Leaders in Pharmaceutical Business Intelligence (LPBI) Group

Roles at http://pharmaceuticalintelligence.com

Research Category OWNER:

Computational Biology/Systems and BioInformatics

Anamika Sarkar Personal Bio

 

I have 8+ yrs of experiences in Computational Physiology/Biology/Cellular/Biochemical research applied to basic sciences and drug development. My experiences are both in academic and industrial settings. My experiences and trainings span in applying Mathematics as tool for Biological and Physiological problems – organ levels (heart, kidney) to micro levels like signaling pathway analysis and gene regulations. I received my Bachelor and Masters degrees in Applied Mathematics from Delhi University, India and Indian Institute of Technology Delhi, respectively. My PhD was in Cardiovascular Fluid Dynamics from Indian Institute of Technology Delhi, where my thesis work was focused to understand error in measuring pressure drops and dispersion of drugs, in a catheterized artery. My postdoctoral work at BioEngineering, University of Washington, Seattle, included modeling of cellular, biochemical pathways and cellular interactions in immune cells, T cells and Dendritic cells. I continued my research in pathway/network modeling of microbial dynamics applying to Interferon β dynamics during flu virus infection at Mt. Sinai School of medicine, as Assistant Scientist, in department of Pharmacology and Systems Therapeutics. I joined Novartis Pharmaceuticals to translate my basic science research experiences into drug discovery R&D. At Novartis, I worked on developing large scale disease modeling of Blood Pressure Regulation by kidney and Heart Failure. The models had proper representations of biochemical pathways as drug targets and pharmacodynamics information of different drugs. The models a were used to compare between different drugs and predict long term drug effects in clinical trial settings. Presently, I work as a consultant in designing and execution of scientific projects.

Anamika Sarkar

535 Eagle Rock Ave, West Orange, NJ 07052

718.916.0557 ~ sarkaranamika@yahoo.com

Education
Part time MBA, Pharmaceutical Management, Rutgers Business School	Spring2012- present

 

PhD, Applied Mathematics, Indian Institute of Technology Delhi, New Delhi, India

 Thesis:  Flow and Dispersion in a Catheterized Artery – A Theoretical Model

 

1994-2000

Master of Science, Applied Mathematics, Indian Institute of Technology Delhi, New Delhi, India

1990-1992

Bachelor of Science , Mathematics, Sri Venkateswara College, University of Delhi, New  Delhi, India

 

1987-1990Research Experiences

 

Consultant – Scientific and Strategy, (project to project), Part time – Entrepreneurial Venture

• Sugar and Heart Clinic, Apollo,  India
• “sys+bio – systems solution worldwide” , USA
• Advanced Technology and Novel Therapeutics, USA

 

May 2011- present

Visiting Scientist, Novartis Pharmaceuticals Corporation, Modeling and Simulation

• Developed multi-scale disease modeling platforms based on mechanistic relationships and biochemical pathways integrated together
  • for renal disease (Diabetic – T2D, Hypertensive patients) –  in 18 months
  • cardiac heart failure model (Reduced Ejection and
  •  Preserved Ejection fraction patients) – in one year
  • Part of the models is published in a chapter of a book, has been presented in multiple conferences both as platform and poster
  • Results from the model will comprise in various manuscripts of peer review journals – writing in progress
  • Learnt physiology of  complex organ kidney in normal and diseased states                   – in six weeks
  • Calibrated  model parameters with PK/PD properties of the drug on targets
  • Developed PBPK and PK/PD modeling to support drugs in early development of Cardiovascular Metabolismas well asOncology
  • Predictive analysis for outcome trial studies for late development
  • Conceptualized and implemented hypothesis driven modeling
    • to provide mechanistic explanation for the dynamic behavior of biomarkers in clinical trials
    • in order to identify subpopulations with different outcomes for a drug
    • Presented results with different focii targeted to diverse audiences – clinicians, academics, medical affairs, sales and marketing
    • Successfully initiated collaboration in modeling support to clinical teams on certain early development drugs  – delivered results in 6 months
    • Initiated and successfully collaborated in model development with external vendors
    • Integral part of a software development team – specialized inputs as an end-user allowed a high level of customization for internal use
    • Successful collaborations with senior and junior level modeling scientists
    • Mentoring – junior scientists and interns

