fulton, D. B., Westgate, M. E., Spalding, M. H., and Shanks, J. V.,

“Development of NMR tools to obtain metabolic flux maps for soybean seeds.” Proc. 32nd Annual

Biochemical Engineering Symposium, Ames, IA, October 5 (2002) 83-89.

46. O. González-Rivera, Sriram, G., and Shanks, J. V., “Determination of the biomass composition of

Catharanthus roseus hairy roots.” Proc. 32nd Annual Biochemical Engineering Symposium, Ames,

IA, October 5, (2002) 65-70.

47. Hong, S. B., Hughes, E. K., Shanks, J. V., San, K. Y., and Gibson, S. “Role of the Non-Mevalonate

Pathway in Indole Alkaloid Production by Catharanthus roseus Hairy Roots,” Biotechnology

Progress, 19, 1105-1108 (2003).

48. Shanks, J. V., Oliver, D. J., Moon H., Rollo, S., and Subramanian, M., “Genetic and Biochemical

Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs) by Plants,” Proceedings of

the American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 16-21

(2003). Paper62d.

49. Moon, H., Subramanian, M., Rollo, S., Oliver, D. J., Shanks, J. V., and Moon, Hangsik, “Use of

Arabidopsis as a Model System for Genetic and Biochemical Studies of TNT Transformation in

Plants,” Proceedings of the First Conference on Sustainable Range Management, B. Alleman and

S. Downes (Eds), New Orleans, LA, January 5-8 (2004), Paper C3-04.

50. Sriram, G. and Shanks, J. V., “Improvements in Metabolic Flux Analysis using Carbon Bond

Labeling Experiments: Bondomer Balancing and Boolean Function Mapping,” Metabol. Eng, 6,

116-132 (2004).

51. Hughes, E., Hong, S.-B., Shanks, J. V., San, K.-Y., and Gibson, S. I. “Expression of a Feedback-

Resistant Anthranilate Synthase in Catharanthus roseus Hairy Roots Provides Evidence for Tight

Regulation of Terpenoid Indole Alkaloid Levels,” Biotechnol. Bioeng., 86, 718-727 (2004).

52. Hughes, E. H., Hong, S.-B., Gibson, S. I., Shanks, J. V., and San, K.-Y., “Metabolic Engineering of

the Indole Pathway in Catharanthus roseus Hairy Roots and Increased Accumulation of Tryptamine

and Serpentine,” Metabolic Engineering, 6, 268-276 (2004).

53. Sriram, G., Fulton, D. B., Iyer, V. V., Peterson, J. M., Zhou, R., Westgate, M. E., Spalding, M. H.,

and Shanks, J. V., “Quantification of Compartmented Metabolic Fluxes in Developing Soybean

(Glycine max) Embryos by Employing Biosynthetically Directed Fractional 13

C Labeling, 2-D

[13

C, 1H] NMR and Comprehensive Isotopomer Balancing,” Plant Physiol. 136, 3043-3057 (2004).

54. Rollo, S., Moon, H., Subramanian, M., Oliver, D. J., and Shanks, J. V., “Toxicity of RDX on

Germination of Arabidopsis thaliana,” Proceedings of the 33rd Annual Biochemical Engineering

Symposium, Lincoln, NE, April (2004).

55. Rollo, S., Moon, H., Subramanian, M., Oliver, D. J., and Shanks, J. V., “Phytoremediation of RDX:

Using Arabidopsis thaliana to Determine the Genetics and Biochemistry of the Transformation

Pathway,” Proceedings of the American Institute of Chemical Engineers Annual Meeting, Austin,

TX, November (2004), Paper 285e.

56. Shanks, J. V., “Phytochemical engineering: Combining Chemical Reaction Engineering with Plant

Science,” AIChE Journal 51, 2-7, (2005).

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57. Peebles, C.A.M., Hong, S.-B., Gibson, S. I., Shanks, J. V., and San, K.-Y., “The Transient Effects

of Over-expressing Anthranilate Synthase α and β subunits in Catharanthus roseus Hairy Roots,”

Biotech. Progress, 21, 1572-1576, (2005).

58. Hong, S.-B., Peebles, C.A.M., Shanks, J. V., San, K.-Y., and Gibson, S. I., “Expression of the

Arabidopsis feedback-insensitive Anthranilate Synthase Induced by Holoenzyme and Tryptophan

Decarboxylase Genes in Catharanthus roseus Hairy Roots,” J. Biotech., 122, 28-38, (2006).

59. Hong, S.-B., Peebles, C.A.M., Shanks, J. V., San, K.-Y., and Gibson, S. I., “Terpenoid Indole

Alkaloid Production by Catharanthus roseus Hairy Roots Induced by Agrobacterium tumefaciens

Harboring rol ABC Genes,” Biotech. Bioeng., 93, 386-390, (2006).

60. Peebles, C. A.M., Hong, S.-B., Gibson, S. I., Shanks, J. V., and San, K.-Y., “Effects of Terpenoid

Precursor Feeding on Catharanthus roseus Hairy Roots Over-expressing the alpha or the alpha and

beta Subunits of Anthranilate Synthase,” Biotech. Bioeng., 93, 534-540, (2006).

61. Subramanian, M., Oliver, D. J. and Shanks, J. V. “TNT Phytotransformation Pathway

Characteristics in Arabidopsis: Role of Aromatic Hydroxylamines,” Biotech. Progress, 22, 208-216,

(2006).

62. Glatz, C. E., Gonzalez, R., Huba, M., Mallapragada, S. K., Narasimhan, B., Reilly, P. J., Saunders,

K., and Shanks, J. V. “Problem-Based Learning Biotechnology Courses in Chemical Engineering,”

Biotechnology Progress, 22, 173-178 (2006).

63. Yoon, J. M., Oliver, D. J., Shanks, J. V., “Phytotransformation of 2,4-Dinitrotoluene in Arabidopsis

thaliana: Toxicity, Fate, and Gene Expression Studies in vitro”, Biotechnology Progress, 22, 1524 -

1531 (2006).

64. Sriram, G., González-Rivera, O. and Shanks, J. V. “Determination of Biomass Composition of

Catharanthus roseus Hairy Roots for Metabolic Flux Analysis,” Biotechnology Progress, 22, 1659

- 1663 (2006).

65. Yoon, J. M., Oliver, D. J., Shanks, J. V., “Phytotransformation and Phytoremediation of 2,6-

Dinitrotoluene using a Model Plant, Arabidopsis thaliana”, Chemosphere, 68,1050–1057 (2007).

66. Hannink, N. K., Subramanian M., Rosser, S. J., Basran A., Murray, J. A. H., Shanks, J. V. and

Bruce, N. C. “Enhanced Transformation of TNT by Tobacco Plants Expressing a Bacterial

Nitroreductase,” International Journal of Phytoremediation, 9, 385-401 (2007).

67. Sriram, G., Fulton, D. B. and Shanks, J. V. “Flux Quantification in Central Carbon Metabolism of

Catharanthus roseus Hairy Roots by 13

C Labeling and Comprehensive Bondomer Balancing”,

Phytochemistry, 68, 2243-2257 (2007).

68. Sriram, G., Iyer, V. V., Fulton, D. B., and Shanks, J. V. “Identification of Hexose Hydrolysis

Products in Metabolic Flux Analytes: A Case Study of Levulinic acid in Plant Protein

Hydrolysate”, Metabolic Engineering, 9, 442-451 (2007).

69. Peebles, C.A.M., Gibson, S. I., Shanks, J. V., and San, K.-Y., “Characterization of an Ethanol

Inducible Promoter System in Catharanthus roseus Hairy Roots,” Biotechnology Progress, 23,

1258 -1260 (2007).

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70. Peebles, C.A.M., Gibson, S. I., Shanks, J. V., and San, K.-Y., “A Study on the Long-Term

Maintenance of a Transgenic Catharanthus roseus Hairy Root Line,” Biotechnology Progress, 23,

1517 -1518, (2007).

71. Iyer, V.V., Sriram, G., Fulton, D. B., Zhou, R., Westgate, M.E., and Shanks, J.V., “Metabolic Flux

Maps Comparing the Effect of Temperature on Protein and Oil Biosynthesis in Developing

Soybean Cotyledons” Plant Cell and Environment, 31 (4), 506–517 (2008).

72. Sander, G.W., Gibson, S.I., San, K.Y., and Shanks, J.V., "Metabolic Engineering of Catharanthus

roseus Hairy Roots for Terpenoid Indole Alkaloid Production under Light and Dark Conditions",

Proceedings of the 37th Annual Biochemical Engineering Symposium, 37, 39 - (2008).

73. Binder, B.Y.K., Peebles, C.A.M., Shanks, J.V., and K.-Y. San, “The Effects of UV-B Stress on the

Production of Terpenoid Indole Alkaloids in Catharanthus roseus Hairy Roots,” Biotechnol. Prog.

25, 861–865 (2009).

74. Peebles, C.A.M., E.H. Hughes, J.V. Shanks, and K.-Y. San, “Transcriptional response of the

terpenoid indole alkaloid pathway to the overexpression of ORCA3 along with jasmonic acid

elicitation of Catharanthus roseus hairy roots over time,” Metabolic Engineering, Metab. Eng., 11,

76-86 (2009).