 

June 2009-July 2011

Research Experiences – continued…

 

Assistant Scientist, Ravi Iyengar lab, Pharmacology and Systems Therapeutics,                   Mt. Sinai School of Medicine, New York

• Large scale biochemical reaction modeling for innate immune response by regulation of Interferon β during viral infection with specific analysis to flu virus
• Initiated and successfully collaborated with world renowned microbiologists to support development of modeling (using qt-PCR data) and validating the results using (image analysis)
• Modeled integration of pathway modeling with 2-D spatial analysis on interdependence of cell shape (in neuron cells) on the local biochemical regulation incorporating fluorescent image analysis to inform and validate the model
• Modeling of MAPK pathway(Oncogene) for analysis cell fate -proliferation,cell death
• Have mentored many graduate and undergraduate students
• Closely involved in grant writing for national funding organizations, eg., NIH, NSF

2005-May 2009

Senior Postdoctoral Fellow, Jose Vilar lab, Computational Biology,                              Memorial Sloan Kettering Cancer Center, New York

• Modeling of apoptosis of cell

2004-2005

Senior Postdoctoral Fellow, RobertB. Franza lab, CSI, Bioengineering,                                        University of Washington, Seattle, WA

• Mathematical modeling of intracellular signaling processes in T cells in response to infection presented by Dendritic cells as ligands.
• Stochastic analysis of probability of discrete molecular interactions for biochemical pathways

 

Played key roles for other  collaborative projects at CSI –

• developing of the software BALSA (Biological Abstraction Layer for Simulation Analysis)
• developing of the stochastic platform SigTran
• designing of  FPGA hardware chip, SCOOBY,to accelerate stochastic simulation

2002-2004

 

Postdoctoral Fellow, James B. Bassingthwaighte lab, NSR, Bioengineering, University of Washington, Seattle, WA

• Reconstruction of Arterial Network from images of sliced rabbit heart

Implementing different models as a part of the resource facility of NSR, especially Electrophysiological models

 

2000-2002

Doctoral Research, Girija Jayaraman lab, Applied Mathematics, Indian Institute of Technology Delhi, India

• Biomechanics: Application of concepts of fluid dynamics to study pressure drop and drug dispersion in catheterized artery

1994-2000

Junior Research Fellow, Girija Jayaraman, Centre for Atmospheric Sciences, Indian Institute of Technology Delhi

Project Title : “Modelling in Cardiovascular Fluid Dynamics with Special Reference to Atherosclerosis’”.

Oct 1993-Dec1993

Junior Research Fellow, H. P. Dixit, Indira Gandhi National Open University, New Delhi, India

Project Title : “Mathematical Modelling of Computer Graphics”.

Jul 1992

– Sept 1993

 

 

Academic Publications

 

1. Sarkar, Anamika*, Nistal-Villan, Estanislao*, Garcia-Saste, Adolfo, Iyengar, Ravi, (2007) Multiple Pinpricks: A general strategy by which viruses deal with the signaling network that controls early host response (in preparation).

 

2. Anamika Sarkar,  Melissa Hallow, Jennifer Beh,  Alan Charney, Hector De Leon,  Sergey Ermakov,  Stuart Friedman,  Anna Georgieva,  Gabriel Helmlinger,  Arthur Lo Manoj Rodrigo, Donald Stanski, and Jeff Trimmer, Ramesh Sarangapani, Integrated model for renin angiotensin aldosterone (RAAS) combination therapies of antihypertensive drugs in blood pressure regulation, (in preparation)

 

3. Anamika Sarkar,  Dean Bottino, David James, Melissa Hallow, Gabriel Helmlinger,  Arthur Lo Manoj Rodrigo, Donald Stanski, and Jeff Trimmer, Ramesh Sarangapani Anna Georgieva,  Aldosterone therapy model predicts better blood pressure reduction in combination with other antihypertensive renin angiotensin aldosterone (RAAS)  drugs. (in preparation)

 

4. Neves, S.R., Tsokas, P., Sarkar, A., Grace, E. A., Rangamani, P., Schaff, J., Blitzer, R.D., Moraru, I.I., Iyengar, R., (2008) Cell shape and negative links in regulatory loops coordinately regulate the propagation of spatial information within signaling network, Cell, 133, 666-680.