75. Peebles, C.A.M., Sander, G.W., Li, M., Gibson, S.I., Shanks, J.V. and K.-Y. San, “Long term

maintenance of a transgenic Catharanthus roseus hairy root line expressing feedback-insensitive

anthranilate synthase holoenzyme,” Biotechnology and Bioengineering, 102, 1521 - (2009).

76. Peebles, C.A.M., Shanks, J.V., and K.-Y. San, “The role of the octadecanoid pathway in the

production of terpenoid indole alkaloids in Catharanthus roseus hairy roots under normal and UV-

B stress conditions,” Biotechnol. Bioeng. 103, 1248-1254 (2009).

77. Murarka, A., Clomburg, J. M., Moran, S., Shanks, J. V. and R. Gonzalez. “Metabolic Analysis of

Wild-Type Escherichia coli and a Pyruvate Dehydrogenase Complex (PDHC)-deficient derivative

reveals the Role of PDHC in the Fermentative Metabolism of Glucose,” J. Biological

Chemistry,285, 31548-31558 (2010).

78. Peebles, C.A.M., Sander, G. W., Hughes, E. H., Peacock, R., J.V. Shanks, and K.-Y. San, “The

Expression of 1-deoxy-D-xylulose Synthase and Geraniol 10-hydroxylase or Anthranilate Synthase

Increases Terpenoid Indole Alkaloid Accumulation in Catharanthus roseus Hairy Roots,”

Metabolic Engineering 13, 234-240 (2011). http://dx.doi.org/10.1016/j.ymben.2010.11.005

79. Li, M., Peebles, C.A.M., J.V. Shanks, and K.-Y. San, “Effect of Nitric Oxide on Growth and

Terpenoid Indole Alkaloid Production in Catharanthus roseus Hairy Root Cultures,” Biotechnology

Progress 27, 625-630 (2011).

80. Choudhary, M.K., Yoon, J.M., Gonzalez, R. and J.V. Shanks, “Re-examination of metabolic fluxes

in Escherichia coli during anaerobic fermentation of glucose using 13

C labeling experiments and 2-

dimensional nuclear magnetic resonance (NMR) spectroscopy,” Biotechnology and Bioprocess

Engineering 16, 419-437 (2011). DOI: 10.1007/s12257-010-0449-5

81. Iyer, V.V., Ling, L. Studham, M., Westgate, M.E., Wurtele, E.S. and Shanks, J.V. “Metabolic

Flux and Transcriptional Profiling of Soybean Isolines with Varying Protein Production,”

Submitted to Biochemical Journal, 2011.

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Books:

Committee on Biobased Industrial Products, “Biobased Industrial Products,” National Research

Council, National Academy Press, August 1999.

Book Foreword:

Foreword by J. V. Shanks. p. v-vi, Plant Metabolic Networks, J. Schwender, Ed. Springer Plant

Sciences, 2009, pp. 409

Book Chapters:

1. Shanks, J. V. and Bhadra, R., “Characteristics of Selected Hairy Root Lines of Catharanthus

roseus,” pp. 51-63 in Hairy Roots, P.M. Doran, Ed., Harwood Academic Publishers, Chur,

Switzerland, ©1997, pp. 237.

2. Morgan, J., Rijhwani, S. K., and Shanks, J. V., “Metabolic Engineering for the Production of Plant

Secondary Metabolites,” pp. 325-352 in Metabolic Engineering, S. Y. Lee and E. T. Papoutsakis,

Eds., Marcel Dekker, ©1999.

3. Rijhwani, S. K., Bhadra, R., Ho, C.-H., Morgan, J., Vani, S., and Shanks, J. V., “Quantification of

Metabolic Fluxes for Metabolic Engineering of Plant Products,” pp 45-60 in Plant Cell and Tissue

Culture for the Production of Food Ingredients, T. J. Fu, G. Singh, and W. R. Curtis, Eds., Plenum

Publishing Corporation, New York, NY, ©1999.

4. Shanks, J. V., “In situ NMR Systems,” in NMR in Microbiology: Theory and Applications, J.-N.

Barbotin and J.-C. Portais, Eds., Horizon Scientific Press, Wymondham, UK. ©2000.

5. Burken, J. G., Shanks, J. V., and Thompson, P. L., “Phytoremediation and Plant Metabolism of

Explosives and Nitroaromatic Compounds,” in Biodegradation of Nitroaromatic Compounds and

Explosives, J. Spain, J. Hughes, and H. Knackmuss, Eds., CRC Press, ©2000.

6. Subramanian, M. and Shanks, J. V., “Role of Plants in Transformation of Explosives” pp. 389-408

in Phytoremediation: Degradation and Control of Contaminants, S. McCutcheon and J.L. Schnoor,

Eds., Wiley and Sons, Inc., ©2003.

7. Yoon, J.M., Oliver, D.J. and Shanks, J. V. “Plant Transformation Pathways of Energetic Materials

(RDX, TNT, DNTs). pp. 103-116 in, Agricultural Biotechnology: Beyond Food and Energy to

Health and the Environment, National Agricultural Biotechnology Council Report 17, A.

Eaglesham, R. Bessin, R. Trigiano, R. W. T. Hardy, Eds. National Agricultural Biotechnology

Council, Ithaca, New York, ©2005.

8. Iyer, V. V., Sriram, G. and Shanks, J. V. “Metabolic Flux Maps of Central Carbon Metabolism in

Plants: Isotope Labeling Analysis.” pp 125-144 In Concepts in Plant Metabolomics, B. J. Nikolau

and E. S. Wurtele, Eds. Springer Publishers. April 2007.

9. Sriram G., Shanks J.V. “Application of Isotopomer Data and Mathematical Modeling in Flux

Quantification.” In: Mathematical Modeling in Nutrition and Health Sciences Hanigan M.D.,

Novotny J.A., Marstaller C.L., Eds., Virginia Tech press, Blacksburg, VA. ©2007.

10. Brown M., Shanks J.V. “Linear Hydrocarbon Producing Pathways in Plants, Algae and Microbes.”

pp 1-12 In: Sustainable Bioenergy and Bioproducts , Gopalakrishnan, K., van Leeuwen J.H.,

Brown R.L., Eds., Springer-Verlag, © 2012, DOI: 10.1007/978-1-4471-2324-8.

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11. Truong, Q., Yoon, J.M., and Shanks, J. V. “Isotopomer Measurement Techniques in Metabolic

Flux Analysis: NMR” In, Plant Metabolism: Methods and Protocols. Methods in Molecular

Biology. Sriram, G. Eds. Humana Press, In press.

Technical Reports:

1. Hughes, J. and Shanks, J. V., “Biochemical Transformations and Pathways From Phytoremediation

of TNT-Contaminated Soils,” Research Brief #11, Hazardous Substance Research Center/South &

Southwest, 1996.

2. Shanks, J. V., “Phytoremediation of TNT: C. roseus Hairy Roots as a Model System,” Course

Notebook, IBC Conference on Phytoremediation, Washington, DC, May 1996.

3. Shanks, J. V., Oliver, D.J., Moon, H. Subramanian, M., Yoon, J.M., Rollo, S. “Genetic and

Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs) by Plants,”

SERDP Final Report, Washington, D.C., April 2007.

Technical Software:

NMR2Flux, ISURF 3399, Iowa State University, Sriram, G. and Shanks, J. V., © 2005.

Educational Publications:

1. Davis, S. H. and Shanks, J. V., “Computer Tools For Chemical Engineering Courses at Rice

University,” ASEE Annual Conference Proceedings, Vol. II, 1459-1463 (1991).

2. Davis, S. H. and Shanks, J. V., “Computer Modules for Chemical Engineering Flowsheet

Simulation,” Annual Meeting, AIChE, Software Presentation, AIChE Manuscript, pp. 24 (1991).

3. Davis, S. H. and Shanks, J. V., “Simulation Programs Used in Chemical Engineering at Rice

University,” ASEE Annual Conference Proceedings, Vol. II, 1034-1037 (1992).

4. Glatz, C. E., Gonzalez, R., Huba, M., Mallapragada, S. K., Narasimhan, B., Reilly, P. J., Saunders,

K., and Shanks, J. V. “Problem-Based Learning Biotechnology Courses in Chemical Engineering,”

Biotechnology Progress, 22, 173-178 (2006).

Textbooks:

Davis, S. H. and Shanks, J. V., Chemical Engineering Fundamentals, Rice University, ©1989,

©1990, ©1991, ©1992, ©1993, ©1994, pp. 231.

Textbook Web Site:

Davis, S. H. and Shanks, J. V., Chemical Engineering Fundamentals, Rice University. 1996, 1997,

1998 http://www.owlnet.rice.edu/~ceng301/

Educational Software:

Macintosh Simulation Programs, Chemical Engineering Dept., Rice University, Davis, S. H. and

Shanks, J. V., © 1991, © 1992.

Lecturer of Continuing-Education Courses:

“NMR Spectroscopy” in Advances in Tissue Engineering, Sponsored by Rice University, Houston,

TX, in August for the years 1993, 1994, 1995, 1996, 1997, 1998.

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Technical Presentations at Conferences-Abstracts:

1. “Application of 31

P NMR Spectroscopy to Fermentation Studies of Recombinant Saccharomyces

cerevisiae,” Annual Meeting, AIChE, New York, NY, November 1987.