 

5. Sarkar, Anamika, Lipshtat, Azi, Berger, Seth and Iyengar, Ravi, (2007) Local propagation of signal transduction: role of cell shape (submitted).

 

6. Sarkar, Anamika, Meila, Marina and Franza, B.R., (2007) IkappaB, NF-kappaB regulation model: simulation analysis of small number of molecules, EURASIP J. of Bioinformatics and Systems Biology Article ID 25250, 10 pages, 2007. doi:10.1155/2007/25250 .

 

7. Sarkar, A., Beard, D. and Franza, B.R., (2006) Effect of binding in cyclic phosphorylation de-phosphorylation process and in energy transformation, Mathematical Biosciences, 202, No:1, 175-193.

 

8. Jayaraman, G. and Sarkar, A., (2005) “Nonlinear analysis of arterial blood flow – steady streaming effect”, Nonlinear Analysis: Theory, Methods & Applications, 63, 880-890.

 

9. Sarkar, A. and Franza, B.R., (2004) The logical analysis of the process of T cell activation: different consequences depending on the state of CD28 engagement, Journal of Theoretical Biology, 226, No:4, 455-466.

 

 

10. Sarkar, A. and Jayaraman, G., (2004) The effect of wall absorption on dispersion in

      oscillatory flow in an annulus: application to catheterized artery, Acta Mechanica,
172, No:3-4, 151 – 167.

 

11. Sarkar, A. and Jayaraman, G., (2002) The effect of wall absorption on dispersion in annular flows, Acta Mechanica, 158, No:122, 105-119.

 

12. Sarkar, A. and Jayaraman, G., (2001) Non linear analysis of oscillatory flow in the annulus of an elastic tube – application to catheterized artery, Physics of Fluids, 13, No:10, 2901-2911.

 

13. Sarkar, A. and Jayaraman, G.,  (1998) Correction to flow rate – pressure drop relation in coronary angioplasty – steady streaming effect, Journal of Biomechanics, 31, 781-791.

 

 

Authored Book Chapter

 

Anamika Sarkar*, Aislyn Wist* and Ravi Iyengar (Nov 2008), Computational and chemical biology approaches to analyzing intracellular signaling networks, Wiley Encyclopedia of Chemical Biology, John Wiley and Sons, New Jersey, USA.

 

Arthur Lo, Jennifer Beh, Hector De Leon, Melissa K. Hallow, Ramprasad Ramakrishna, Manoj Rodrigo, Anamika Sarkar, Ramesh Sarangapani, and Anna Georgieva, (Nov 2010) Using a Systems Biology Approach to Explore Hypotheses Underlying Clinical Diversity of the Renin Angiotensin System and the Response to Antihypertensive Therapies, AAPS Advances in the Pharmaceutical Sciences Series, Vol. 1, Springer, USA

 

Invited Platform Presentations

 

• Disease modeling and its applications in model-based drug R&D: The example of an integrated model of hypertension, renal disease progression and therapeutic modulation of the renin-angiotensin-aldosterone system (RAAS), at Innovation in Life Science & Healthcare, Bryn Mawr, Oct 2009

 

• “Computation model for viral infection: small perturbations to large effects” at World Congress in Nonlinear Analysis, Orlando, July 2008.

 

• “Dynamic regulation of Interferon beta in early viral infection”at Symposium on Modeling Dendritic Cell Responses To Viral Infection, New York, Sept 2006.

 

• “Stochastic modeling and sensitivity analysis of signal transduction processes in T Cell Dendritic Cell interactions”, at SIAM Conference on the Life Sciences, Portland, July 2004.

 

• “Understanding cell signaling processes by mathematical modeling: some applications and limitations”, Bioengineering, University of California at San Diego, February 2004.

 

• “Introduction and overview of systems biology: cellular modeling – Part 1”, for lecture in a seminar course CSE590 – Modeling and Simulation in Systems Biology – at Computer Science Engineering Department, University of Washington, Seattle, Jan 2004.

 

• “Modeling and simulation of signal transduction process in T Cell, Dendritic Cell interactions”at Annual Fall Meeting of Biomedical Society (BMES), Nashville, Oct 2003.

 

 

Conference Platform Presentations

 

• Anamika Sarkar, Estanis Nistal-Villán, Antonio Borderia-Giner, Ana Fernandez-Sesma, Stuart Sealfon, Adolfo García-Sastre, Ravi Iyengar, “Regulation of Interferon β transcription during the early phase of virus invasion”, Annual Fall Meeting of Biomedical Society (BMES), Los Angeles, Sept 2007.
• Sarkar, A. and Jayaraman, G., “Nonlinear model of  flow in a catheterized artery : steady streaming effect”, 3^rd World Congress in Biomechanics, Sapporo, Japan,1998.
•  Sarkar, A. and Jayaraman, G., “Estimation of mean pressure in a catheterized stenosed artery:   steady streaming effect”, 24^th National Conference of Fluid Mechanics and Fluid Power, Calcutta,   India, 1997.
•  Sarkar, A., Jayaraman, G. and Iyengar, S. R. K. , “Effect of steady streaming in  flow between a clot  model and a stenosis” 5th National Conference of Biomechanics, Chennai, India, 1996.

 

Conference Poster Presentations

 

• Anamika Sarkar,  Melissa K. Hallow, Antoine Soubret, Gabriel Helmlinger, Ramesh Sarangapani, Anna Georgieva, Multiscale disease model of heart failure and renal disease with therapeutic application in drug R&D, BMES, Austin,TX, Oct 2010.

 

• Anamika Sarkar,  Melissa Hallow, Ramesh Sarangapani,  Jennifer Beh,  Alan Charney, Hector De Leon,  Sergey Ermakov,  Stuart Friedman,  Anna Georgieva,  Gabriel Helmlinger,  Arthur Lo, Ramprasad Ramakrishna,  Manoj Rodrigo, Donald Stanski, and Jeff Trimmer, Of Mechanisms Involved In GFR Decline and Albuminuria Using The RAAS Hypertension PhysioLab: A Systems Biology Approach To Simulate Diabetic And Hypertensive Nephropathy, American Society of Nephrology, San Diego, Oct 2009.

 

• Jennifer Beh, Hector De Leon, Sergey Ermakov, Stuart Friedman, Anna Georgieva, K. Melissa Hallow, Gabriel Helmlinger, Arthur Lo, Ramprasad Ramakrishna, Mano Rodrigo, Ramesh Sarangapan, Anamika Sarkar, Donald Stanski; Jeff Trimmer, Local generation of Ang I and Ang II in the kidney do not contribute to systemic peptide levels in a dynamic model of systemic and tissue renin-angiotensin system (RAAS) kinetics, AAPS annual meeting, Los Angles, CA, Nov. 8 -12, 2009

 

• Jennifer Beh, Hector De Leon, Sergey Ermakov, Stuart Friedman, Anna Georgieva, K. Melissa Hallow, Gabriel Helmlinger, Arthur Lo, Ramprasad Ramakrishna, Mano Rodrigo, Ramesh Sarangapan, Anamika Sarkar, Donald Stanski; Jeff Trimmer, Integrated model to simulate long-term blood pressure (BP) control, hypertension development and the responses to antihypertensive therapies: the renin angiotensin aldosterone (RAAS) Hypertension PhysioLab Platform. American College of Clinical Pharmacology, San Antonio, Texas, Sep. 13-15, 2009
• Anamika, Sarkar, Lipshtat, Azi, Berger, Seth and Ravi Iyengar, ”Role of cell shape on the local propagation of cell signaling events”, Computational cell Biology Meeting, Cold Spring Harbor, March 2007.