2. “Comparison of Wild-Type and Reg1 Mutant Saccharomyces cerevisiae Metabolic Levels and

Rates Using in vivo 31

P NMR,” Annual Meeting, AIChE, Washington, DC, November 1988.

3. “Measurements of Intracellular Levels and pH using 31

P NMR,” Seventh Annual Conference on

Biomedical Research in Houston, Houston, TX, February 1989.

4. “Establishment and Cultivation of Hairy Root Lines of Catharanthus roseus,” Bhadra, R.,

Ho, C.-H., Rosi, S., and Shanks, J. V., Annual Meeting, Tissue Culture Association, In Vitro Cell.

Dev. Biol., 26, 69A (1990).

5. “Establishment and Cultivation of Hairy Root Lines of Catharanthus roseus,” Bhadra, R.,

Ho, C-H., and Shanks, J. V., Annual Meeting, AIChE, Chicago, IL, November 1990.

6. “Identification of Growth and Morphological Characteristics for the Selection of Hairy Root Lines

of C. roseus,” Bhadra, R. and Shanks, J. V., Ninth Annual Conference on Biomedical Engineering

Research in Houston, Houston, TX, February 1991.

7. “Selection and Growth Characteristics of Hairy Root Lines of Catharanthus roseus,” Bhadra, R.

and Shanks, J. V., Spring Meeting of the ACS, Atlanta, GA, April 1991.

8. “Use of NMR in Metabolic Engineering,” Biomedical and Biological Applications of Nuclear

Magnetic Resonance, Galveston-Houston Biological NMR Symposium, Galveston, TX, May 1991.

9. “Growth Characteristics of Hairy Root Lines of Catharanthus roseus,” Bhadra, R., Ho, C.-H., and

Shanks, J. V., Annual Meeting, Tissue Culture Association, In Vitro Cell. Dev. Biol., 27, 109A

(1991).

10. “Nutrient Utilization by Hairy Root Lines of Catharanthus roseus,” Bhadra, R., Vani, S. N., and

Shanks, J. V., Annual Meeting, AIChE, Los Angeles, CA, November 1991.

11. “A Novel Reactor for In Situ Studies of Organ Metabolism,” Ho, C.-H. and Shanks, J. V., Tenth

Annual Conference on Biomedical Engineering Research in Houston, Houston, TX, March 1992.

12. “Alkaloid Yields from Hairy Root Lines of C. roseus,” Vani, S. and Shanks, J. V., Tenth Annual

Conference on Biomedical Engineering Research in Houston, Houston, TX, March 1992.

13. “Alkaloid Production by Hairy Root Lines of Catharanthus roseus,” Bhadra, R., Vani, S., and

Shanks, J. V., Spring Meeting of the ACS, San Francisco, CA, April 1992.

14. “Transgenic Hairy Root Clones for Production of Indole Alkaloids,” Bhadra, R., Ho, C.-H.,

Vani, S. N., and Shanks, J. V., Ninth International Biotechnology Symposium and Exposition,

ACS, Crystal City, VA, August 1992.

15. “31

P and 13

C NMR Spectroscopy for Metabolic Studies of Hairy Roots: A Novel Micro-Reactor,”

Ho, C.-H. and Shanks, J. V., Annual Meeting, AIChE, Miami Beach, FL, November 1992.

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16. “NMR Spectroscopy Studies of Yeast in an Air-lift Reactor: Comparison of High to Low Cell

Densities,” Rodriguez, M., Mann, B., Fernet, M., and Shanks, J. V., Annual Meeting, AIChE,

Miami Beach, FL, November 1992.

17. “Effects of Initial Medium pH on Hairy Root Metabolism — A Study with 31

P and 13

C NMR

Spectroscopy,” Ho, C.-H. and Shanks, J. V., Annual Meeting, AIChE, Miami Beach, FL,

November 1992.

18. “31

P NMR Studies of Elicitor-Treated Catharanthus roseus Hairy Root Cultures,” Ho, C.-H. and

Shanks, J. V., Eleventh Annual Conference on Biomedical Engineering Research in Houston,

Houston, TX, February 1993.

19. “Effect of Illumination on Hairy Root Cultures of Catharanthus roseus,” Bhadra, R. and Shanks,

J. V., Annual Meeting, AIChE, St. Louis, MO, November 1993.

20. “Growth, Nutrient Utilization and Alkaloid Productivity of C. roseus Hairy Roots in Bioreactors,”

Vani, S. and Shanks, J. V., Annual Meeting, AIChE, St. Louis, MO, November 1993.

21. “NMR Studies of Catharanthus roseus Hairy Root Cultures in Response to Elicitation,”

Ho, C.-H. and Shanks, J. V., Annual Meeting, AIChE, St. Louis, MO, November 1993.

22. “Measurement of Oxygen Uptake Rates and Growth C. roseus Hairy Roots in a Bioreactor,”

Vani, S. and Shanks, J. V., Twelfth Annual Conference on Biomedical Engineering Research in

Houston, Houston, TX, February 1994.

23. “The Response of Hairy Root Cultures of Catharanthus roseus to Illumination” Bhadra, R. and

Shanks, J. V., Twelfth Annual Conference on Biomedical Engineering Research in Houston,

Houston, TX, February 1994.

24. “Reactor Studies of the Effect of CO2 Levels on the Metabolism of Catharanthus roseus Hairy

Roots,” Vani, S. and Shanks, J. V., Annual Meeting, AIChE, San Francisco, CA, November 1994.

25. “Effect of Scaleup on Metabolism of C. roseus Hairy Root Cultures,” Vani, S. and Shanks, J. V.,

Thirteenth Annual Conference on Biomedical Engineering Research in Houston, Houston, TX,

February 1995.

26. “Photoheterotrophic Culture of Hairy Roots of Catharanthus roseus for the Synthesis of Indole

Alkaloids,” Bhadra, R. and Shanks, J. V., Spring Meeting of the ACS, Anaheim, CA, April 1995.

27. “In vivo 13

C NMR Spectroscopy as a Tool to Study Aromatic Hydrocarbon Degradation,”

Melvin, B. K. and Shanks, J. V., Annual Meeting of the AIChE, November 1995.

28. “Elicitation Studies of Catharanthus roseus Hairy Root Cultures,” Rijhwani, S. K. and Shanks,

J. V., Annual Meeting of the AIChE, Miami Beach, FL, November 1995.

29. “Effect of Pectinase on Synthesis of Therapeutically Valuable Secondary Metabolites by

Catharanthus roseus Hairy Root Cultures,” Rijhwani, S. K. and Shanks, J. V., 14th Annual Houston

Conference on Biomedical Engineering Research, Houston, TX, February 1996.

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30. “Effect of Fungal Wall Components on Indole Alkaloid Synthesis by Catharanthus roseus Hairy

Root Cultures,” Rijhwani, S. K. and Shanks, J. V., National Meeting of the ACS, New Orleans, LA,

March 1996.

31. “An Inhibition ELISA for Measurement of Low Concentrations of Vinblastine, A Plant Secondary

Metabolite,” Budd, S. M. and Shanks, J. V., National Meeting of the ACS, New Orleans, LA,

March 1996.

32. “Phytoremediation of TNT: C. roseus Hairy Roots as a Model System,” Lauritzen, J., Hughes, J.,

and Shanks, J. V., Fifth World Congress of Chemical Engineering, San Diego, CA, July 1996.

33. “Phytoremediation of Explosives,” Hughes, J., Bhadra, R., Lauritzen, J., Vanderford, M., and

Shanks, J. V., Second Annual Symposium on Energy and the Environment, Energy and

Environmental Systems Institute, Rice University, Houston, TX, September 1996.

34. “Quantification of Fluxes in the Indole Alkaloid Pathways of Catharanthus roseus: Implications

for Metabolic Engineering,” Bhadra, R., Budd, S., Ho, C.-H., Morgan, J., Rijhwani, S., Vani, S.,

and Shanks, J. V., Engineering Foundation Conference, Recombinant DNA, Metabolic

Engineering, Danvers, MA, October 1996.

35. “Kinetics and Fate of Transformation of 2,4,6-Trinitrotoluene by Aquatic Plants and Plant Tissue

Cultures,” Bhadra, R., Lauritzen, J., Hughes, J., and Shanks, J. V., Annual Meeting of the AIChE,

Chicago, IL, November 1996.

36. “Metabolism of C. roseus Hairy Root Cultures: A NMR Spectroscopy Based Study,” Rijhwani, S.

and Shanks, J. V., Annual Meeting of the AIChE, Chicago, IL, November 1996.

37. “Metabolic Engineering for the Production of Plant Pharmaceuticals,” Morgan, J., Rijhwani, S.,

Vani, S. and Shanks, J. V., Fifteenth Annual Conference on Biomedical Engineering Research in

Houston, Houston, TX, February 1997.

38. “Effects of Precursor Feeding upon Alkaloid Biosynthesis in Catharanthus roseus Hairy Root

Cultures,” Morgan, J. and Shanks, J. V., National Meeting of the ACS, San Francisco, CA, April

1997.

39. “In situ NMR Spectroscopy as a Technique to Study Elicitation-Induced Metabolic Changes in

Plant Organ Cultures,” Rijhwani, S. and Shanks, J. V., National Meeting of the ACS, San

Francisco, CA, April 1997.