 

• Anamika Sarkar, Estanislao Nistal-Villán, Antonio Borderia-Giner, Ana Fernandez-Sesma, Stuart Sealfon, Adolfo García-Sastre, Ravi Iyengar, “Regulation of Interferon b induction during the early phase of viral infection”, Emerging Science of Emerging Pathogens: from atoms to the world, New York, May 2007.

 

• Sonali Patil, Ganesh Viswanathan, Anamika Sarkar, Jianzhong Hu, Avi Ma’ayan, Myung-June Park, Fernand Hayot, James Wetmur, Adolfo Garcia-Sastre, Ravi Iyengar and Stuart Sealfon, Bioinformatics-based Dendritic Cell Signaling Network and Modeling, Infection and Immunity, New York, September 2006

 

• Sarkar, A., Meila, M., Franza, B.R., Mathematical Modeling of T-cell and Dendritic cell interaction: Signals from very low number of molecules, Computational Physiology: From

Genome to Physiome, San Diego, March 2005.

 

• Pettigrew, Michel F. Sarkar, Anamika , Kellen, M. and  Li, Z., Mathematical models and stochastic simulation of T Cell activation by Antigen Presenting Cells (APC), SIAM Workshop on Computational Models and Simulation for Intra-cellular Processes (CM02),  Washington, D.C., October 2002.

 

• Sarkar, A., Pettigrew, Michel F., Keane, J., Crowther,G., P. Loriaux and Franza, B., A Model for a Network of  T-cell Signaling in Presence of Antigen Presenting Cell ,Annual meeting of American Society for Cell Biology, San Francisco, December 2002.

 

• Sarkar, A. and Jayaraman, G,, “Dispersion in a Catheterized Artery”, Annual Fall Meeting of Biomedical Engineering Society (BMES), Seattle, October 2000.

 

Awards and Fellowships

 

Recipient of travel award from Department of Energy for attending and chairing a session at SIAM Conference on the Life Sciences at Portland.	2004
Recipient of post doctoral Fellowship of Pacific Northwest National Laboratory (PNNL) and University of Washington (UW) Joint Program in Cell.	2002
Recipient of travel grant from both Japanese and Indian Governments for attending          3rd World Congress in Biomechanics at Sapporo, Japan	1998
Recipient of Dr M G Deshpande Memorial Prize for best paper, from Academic and Research Organisation, presented at                                                                                                  24th National Conference of Fluid Mechanics and Fluid Power, Calcutta, India.	1997
Senior Research Fellowship from the Indian Government	1996-1999
Junior Research Fellowship from the Indian Government Software Skills MATLAB and R, SimBiology, Ingenuity, worked in PC and Linux environment	1994-1999

Teaching Experiences

 

TA for pre-PhD core course “Systems Biomedicine” at Pharmacology and Systems Therapeutics, Mt. Sinai School of Medicine, New York	Oct 2007
Mentored Alina Peterson, a rotation PhD student in Ravi Iyengar’s lab, Mt. Sinai School of Medicine, New York.	Jan 2007 – Mar 2007
Mentored René van Ee, from Leiden University Medical Center, Amsterdam, as a part of the International Exchange Program between Universities.	Dec 2004
Mentored Afshin M. Hossain, Bioengineering undergraduate as part of the Work Study program at University of Washington, Seattle.	2003-2004
Taught biological modelling to High-School students of Ballard High School, Seattle, as part of an outreach program at UW/CSI, Seattle.	Summer of 2002 & 2003
TA for pre-PhD course Bioengineering 589 “Bioengineering Principles of Physiology” at Bioengineering, University of Washington, Seattle	Winter 2002
TA for pre-PhD course Bioengineering 550 “Biological Mass Transport” at Bioengineering, University of Washington, Seattle	Spring 2001
Mentored Gregory F. Byrd “Validation of 3-D morphometric and topologic data in the heart” for submitting thesis to School of Medicine, University of Washington, Seattle, for ISMS (The Independent study in Medical Science) requirement.	2001 -2002
Classroom Tutorials  for under-graduate and post-graduate students in Indian Institute of Technology Delhi, India for courses -Differential Equations, Boundary Value Problems, Numerical Analysis, Complex Analysis, Mathematical Modeling	1995-2000

 

Organizational Experiences :

 

Co-organizer for the Track Session “Modeling Non-linear Dynamics of Natural Systems” at World Congress of Nonlinear Analysis at Orlando,	July 2008
Organized Minisymposium titled “Mathematical Modeling of Cellular Dynamics” at SIAM Conference on the Life Sciences at Portland.	July 2004

Professional Affiliations:

 

• Member of American Association for Advancement of Science (AAAS)
• Member of Biomedical Engineering Society (BMES)
• Member of Society for Industrial and Applied Mathematics (SIAM)
• Member of Mathematical Society, Indian Institute Technology Delhi, New Delhi, India

 

University and Academic Services:

 

Reviewed manuscripts for the journals Physics of Fluids Annals of Biomedical Engineering Mathematical Biosciences IEE Systems Biology Applied Mathematics and Computation
Selected as review panel for improvement of Nature	2009-2010
Selected as postdoctoral representative for the Members of Student Affairs Committee of Bioengineering department, University of Washington, Seattle.	2001-2004
Secretary of BEPA (Bioengineering Postdoctoral Association), University of Washington, Seattle.	2001
Organising member for Summer Workshop on “Computational Modeling” hosted by NSR, UW Seattle.          Developed teaching materials and conducted classes, especially on Electrophysiological problems.	Aug 2000 and 2001
Organised MQWEST (Math Quiz) at a local school level while at Indian Institute Technology Delhi, New Delhi, India.	1998
Vice-president Mathematical Society, Indian Institute Technology Delhi, New Delhi, India.	1996-1997

 

 

535 Eagle Rock Ave, West Orange, NJ 07052

718.916.0557 ~ sarkaranamika@yahoo.com

Education

Part time MBA, Pharmaceutical Management, Rutgers Business School Spring2012‐

present

PhD, Applied Mathematics, Indian Institute of Technology Delhi, New Delhi, India

Thesis: Flow and Dispersion in a Catheterized Artery – A Theoretical Model

1994‐2000

Master of Science, Applied Mathematics, Indian Institute of Technology Delhi, New Delhi,

India

1990‐1992

Bachelor of Science , Mathematics, Sri Venkateswara College, University of Delhi, New

Delhi, India

1987‐1990

Research Experiences

Consultant ‐ Scientific and Strategy, (project to project) , Part time – Entrepreneurial Venture

 Sugar and Heart Clinic, Apollo, India

 “sys+bio – systems solution worldwide” , USA

 Advanced Technology and Novel Therapeutics, USA

May 2011‐

present

Visiting Scientist, Novartis Pharmaceuticals Corporation, Modeling and Simulation

 Developed multi‐scale disease modeling platforms based on mechanistic

relationships and biochemical pathways integrated together

o for renal disease (Diabetic ‐ T2D, Hypertensive patients) ‐ in 18 months

o cardiac heart failure model (Reduced Ejection and

o Preserved Ejection fraction patients) ‐ in one year

o Part of the models is published in a chapter of a book, has been presented in

multiple conferences both as platform and poster

o Results from the model will comprise in various manuscripts of peer review

journals ‐ writing in progress

 Learnt physiology of complex organ kidney in normal and diseased states

‐ in six weeks

 Calibrated model parameters with PK/PD properties of the drug on targets

 Developed PBPK and PK/PD modeling to support drugs in early development of

Cardiovascular Metabolism as well as Oncology

 Predictive analysis for outcome trial studies for late development

 Conceptualized and implemented hypothesis driven modeling

o to provide mechanistic explanation for the dynamic behavior of biomarkers

in clinical trials

o in order to identify subpopulations with different outcomes for a drug

 Presented results with different focii targeted to diverse audiences – clinicians,

academics, medical affairs, sales and marketing

 Successfully initiated collaboration in modeling support to clinical teams on certain

early development drugs ‐ delivered results in 6 months

June 2009‐

July 2011

Anamika Sarkar/Curriculum Vitae

2

 Initiated and successfully collaborated in model development with external vendors