40. “Phytoremediation of Explosives: Hairy Root Cultures as a Model System,” Fourteenth Biennial

Estuarine Research Federation International Conference, Providence, RI, October 1997.

41. “Quantitative Analysis of the Tabersonine Branchpoint in Catharanthus roseus Hairy Root

Cultures,” Morgan, J. and Shanks, J. V., Annual Meeting of the AIChE, San Francisco, CA,

November 1997.

42. “Phytoremediation of 2,4,6-TNT: Plant Transformation Processes,” Bhadra, R., Wayment, D. G.,

Hughes, J., and Shanks, J. V., National Meeting of the ACS, Boston, MA, August 1998.

43. “Strategies to determine Flux Limitations in Indole Alkaloid Pathways of Catharanthus roseus,”

Morgan, J. and Shanks, J. V., National Meeting of the ACS, Boston, MA, August 1998.

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44. “Quantification of Metabolic Flux in Plant Secondary Metabolism by a Biogenetic Organizational

Approach,” Morgan, J. and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,

November 1998.

45. “Phytoremediation of HMX and RDX in Hairy Root Cultures of Catharanthus Roseus,” Barman,

S., Williams, R., Bhadra, R., and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,

November 1998.

46. “Biochemical Pathways of 2,4,6-Trinitrotoluene Abatement by Phytoremediation,” Bhadra, R.,

Wayment, D. G., Hughes, J., and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,

November 1998.

47. “Fate of RDX and HMX in Phytoremediation Systems,” Williams, R., Stone, M., Barman, S.,

Bhadra, R., Hughes, J., and Shanks, J. V., Annual Meeting of the AIChE, Miami Beach, FL,

November 1998.

48. “Phytoremediation of TNT and the Monoaromatics,” Wayment, D. G., Bhadra, R., Hughes, J., and

Shanks, J. V., National Meeting of the ACS, Anaheim, CA, March 1999.

49. “Conjugate Formation During the Metabolism of 2,4,6-Trinitrotoluene in Plant Roots,” Bhadra, R.,

Wayment, D. G., Hughes, J., and Shanks, J. V., Battelle In Situ Conference for Bioremediation, San

Diego, CA, April 1999.

50. “Plant Metabolism of 2,4,6-Trinitrotoluene and Related Nitroaromatic Compounds,” Second

International Symposium on Biodegradation of Nitroaromatic Compounds and Explosives, Xerox

University, VA, September 1999.

51. “The Characterization of Oxidation Products of TNT Metabolism in Aquatic Phytoremediation

Systems of Myriophyllum aquaticum,” Bhadra, R., Hughes, J. B., Wayment, D., and Shanks, J. V.,

Annual Meeting of the AIChE, Dallas, TX, November 1999.

52. “Indole Alkaloid Production in C. roseus Hairy Roots,” Annual Meeting of the AIChE, Dallas, TX,

November 1999.

53. “Challenges in Engineering Overproduction of Plant Alkaloids,” Engineering Foundation

Conference, Metabolic Engineering III, Colorado Springs, CA, October 2000.

54. “Protein and Nonprotein Nitrogen in C. roseus Hairy Roots,” Hughes, E., San, K. Y., and Shanks, J.

V., Annual Meeting of the AIChE, Los Angeles, CA, November 2000.

55. “Phytoremediation of TNT: Pathway Studies,” Subramanian, M. and Shanks, J. V., Annual Meeting

of the AIChE, Los Angeles, CA, November 2000.

56. “A Strategy for Manipulation of Alkaloid Flux in Catharanthus roseus Hairy Roots,” Hughes, E.,

Hong, S.-B., Gibson, S., San, K.-Y., and Shanks, J. V., Houston Conference on Biomedical

Engineering Research, Houston, TX, February 2001.

57. “A Strategy for Manipulation of Indole Alkaloid Flux in Catharanthus roseus Hairy Roots,” Hong,

S.-B., Hughes, E., Shanks, J. V., San, K.-Y., and Gibson, S., American Society of Plant

Physiologists Annual Meeting, Providence, RI, July 2001.

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58. “TNT Transformation by Plants: Role of Hydroxylamines,” Subramanian, M. and Shanks, J. V.,

Annual Meeting of the AIChE, Reno, NV, November 2001.

59. “An Inducible Promoter for the Study of Alkaloid Flux in Catharanthus roseus Hairy Roots,”

Hughes, E., Hong, S.-B., Gibson, S., San K. Y., and Shanks, J. V., Annual Meeting of the AIChE,

Los Angeles, CA, November 2001.

60. “A Mathematical Model for Carbon-Bond Labeling Experiments,” Sriram, G. and Shanks J. V.,

Annual Meeting of the AIChE, Reno, NV, November 2001.

61. “Find a Way to Use NMR: Tribute to Jay Bailey,” Annual Meeting of the AIChE, Reno, NV,

November 2001.

62. “Development of a Stoichiometric Model to Describe Primary and Intermediary Metabolism in

Catharanthus roseus Hairy Roots,” Gonzalez-Riviera, O., Denefe, E. L., Sriram, G., and

Shanks, J. V., National Meeting of the ACS, Boston, MA, August 2002.

63. “Development of a Stoichiometric Model for Metabolic Flux Analysis in Catharanthus roseus

Hairy Roots,” Sriram, G., Gonzalez-Riviera, O., and Shanks, J. V., Annual Meeting of the AIChE,

Indianapolis, IN, November 2002.

64. “Metabolic Engineering of the Indole Pathway in Catharanthus roseus Hairy Roots,” Hughes, E.,

Hong, S.-B., Gibson, S., San, K. Y., and Shanks, J. V., Annual Meeting of the AIChE, Indianapolis,

IN, November 2002.

65. “Metabolic Flux Analysis of Developing Soybean (Glycine max) Embryos using a Carbon-Bond

Labeling Experiment,” Sriram, G., Fulton, D. B., Peterson, J., Westgate, M., Spalding, M., and

Shanks, J. V., Annual Meeting of the AIChE, Indianapolis, IN, November 2002.

66. “Phytoremediation of TNT: Pathway Analysis,” Subramanian, M. and Shanks, J. V., Annual

Meeting of the AIChE, Indianapolis, IN, November 2002.

67. “Phytotransformation of TNT through Hydroxylamine Intermediates-Pathway Confirmation,”

Subramanian, M. and Shanks, J. V., Partners in Environmental Technology Technical Symposium

and Workshop, SERDP, Washington, DC, December 2002.

68. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Hughes,

E., Hong, S.-B., Gibson, S., Shanks, J. V., San, K.-Y., 225th ACS National Meeting, New Orleans,

LA, March 23-27, 2003.

69. “Role of the non-mevalonate pathway in indole alkaloid production by Catharanthus roseus hairy

roots,” Hong, S.-B., Hughes, E. H., Shanks, J. V., San, K.-Y., and Gibson, S. I., 225th ACS National

Meeting, New Orleans,LA, March 23-27, 2003.

70. “Role of the non-mevalonate pathway in indole alkaloid production by Catharanthus roseus hairy

roots,” Hong, S.-B., Hughes, E. H., Shanks, J. V., San, K.-Y., and Gibson, S. I., Twentieth

Conference on Biomedical Engineering Research in Houston, Houston, TX, April 3-4, 2003.

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71. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Hughes,

E., Hong, S.-B., Gibson, S., Shanks, J., and San, K.-Y., Twentieth Conference on Biomedical

Engineering Research in Houston, Houston, TX, April 3-4, 2003.

72. “Using Rubrics to Facilitate Students’ Development of Problem Solving Skills,” Saunders, K. P.,

Glatz, C. E., Huba, M. E., Griffin, M. H., Mallapragada, S. K., and Shanks, J. V., a Multimedia

presentation at the ASEE Annual Meeting, Nashville, TN, June 24, 2003.

73. “PBL Approach to Bioprocessing Lab,” Glatz, C., Saunders, K., Huba, M., Mallapragada, S.,

Narasimhan, B., Reilly, P., and Shanks, J., a poster presented at the NSF Grantees Conference,

Washington, DC, September 2003.

74. “Development of NMR tools to obtain metabolic flux maps for soybean seeds,” Iyer, V. V., Sriram,

G., Westgate, M. E., and Shanks, J. V., AIChE, Annual Meeting, San Francisco, CA, November 16-

21, 2003.

75. “Metabolic flux analysis of sucrose metabolism into protein, oil and starch in soybean seeds,”

Sriram, G., Iyer, V. V., Zhou, R., Fulton, D. B., Westgate, M. E., Spalding, M. H., and Shanks,

J. V., Annual meeting, American Society of Agronomy, Denver, Co, November 2-6, 2003.

76. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Peebles,

C. A., Hughes, E., Hong, S.-B., Gibson, S., Shanks, J. V., and San, K.-Y., 2003 Annual AIChE

meeting, San Francisco, CA, November 16-21, 2003.

77. “Phytoremediation of RDX: Screening Studies on Arabidopsis thaliana,” Rollo, S., Moon, H.,

Subramanian, M., Oliver, D. J., and Shanks, J. V., Annual Meeting of the AIChE, San Francisco,

CA, November 16-21, 2003.

78. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)

by Plants,” Shanks, J. V., Oliver, D. J., Moon H., Rollo, S., and Subramanian, M., Annual Meeting

of the AIChE, San Francisco, CA, November 16-21, 2003.

79. “Genetic and Biochemical Basis for Plant Transformation of Energetic Materials,” Subramanian,

M., Moon H, Oliver, D, and Shanks, J. V., Partners in Environmental Technology Technical

Symposium and Workshop, SERDP, Washington, DC, December 2003.

80. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)

by Plants,” Shanks, J. V, Battelle Conference on Range Management, New Orleans, LA, January 6,

2004.

81. “Plant Metabolic Engineering under Construction,” Fourth Interagency Conference on Metabolic

Engineering, NSF, February 6, 2004.

82. “Metabolic engineering of indole alkaloid pathways in Catharanthus roseus hairy roots,” Peebles,

C. A., Hughes, E., Hong, S.-B., Gibson, S., Shanks, J. V., and San, K.-Y., Twenty First Conference

on Biomedical Engineering Research in Houston, Houston, TX, February 12-13, 2004.

83. “Metabolic engineering of the terpenoid indole alkaloid pathways in Catharanthus roseus hairy

roots: The effects of terpenoid precursor feeding on transgenic AS hairy roots,” Peebles, C. A.,

Hughes, E., Hong, S.-B., Gibson, S., Shanks, J. V., and San, K.-Y., 227th ACS National Meeting,

Anaheim, CA, March 28-April 1, 2004.

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84. “Toxicity of RDX on Germination of Arabidopsis thaliana,” Rollo, S., Moon, H., Subramanian, M.,

Oliver, D. J., and Shanks, J. V., 33rd

Annual Biochemical Engineering Symposium, Lincoln, NE,

April 2004.

85. “Phytotransformation pathways of the energetic material TNT,” Subramanian M., Moon, H., Rollo,

S., Oliver, D., and Shanks J. V., American Association of Ecological Engineers, Fayetteville, AR,

June 2004.

86. Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Third International Congress on

Plant Metabolomics, Ames, IA, June 3-6, 2004.

87. “Metabolic Flux Analysis of Sucrose Metabolism into Protein, Oil, Starch in Soybean Seeds,”

Iyer, V. V., Sriram, G., Fulton, B., Zhou, R., Westgate, M. E., and Shanks, J. V., Third International

Congress on Plant Metabolomics, Ames, IA, June 3-6, 2004.

88. “Quantification of Metabolic Fluxes in Plants from 2-D NMR Data: Mathematical Framework and

Flux Identifiability,” Sriram, G. and Shanks, J. V., Third International Congress on Plant

Metabolomics, Ames, IA, June 3-6, 2004. Poster Award.

89. “Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of

Sugar Mixtures,” Dharmadi, Y., Moon, Y., Shanks, J. V., San, K-Y., and Gonzalez, R., Metabolic

Engineering V: Genome to Product, Lake Tahoe, CA, September 19-23, 2004.

90. “An Integrated Metabolic Engineering Study of Hairy Roots for Alkaloid Production,” Shanks,

J. V., San, K.-Y., Gibson, S. I., Hong, S.-B., Hughes, E., Sriram, G., Peebles, C., and Sander, G.,

Metabolic Engineering Conference, Lake Tahoe, September 19-23, 2004.

91. “Quantification of Metabolic Fluxes in Plants from 2-D NMR Data: Mathematical Framework and

Flux Identifiability,” Sriram, G. and Shanks, J. V., Metabolic Engineering V: Genome to Product,

Lake Tahoe, CA, September 19-23, 2004.

92. “A Genetic Network Driven Metabolic Flux Analysis Scheme,” San, K-Y., Bennett, G. N.,

Levanon, S. S., Cox, S., Percy, B., Shanks, J. V., and Gonzalez, R., Metabolic Engineering V:

Genome to Product, Lake Tahoe, CA, September 19-23, 2004.

93. “Integrating Genetic and Environmental Impacts on Seed Composition using Metabolic Flux

Analysis,” Shanks, J. V, Sriram, G., Iyer, V. V., Zhou, R., Fulton, D. B., Westgate, M. E., Annual

Meeting, American Society of Agronomy, Seattle, WA, November 2-6, 2004.

94. “Application of NMR Flux Maps for Analysis of Metabolically Engineered Plant

Tissues,” Sander, G., Hughes, E., San, Ka-Yiu, Gibson, S. I., and Shanks, J. V., Annual Meeting of

the AIChE, Austin, TX November 7-12, 2004.

95. “A Systems Biology Approach for Metabolic Engineering of Escherichia coli Sugar-Utilization

Regulatory Systems,” Dharmadi, Y., Moon, Y., Shanks, J. V., San, K-Y., and Gonzalez, R., Annual

Meeting of the AIChE, Austin, TX, November 7-12, 2004.

96. “Development of a Genetic Network Driven Model for Sugar-Utilization Regulatory Systems,”

San, K-Y., Gonzalez, R., Shanks, J. V., and Peacock, R., Annual Meeting of the AIChE, Austin,

TX, November 7-12, 2004.

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97. “Metabolic Engineering of the Terpenoid and Indole Pathways in Catharanthus roseus hairy roots,”

Peebles, C. A., Gibson, S., Shanks, J. V., and San, K-Y., Annual Meeting of the AIChE, Austin,

TX, November 7-12, 2004.

98. “Transient Effect of Overexpressing AS on Terpenoid Indole Alkaloid Production in

Catharanthus roseus Hairy Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y., Annual

Meeting of the AIChE, Austin, TX, November 7-12, 2004.

99. “Phytoremediation of RDX: Using Arabidopsis thaliana to Determine the Genetics and

Biochemistry of the Transformation Pathway,” Rollo, S., Moon, H., Subramanian, M.,

Oliver, D. J., and Shanks, J. V., Annual Meeting of the AIChE, Austin, TX, November 7-12, 2004.

100. “Genetic and Biochemical Basis for Plant Transformation of Energetic Materials,” Oliver, D.,

Moon, H., Rollo, S., Subramanian, M., Yoon, Y. M., and Shanks, J. V., Partners in Environmental

Technology Technical Symposium and Workshop, SERDP, Washington, DC, December 2004.

101. “Prospects for Metabolic Engineering,” Realizing the Vision: Leading Edge Technologies in

Biological Systems, Cosmos Club, Washington DC, December 14, 2004.

102. “Transient Effect of Overexpressing Asαβ on Terpenoid Indole Alkaloid Production in

Catharanthus Roseus Hairy Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y.,

Twenty Second Conference on Biomedical Engineering Research in Houston, Houston, TX,

February 10-11, 2005.

103. “Metabolic Engineering of the Terpenoid Indole Alkaloid Pathways in Catharanthus roseus Hairy

Roots: Overexpression of the Terpenoid Branch Genes for Geraniol 10-hydroxylase and 1-deoxy-

D-xylulose 5-phosphate Synthase,” Peacock, R., Peebles, C. A., Gibson, S, Shanks, J. V., and San,

K-Y., ACS National Meeting, San Diego, CA, March 2005.

104. “Metabolic Engineering of the Terpenoid Indole Alkaloid Pathways in Catharanthus roseus Hairy

Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y., ACS National Meeting, San Diego,

CA, March 2005.

105. “The Effect of Overexpressing ASα and DXS in Catharanthus roseus Hairy Roots on the

Terpenoid Indole Alkaloid Pathway,” Peebles, C. A., Gibson, S, Shanks, J. V., and San, K-Y., ACS

National Meeting, San Diego, CA, March 2005.

106. “Plant Transformation Pathways of Energetic Materials (RDX, TNT, DNTs),” NABC Conference,

Nashville, TN, June, 2005.

107. “ Metabolic Engineering for the Production of Tryptophan and Indole Alkaloids in C. roseus,”

Gordon Research Conference on Plant Metabolic Engineering, Tilton, NH, July 14, 2005.

108. “Phytoremediation of Energetic Materials (DNTs and RDX) Using Arabidopsis thaliana”, Yoon, J.

M., Rollo, S., Oliver, D. J., Shanks, J. V., Annual Meeting of the AIChE, Cincinnati, OH, October

2005.

109. “Characterization of the Ecdysone Agonist-Inducible Promoter and the Ethanol Inducible

Promoter in Catharanthus roseus Hairy Roots,” Peebles, C. A., Gibson, S, Shanks, J. V., and San,

K-Y., Annual Meeting of the AIChE, Cincinnati, OH, October 2005.

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110. “Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems,” Peacock, R.,

Zhu, J., Shanks, J. V., Gonzalez, R. and K.-Y. San. Annual Meeting of the AIChE, Cincinnati, OH,

October 2005.

111. “Overexpression of the Terpenoid Branch Genes for Geraniol 10-hydroxylase and 1-deoxy-D-

xylulose 5-phosphate Synthase,” Peacock, R., Peebles, C. A., Gibson, S, Shanks, J. V., and San,

K-Y., Annual Meeting of the AIChE, Cincinnati, OH, October 2005.

112. “Phytotoxicity and Uptake of Dinitrotoluenes Using Arabidopsis thaliana”, Yoon J. M., Oliver,

D. J., Shanks, J. V., Partners in Environmental Technology Technical Symposium and Workshop,

SERDP, Washington, DC, November 2005.