 Integral part of a software development team – specialized inputs as an end‐user

allowed a high level of customization for internal use

 Successful collaborations with senior and junior level modeling scientists

 Mentoring ‐ junior scientists and interns

Research Experiences – continued…

Assistant Scientist, Ravi Iyengar lab, Pharmacology and Systems Therapeutics,

Mt. Sinai School of Medicine, New York

 Large scale biochemical reaction modeling for innate immune response by

regulation of Interferon β during viral infection with specific analysis to flu virus

 Initiated and successfully collaborated with world renowned microbiologists to

support development of modeling (using qt‐PCR data) and validating the results

using (image analysis)

 Modeled integration of pathway modeling with 2‐D spatial analysis on

interdependence of cell shape (in neuron cells) on the local biochemical regulation

incorporating fluorescent image analysis to inform and validate the model

 Modeling of MAPK pathway(Oncogene) for analysis cell fate ‐proliferation,cell death

 Have mentored many graduate and undergraduate students

 Closely involved in grant writing for national funding organizations, eg., NIH, NSF

2005‐May

2009

Senior Postdoctoral Fellow, Jose Vilar lab, Computational Biology,

Memorial Sloan Kettering Cancer Center, New York

 Modeling of apoptosis of cell

2004‐2005

Senior Postdoctoral Fellow, RobertB. Franza lab, CSI, Bioengineering,

University of Washington, Seattle, WA

 Mathematical modeling of intracellular signaling processes in T cells in response to

infection presented by Dendritic cells as ligands.

 Stochastic analysis of probability of discrete molecular interactions for biochemical

pathways

Played key roles for other collaborative projects at CSI –

 developing of the software BALSA (Biological Abstraction Layer for Simulation

Analysis)

 developing of the stochastic platform SigTran

 designing of FPGA hardware chip, SCOOBY, to accelerate stochastic simulation

2002‐2004

Postdoctoral Fellow, James B. Bassingthwaighte lab, NSR, Bioengineering, University of

Washington, Seattle, WA

 Reconstruction of Arterial Network from images of sliced rabbit heart

Implementing different models as a part of the resource facility of NSR, especially

Electrophysiological models

2000‐2002

Doctoral Research, Girija Jayaraman lab, Applied Mathematics, Indian Institute of

Technology Delhi, India

 Biomechanics: Application of concepts of fluid dynamics to study pressure drop and drug

1994‐2000

Anamika Sarkar/Curriculum Vitae

3

dispersion in catheterized artery

Junior Research Fellow, Girija Jayaraman, Centre for Atmospheric Sciences, Indian Institute

of Technology Delhi

Project Title : “Modelling in Cardiovascular Fluid Dynamics with Special Reference to

Atherosclerosis’”.

Oct 1993‐

Dec1993

Junior Research Fellow, H. P. Dixit, Indira Gandhi National Open University, New Delhi, India

Project Title : “Mathematical Modelling of Computer Graphics”.

Jul 1992

‐ Sept 1993

Academic Publications

1. Sarkar, Anamika*, Nistal‐Villan, Estanislao*, Garcia‐Saste, Adolfo, Iyengar, Ravi, (2007) Multiple

Pinpricks: A general strategy by which viruses deal with the signaling network that controls early

host response (in preparation).