113. “Metabolic and Gene Expression Profiling of Terpenoid Indole Alkaloid (TIA) Pathways in

Periwinkle Plants Treated with Methyl Jasmonic Acid and Fungal Elicitor,” Wei, S. and S. I.

Gibson, Plant Biology 2006, Boston, MA, 2006.

114. “Metabolic Engineering of Catharanthus roseus Hairy Roots for Production of Indole Alkaloids,”

Shanks, J. V., C. A. M. Peebles, K.-Y. San, S. I. Gibson, S. Wei, and G. Sander, Natural Products

Discovery and Production: New Challenges; New Opportunities, Sante Fe, NM, 2006.

115. “Metabolic Flux Maps of Central Carbon Metabolism in Soybean Embryos,” J. V. Shanks,

Molecular and Cellular Biology of the Soybean, 11th Biennial Meeting, Lincoln, NE, August, 2006.

116. “Metabolic Engineering of the Terpenoid and Indole Pathways in Catharanthus roseus Hairy

Roots,” Peebles, C. A. M., S. I. Gibson, J. V. Shanks, and K.-Y. San, American Institute of

Chemical Engineers Annual Meeting, San Francisco, CA, November 2006.

117. “The Transient Effect of Jasmonic Acid Feeding along with Orca3 Overexpression in Catharanthus

roseus Hairy Roots.” Peebles, C. A. M., S. I. Gibson, J. V. Shanks, and K.-Y. San, American

Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 2006.

118. “Design of Isotope Labeling Experiments for Metabolic Flux Analysis in Escherichia coli under

Anaerobic Condition.” Choudhury, M., Y. Dharmadi, R. Gonzalez, K.-Y. San and J. V. Shanks,

American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November 2006.

119. “Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems” Zhu, J., R.

Peacock, J. V. Shanks, R. Gonzalez, and K.-Y. San, American Institute of Chemical Engineers

Annual Meeting, San Francisco, CA, November 2006.

120. “Perspectives in Metabolic Flux Mapping,” J.V. Shanks, Joint Genomics: GTL Awardee Workshop

V and Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy

Awardee Workshop 2007, Bethesda, MD., February 13, 2007.

121. “Metabolic Flux Analysis on Soybean Isolines With Different Seed Compositions,” Vidya V. Iyer,

Matthew E. Studham, Mark E. Westgate, Julie Dickerson, Eve S. Wurtele, Jacqueline V. Shanks.

American Institute of Chemical Engineers Annual Meeting, Salt Lake City, UT, November 2007.

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122. “Metabolic Engineering of the Terpenoid and Indole Pathways in Catharanthus roseus Hairy

Roots,” Peebles, C.A.M., S. I. Gibson, J. V. Shanks, and K.-Y. San. American Institute of Chemical

Engineers Annual Meeting, Salt Lake City, UT, November 2007.

123. “Exploration of the Role of the Octadecanoid Pathway for Terpenoid Indole Alkaloid Production

in Catharanthus roseus Hairy Roots.” Peebles, C.A.M., J.V. Shanks, and K.-Y. San. American

Institute of Chemical Engineers Annual Meeting, Salt Lake City, UT, November 2007.

124. “The Effect of UVB Light on Terpenoid Indole Alkaloid Production in Catharanthus roseus Hairy

Roots.” Binder, B.Y.K., C.A.M. Peebles, K.-Y. San, American Institute of Chemical Engineers

Annual Meeting, Salt Lake City, UT, November 2007.

125. “Unraveling the Sugar Utilization Regulatory Systems in Escherichia coli,” Dharmadi, Y., J. V.

Shanks, K.-Y. San, and R. Gonzalez. American Institute of Chemical Engineers Annual Meeting,

Salt Lake City, UT, November 2007.

126. “Development of a Mechanistic Model for Sugar-Utilization Regulatory Systems,” Zhu, J., R.

Gonzalez, J. V. Shanks, and K.-Y. San. American Institute of Chemical Engineers Annual Meeting,

Salt Lake City, UT, November 2007.

127. “Toxicity and Transformation of Dinitrotoluenes using Arabidopsis thaliana,” Yoon J. M., Oliver,

D. J., Shanks, J. V., The Society of Environmental Toxicology and Chemistry (SETAC) North

America 28th Annual Meeting, Milwaukee, WI, USA, November 2007.

128. “Transient Effects of Overexpressing Anthranilate Synthase α and β Subunits in Catharanthus

roseus Hairy Roots in Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.

Shanks, American Society of Plant Biologists, Midwestern Section Annual Meeting, Ames, IA,

March 2008. Poster Award.

129. “Metabolic Engineering of Catharanthus roseus Hairy Roots for Terpenoid Indole Alkaloid

Production under Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.

Shanks, 37th Annual Biochemical Engineering Symposium, Ames, IA, April 2008.

130. “Transient Effects of Overexpressing Anthranilate Synthase α and β Subunits in Catharanthus

roseus Hairy Roots in Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.

Shanks, 37th Annual Biochemical Engineering Symposium, Ames, IA, April 2008.

131. “The transient effect of overexpressing ORCA3 plus jasmonic acid feeding in Catharanthus roseus

hairy roots,” Peebles, C. A. M., S. I. Gibson, J. V. Shanks, and K.-Y. San, Natural Products

Discovery and Production II: Celebrating Successes of Traditional and Novel Cultures; New

Opportunities, Whistler, British Columbia, Canada, 2008.

132. “Metabolic Engineering of Catharanthus roseus Hairy Roots for Terpenoid Indole Alkaloid

Production under Light and Dark Conditions,” Sander, G.W., Gibson, S.I., San, K.Y., and J. V.

Shanks, Natural Products Discovery and Production II: Celebrating Successes of Traditional and

Novel Cultures; New Opportunities, Whistler, British Columbia, Canada, 2008.

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133. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” J. V. Shanks,

Phytochemistry Society of North America Annual Meeting, Pullman, WA June 2008.

134. “Metabolic Flux Analysis on Soybean Isolines With Different Seed Compositions” J. V. Shanks,

Metabolic Engineering VII, Puerto Vallarta, Mexico, September, 2008.

135. “Metabolic Flux Analysis of Maize (Zea mays, GS3 X Gaspe) Cell Suspension Culture by Using 13

C Labeling Experiment and 2-Dimensional Nuclear Magnetic Resonance (NMR) Spectroscopy”

J. M.Yoon, Y.Li, H. Kanani, K. Dhugga, J. Lightner, J. V. Shanks, Metabolic Engineering VII,

Puerto Vallarta, Mexico, September, 2008.

136. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” J. V. Shanks,

Danforth Plant Science Symposium, St Louis, MI, October, 2008.

137. “Effects of Nitric Oxide on Growth and Terpenoid Indole Alkaloid Production In Catharanthus

Roseus Hairy Root Cultures Li, M. , Peebles, C.A.M., J. V. Shanks, and K.-Y. San. American

Institute of Chemical Engineers Annual Meeting, Philadelphia, PA, November 2008.

138. “Systems biology approach to understand seed composition: A convergence of metabolomics,

transcriptomics and metabolic flux data to expand the metabolic and regulatory network of

developing soybean seeds”, Li L, Zhou WX, Zhou WG, Demirkale Y, Ransom N, Shanks J, Iyer V,

Nettleton D, Westgate M, Nikolau B, and Wurtele ES International Conference on Legume

Genomics and Genetics 4, Puerto Vallarta, Mexico. September, 2008.

139. “Systems biology approach to understand seed composition: a convergence of bioinformatics,

metabolomics, transcriptomics and metabolic flux data to expand the metabolic and regulatory

network of developing soybean seeds”, Li L, Zhou WX, Yu XM, Zhou WG, Demirkale Y, Ransom

N, Shanks J, Iyer V, Nettleton D, Westgate M, Nikolau B, and Wurtele ES 18th annual Growth

Factor and Signal Transduction Symposium Ames, Iowa. June, 2009.

140. “Harnessing Plant Biochemistry for Industrial Chemicals - Beyond Fuels?”, J.V. Shanks, Plenary

Speaker, Gordon Research Conference on Plant Metabolic Engineering, Waterville Valley Resort in

the White Mountains of New Hampshire, NH, July, 2009.

141. "Flux Cartography in Oil Seeds - Analysis of Metabolic Roadblocks" J.V. Shanks, Intl. Congress

of Plant Molecular Biology, St. Louis, MI, October 26, 2009.

142. “Effects of Nitric Oxide on Growth, Terpenoid Indole Alkaloid Production and Some of the TIA

Gene Transcripts in Catharanthus Roseus Hairy Root Cultures.” Li, M. , Peebles, C.A.M., J. V.

Shanks, and K.-Y. San. American Institute of Chemical Engineers Annual Meeting, Nashville, TN,

November 11, 2009.

143. “Overexpression of Multiple Terpenoid Indole Alkaloid Genes Increases Alkaloid Accumulation in

Catharanthus Roseus Hairy Root Cultures.” Peebles, C.A.M., J. V. Shanks, and K.-Y. San.

American Institute of Chemical Engineers Annual Meeting, Nashville, TN, November 13, 2009.

144. “Alkaloid Extraction and Purification From Catharanthus Roseus Hairy Root Tissue.” Brown, D.,

G. Sander, and J. V. Shanks. American Institute of Chemical Engineers Annual Meeting, Nashville,

TN, November 9, 2009.

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145. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for Biofuels,”

American Chemical Society Fall Meeting, Boston, MA, August 2010.

146. “Systems Analysis of the Fermentative Metabolism of Escherichia coli”, R. Gonzalez, A. Murarka,

J. M. Clomburg, S.Moran and J. V. Shanks, American Institute of Chemical Engineers Annual

Meeting, Salt Lake City, Utah, November 2010

147. “The Top 10 Reasons ChE’s Should be Interested in (Living) Plants” J. V. Shanks, American

Institute of Chemical Engineers Annual Meeting, AIChE Food, Pharmaceutical and Bioengineering

Division, Area 15c Plenary, Salt Lake City, Utah, November 2010.

148. "Influence of SHaM Media Carbon-to-Nitrogen Ratios on Soybean Somatic Embryos (cv. Jack)

Growth and Composition", Q. Truong and J. V. Shanks, Plant Metabolic Engineering Gordon

Conference, Waterville Valley, New Hampshire, July 2011.

149. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for Biofuels”, M.

Brown, G. Ding, W. Qin, J. Chmielowski, A. Jose, L. Wallace, S. Hoddick, E. Justiniano, M.

Nelson, G. Nadathur, G. Wolfe, B. Nikolau and J. V. Shanks, American Institute of Chemical

Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.

150. “Metabolic Flux Analysis of Escherichia coli MG1655 Under Octanoic Acid Stress”, Y. Fu,

J.M.Yoon, L. Royce, M. Rodriguez-Moya, R. Gonzalez, L.Jarboe and J. V. Shanks, American

Institute of Chemical Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.

151. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for Biofuels”, M.

Brown, G. Ding, W. Qin, J. Chmielowski, A. Jose, L. Wallace, S. Hoddick, E. Justiniano, M.

Nelson, G. Nadathur, G. Wolfe, B. Nikolau and J. V. Shanks, American Institute of Chemical

Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.

152. “Structural Elucidation of Unknown Alkaloids Present in Catharanthus roseus by Precursor Ion

Fingerprinting”, C.D. Flores, G. W. Sander, M.A. Perera and J. V. Shanks, American Institute of

Chemical Engineers Annual Meeting, Minneapolis, Minnesota, October 2011.

153. “Integrating Biological and Chemical Catalysts to Create a Generalized Framework for Producing

Biorenewable Chemicals”, J.V. Shanks, The 6th Sino-US Joint Conference of Chemical

Engineering, SINOPEC Conference Centre, Beijing, China, Nov. 7-10, 2011.

Invited Lectures at Universities, Companies, and Conferences:

1. “Application of in vivo NMR Spectroscopy to Cellular Metabolism from an Engineering

Perspective,” Molecular Biology and Chemistry Program, University of Massachusetts, Amherst,

MA, November 24, 1987.

2. “Use of in vivo NMR Spectroscopy for Metabolic Engineering Applications,” Chemistry Dept.,

University of TX at Dallas, Dallas, TX, November 29, 1989.

3. “Use of in vivo NMR Spectroscopy for Metabolic Engineering Applications,” Chemical

Engineering Dept., Iowa State University, Ames, IA, March 1, 1990.

4. “Establishment and Cultivation of Hairy Root Lines of Catharanthus roseus,” Chemical

Engineering Dept., University of California Davis, Davis, CA, January 14, 1991.

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5. “Use of NMR in Metabolic Engineering Applications,” Biochemical Engineering Program, Duke

University, Durham, NC, April 1991.

6. “Use of NMR in Metabolic Engineering,” Biomedical and Biological Applications of Nuclear

Magnetic Resonance, Galveston-Houston Biological NMR Symposium, Galveston, TX, May 1991.

7. “Production of Indole Alkaloids by Hairy Root Cultures of Catharanthus roseus,” Biotechnology

Institute and Plant Physiology Program, Penn State University, State College, PA, October 28,

1992.

8. “Production of Indole Alkaloids by Hairy Root Cultures of Catharanthus roseus,” Procter and

Gamble, Corporate Research Center, Cincinnati, OH, November 17, 1992.

9. “Transgenic Root Cultures of Catharanthus roseus: Metabolism and Alkaloid Synthesis,” NIH

Conference: Research Opportunities in Biomolecular Engineering: The Interface Between

Chemical Engineering and Biology, Washington, DC, December 7, 1992.

10. “Production of Indole Alkaloids by Hairy Root Cultures of Catharanthus roseus,” School of

Chemical Engineering, Purdue University, West Lafayette, IN, September 9, 1993.

11. “Building Bridges for Women in Biomedical Engineering and Sciences,” Panel Discussant, Twelfth

Annual Conference on Biomedical Research in Houston; Houston, TX, February 1994

12. “In Situ NMR Spectroscopy as a Research Tool in Plant Biotechnology,” Procter and Gamble,

Corporate Research Center, Cincinnati, OH, May 17, 1994.

13. “Transgenic Root Cultures as Chemical Factories,” Dept. of Chemical Engineering, University of

Houston, Houston, TX, November 1994.

14. “Opportunities and Challenges in the Use of Plant Cell and Tissue Cultures as Production

Systems,” Bristol-Myers Squibb, Seattle, WA, April 28, 1995.

15. “Phytoremediation of TNT: Hairy Root Cultures as a Model System,” IBC Conference on

Phytoremediation, Washington, DC, May 9, 1996.

16. “Chemical Engineering with (Living) Plants,” Dept. of Chemical Engineering, Michigan State

University, East Lansing, MI, November 1996.

17. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Products,” National

Meeting of the ACS, San Francisco, CA, April 1997.

18. “Phytoremediation of Explosives: Hairy Root Cultures as a Model System,” Fourteenth Biennial

Estuarine Research Federation International Conference, Providence, RI, October 1997.

19. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Products,” DuPont Central

R&D, Wilmington, DE, January 27, 1998.

20. “Quantification of Metabolic Fluxes for Metabolic Engineering in Plants,” Society of In Vitro

Biology, Las Vegas, NV, June 1, 1998.

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21. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Chemical

and Biochemical Engineering, University of Iowa, Iowa City, IA, October 22, 1998.

22. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Biotechnology

Series, University of Minnesota, MN, December 3, 1998.

23. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Chemical

Engineering, Iowa State University, Ames, IA, December 17, 1998.

24. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Plant

Science, Rutgers University, NJ, February 19, 1999.

25. “Plant Metabolism of 2,4,6-Trinitrotoluene and Related Nitroaromatic Compounds,” Second

International Symposium on Biodegradation of Nitroaromatic Compounds and Explosives, Xerox

University, VA, September 8, 1999.

26. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” ACS Lectureship,

Dept. of Chemical Engineering, University of Wisconsin, Madison, WI, November 16, 1999.

27. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Secondary Metabolites,”

Dept. of Food Science and Human Nutrition, Iowa State University, Ames, IA, April 5, 2000.

28. “Quantification of Metabolic Fluxes for Metabolic Engineering of Plant Products,” Malaysian MIT

Biotechnology Partnership Program Workshop, Bioreactor Processes for Plant Cell Cultures,

Massachusetts Institute of Technology, Cambridge, MA, May 24, 2000.

29. “Phytocatalysis: Applications in Metabolic Engineering and Bioremediation,” Dept. of Chemical

Engineering, Cornell University, Ithaca, NY, November 20, 2000.

30. “Plant Metabolism of TNT, RDX, and HMX,” Presentation, Defense Threat Reduction Agency,

Vegetative Effects Environmental Sensing Program Planning Meeting, Arlington, VA, October 4,

2001.

31. “Applications of Nuclear Magnetic Resonance (NMR) in Metabolic Engineering,” Cargill-Dow

LLC, Minnetonka, MN, October, 2001“Find a Way to Use NMR: Tribute to Jay Bailey,”

Presentation, Annual Meeting of the AIChE, Reno, NV, November 2001.

33. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)

by Plants,” SERDP Scientific Advisory Board Meeting, Arlington, VA, March 7, 2002.

34. “Plant Metabolic Engineering: Entering the S Curve,” Dept. of Horticulture and Landscape

Architecture, Purdue University, West Lafayette, IN, March 28, 2002.

35. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)

by Plants,” Presentation, Eglin Airforce Base Range Meeting, Fort Walton Beach, FL, September 7,

2002.

36. “Evolution of Metabolic Engineering,” Annual Meeting of the AIChE, Indianapolis, IN,

November 2002.

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37. “What Does Plant Metabolism Have to Do With Chemical Engineering?” Dept. of Chemical

Engineering, University of Virginia, December 5, 2002.

38. “Systems Biology: Pathway Engineering Revisited?” Dept. of Chemical Engineering, Rice

University, January 30, 2003.

39. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)

by Plants,” SERDP Progress Review, Arlington, VA, March, 2003.

41. “Plant Metabolic Engineering: Entering the S Curve,” Keynote Address, Lehman College, City

University of New York, September 15, 2003.

42. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)

by Plants,” Battelle Conference on Range Management, New Orleans, LA, January 6, 2004.

43. “Genetic and Biochemical Basis for the Transformation of Energetic Materials (RDX, TNT, DNTs)

by Plants,” Joint Interagency Program on Phytoremediation Research, Principal, Investigators

Meeting, NSF, January 21, 2004.

44. “Plant Metabolic Engineering Under Construction,” Fourth Interagency Conference on Metabolic

Engineering, NSF, February 6, 2004.

45. “Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Third International Congress on

Plant Metabolomics, Ames, IA June 3-6, 2004.

46. “Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Iowa State University and

University of Iowa Joint Bioinformatics Workshop, Ames, IA August 6, 2004.

47. “Plant Metabolic Engineering: Under Construction,” Dept. of Horticulture, Iowa State University,

Ames, IA October, 2004.

48. “Integrating Genetic and Environmental Impacts on Seed Composition using Metabolic Flux

Analysis” Presentation, Annual meeting, American Society of Agronomy, Seattle, WA,

November 2-6, 2004.

49. “Prospects for Metabolic Engineering,” Presentation, Realizing the Vision: Leading Edge

Technologies in Biological Systems, Cosmos Club, Washington, DC, December 14, 2004.

50. “Metabolic Flux Maps of Central Carbon Metabolism in Plants,” Presentation, Pioneer Hi-Bred

International, Inc., Johnston, IA March 22, 2005.

51. “Plant Transformation Pathways of Energetic Materials (RDX, TNT, DNTs),” NABC Conference,

Nashville, TN, June, 2005.

52. “Metabolic Engineering for the Production of Tryptophan and Indole Alkaloids in C. roseus,”

Gordon Research Conference on Plant Metabolic Engineering, Tilton, NH, July 14, 2005.

53. “Flux Maps of Plant Metabolic Networks,” Presentation, Graduate Program in Plant Molecular

Biosciences, Washington State University, Pullman, WA, March 28, 2006.

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54. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”

Presentation, Department of Chemical Engineering, University of Delaware, DE, April 21, 2006.

55. “Metabolic Flux Maps of Central Carbon Metabolism in Soybean Embryos,” Molecular and

Cellular Biology of the Soybean, 11th Biennial Meeting, Lincoln, NE, August, 2006.

56. “Metabolic Flux Maps of Central Carbon Metabolism in Soybean Embryos,” Molecular and

Cellular Biology of the Soybean, Bioinformatics and Computational Biology Faculty Seminar

Series, Iowa State University, Ames, IA October 20, 2006.

57. “Perspectives in Metabolic Flux Mapping,” Joint Genomics: GTL Awardee Workshop V and

Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee

Workshop 2007, Bethesda, MD., February 13, 2007.

58. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” 2007 Plant

Science Symposium on Metabolic Engineering, Lincoln, Nebraska, October 4, 2007.

59. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Interdepartmental

Plant Physiology Symposium, Iowa State University, Ames, IA October 17, 2007.

60. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”

Presentation, Department of Chemical Engineering, Illinois Institute of Technology, Chicago, IL,

November 28, 2007.

61. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Phytochemistry

Society of North America Annual Meeting, Pullman, WA June 2008.

62. “Metabolic Flux Analysis on Soybean Isolines With Different Seed Compositions” Metabolic

Engineering VII, Puerto Vallarta, Mexico, September, 2008.

63. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Danforth Plant

Science Symposium, St Louis, MI, October, 2008.

64. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”

Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, presented November

6th, 2008.

65. “Cathedral roseus –and Other Interesting Tales in Plant Metabolic Engineering,” Center for Plant

Cell Biology, University of California Riverside, Riverside, CA presented December 12th, 2008.

66. “Phytochemical Engineering: Combining Chemical Reaction Engineering with Plant Science,”

Presentation, Department of Chemical Engineering, Washington State University, Pullman, WA

March 30, 2009.

67. “Harnessing Plant Biochemistry for Industrial Chemicals - Beyond Fuels?”, Plenary Speaker,

Gordon Research Conference on Plant Metabolic Engineering, Waterville Valley Resort in the

White Mountains of New Hampshire, NH, July, 2009.

68. "Flux Cartography in Oil Seeds - Analysis of Metabolic Roadblocks" BASF, Raleigh-Durham, NC,

September 18, 2009

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69. "Flux Cartography in Oil Seeds - Analysis of Metabolic Roadblocks" Intl. Congress of Plant

Molecular Biology, St. Louis, MI, October 26, 2009.

70. “Bioengineering a System for the Direct Production of Biological Hydrocarbons for

Biofuels,” American Chemical Society Fall Meeting, Boston, MA, August 2010.

71. " Metabolic Flux Cartography – On the Road to Sustainable Food, Feed, Fuels and

Chemicals” Presentation, Department of Chemical Engineering, Colorado State University, Fort

Collins, CO, October, 2010.

72. “The Top 10 Reasons ChE’s Should be Interested in (Living) Plants” American Institute of

Chemical Engineers Annual Meeting, AIChE Food, Pharmaceutical and Bioengineering Division,

Area 15c Plenary, Salt Lake City, Utah, November 2010

73. “Metabolic Flux Cartography – On the Road to Sustainable Food, Feed, Fuels and

Chemicals”, Minnesota Biotechnology Institute, University of Minnesota, St Paul, MN, April

2011.

74. “Metabolic Flux Cartography – On the Road to Sustainable Food, Feed, Fuels and Chemicals”

Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio,

June 2011.

75. “Integrating Biological and Chemical Catalysts to Create a Generalized Framework for Producing

Biorenewable Chemicals”, The 6th Sino-US Joint Conference of Chemical Engineering, SINOPEC

Conference Centre, Beijing, China, Nov. 7-10, 2011.

Postdoctoral Research Fellows Supervised:

Rajiv Bhadra 1996-1999

Darcey Wayment 1997-1999

Jong Moon Yoon 2004 –2010

Guy Sander 2009 - 2010

Graduate Students Supervised:

Hei-Chan Lee 1991-1992

Rajiv Bhadra 1989-1994

Chih-Huang Ho 1989-1994

Marie-Dominique Fernet 1990-1992

Sundeep Vani 1990-1996

Brenda Mann 1992-1996

Sushil Rijhwani 1992-1997

Steven Budd 1993-1996

John Lauritzen 1993-1998

John Morgan 1994-1999

Matt Ring 2000-2001

Erik Hughes 1998-2003

Murali Subramanian 1998-2004

Ganesh Sriram 1999-2004

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Sarah Rollo 2002-2005

Vidya Iyer 2001-2006

Guy Sander 2003-2009

Madhuresh Choudhary 2003-2008

Yanfen Fu 2009- 2011

Gwen Truong 2007-present

Marvin Mercado 2008-2010

Ting-wei Tee 2009-present

Mark Brown 2009-present

Erin Boggess, BCB (co-advised by Julie Dickerson) 2009-present

Daniel Flores 2011-2011

Preparing Future Faculty Graduate Students Mentor:

Daniela Faas 2007-2010

Biorenewables Resource Laboratory Graduate Student Mentor:

Basak Cinar 2007

Undergrad Research Students Supervised:

Stephanie Rosi 1989-1990

Tom Robbins 1989

Neil Leatherbury 1990-1991

Kathy Hazelton 1990

Mike Janicke 1991-1992

Manuel M. Rodriguez (NSF Graduate Fellowship) 1992-1993

Brian Hamill 1993

Celeste Campbell 1994

Christine Farrier 1994-1995

Jennifer Lynn Miller 1996

Alex Penn (Whitaker Graduate Fellowship) 1997

Christin Barney 1997

Angélica Rodríguez 1997

Soumendra Barman 1998-1999

Rebekah Williams 1998-1999

Rafaél Verduzco 1998

Jason Simmons 1998-1999

Janet Huang 1999

Michael Wald 2000

Nicole Felkey 2000

Erin Denefe 2001

Omar Gonzalez-Riviera 2001-2005

Melissa Swartz 2001

Amish Dalal 2002

Jennifer Rose 2002

Mason McGrady 2002

Chase Beisel (NSF Graduate Fellowship) 2002-2004

Tanya Phillips 2003

Christine Westgate 2003-2004

Hong-Kee Ng 2004

Jennifer Mayard 2004-2005

Shannon Parker 2005-2005

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James (Doug) Vandermyde 2006- 2007, 2008 - 2010

Bonnie Grider 2006

Ricardo Guraieb 2006

Joe Charlson 2006

John Tjaden 2007

Genevieve Lozier 2007

John Hollerung 2007

Sonali Patel 2007

Michelle Kozmik 2007

Lee Rudebusch 2007-2010

Meredith Breton 2008

Diane Brown (NSF Graduate Fellowship) 2008-2009

Kaelynn Koch 2009

Ezinne Archinivu 2009

Erin Jun 2010-2011

Sian Yun Wong 2010-2011

Miya Williams 2011-present

Trent Lamar 2011

Undergrad “Labbie” Students Supervised, Iowa State University:

Nate Morris 2000

Undergrad Education (Computation) Students Supervised (with S.H. Davis), Rice University:

Tom Robbins 1989

Jagjit Virk 1990

Luis Moreno 1990

Joseph De Vincentis 1990-1992

Tammy Chan 1992

Duke York 1992

David Jaber 1992-1993

Adrian Pennisson 1992-1993

Marcel Levi 1993

John Pérez 1994

Alex Penn 1996

Andrew Duryea 1997

High School Research Students Supervised:

Rubin Flores 1989

Esmerélda Hinosa 1994

Jason Simmons 1995

Christine Westgate 2003