2. Anamika Sarkar, Melissa Hallow, Jennifer Beh, Alan Charney, Hector De Leon, Sergey Ermakov,

Stuart Friedman, Anna Georgieva, Gabriel Helmlinger, Arthur Lo Manoj Rodrigo, Donald Stanski,

and Jeff Trimmer, Ramesh Sarangapani, Integrated model for renin angiotensin aldosterone

(RAAS) combination therapies of antihypertensive drugs in blood pressure regulation, (in

preparation)

3. Anamika Sarkar, Dean Bottino, David James, Melissa Hallow, Gabriel Helmlinger, Arthur Lo

Manoj Rodrigo, Donald Stanski, and Jeff Trimmer, Ramesh Sarangapani Anna Georgieva,

Aldosterone therapy model predicts better blood pressure reduction in combination with other

antihypertensive renin angiotensin aldosterone (RAAS) drugs. (in preparation)

4. Neves, S.R., Tsokas, P., Sarkar, A., Grace, E. A., Rangamani, P., Schaff, J., Blitzer, R.D., Moraru, I.I.,

Iyengar, R., (2008) Cell shape and negative links in regulatory loops coordinately regulate the

propagation of spatial information within signaling network, Cell, 133, 666‐680.

5. Sarkar, Anamika, Lipshtat, Azi, Berger, Seth and Iyengar, Ravi, (2007) Local propagation of signal

transduction: role of cell shape (submitted).

6. Sarkar, Anamika, Meila, Marina and Franza, B.R., (2007) IkappaB, NF‐kappaB regulation model:

simulation analysis of small number of molecules, EURASIP J. of Bioinformatics and Systems

Biology Article ID 25250, 10 pages, 2007. doi:10.1155/2007/25250 .

7. Sarkar, A., Beard, D. and Franza, B.R., (2006) Effect of binding in cyclic phosphorylation dephosphorylation

process and in energy transformation, Mathematical Biosciences, 202, No:1,

175‐193.

8. Jayaraman, G. and Sarkar, A., (2005) “Nonlinear analysis of arterial blood flow ‐ steady streaming

effect”, Nonlinear Analysis: Theory, Methods & Applications, 63, 880‐890.

Anamika Sarkar/Curriculum Vitae

4

9. Sarkar, A. and Franza, B.R., (2004) The logical analysis of the process of T cell activation: different

consequences depending on the state of CD28 engagement, Journal of Theoretical Biology, 226,

No:4, 455‐466.

Academic Publications – continued…

10. Sarkar, A. and Jayaraman, G., (2004) The effect of wall absorption on dispersion in

oscillatory flow in an annulus: application to catheterized artery, Acta Mechanica,

172, No:3‐4, 151 ‐ 167.

11. Sarkar, A. and Jayaraman, G., (2002) The effect of wall absorption on dispersion in annular flows,

Acta Mechanica, 158, No:122, 105‐119.

12. Sarkar, A. and Jayaraman, G., (2001) Non linear analysis of oscillatory flow in the annulus of an

elastic tube ‐ application to catheterized artery, Physics of Fluids, 13, No:10, 2901‐2911.

13. Sarkar, A. and Jayaraman, G., (1998) Correction to flow rate – pressure drop relation in coronary

angioplasty ‐ steady streaming effect, Journal of Biomechanics, 31, 781‐791.

Authored Book Chapter

Anamika Sarkar*, Aislyn Wist* and Ravi Iyengar (Nov 2008), Computational and chemical biology

approaches to analyzing intracellular signaling networks, Wiley Encyclopedia of Chemical Biology,

John Wiley and Sons, New Jersey, USA.

Arthur Lo, Jennifer Beh, Hector De Leon, Melissa K. Hallow, Ramprasad Ramakrishna, Manoj Rodrigo,

Anamika Sarkar, Ramesh Sarangapani, and Anna Georgieva, (Nov 2010) Using a Systems Biology

Approach to Explore Hypotheses Underlying Clinical Diversity of the Renin Angiotensin System and

the Response to Antihypertensive Therapies, AAPS Advances in the Pharmaceutical Sciences Series,

Vol. 1, Springer, USA

Invited Platform Presentations

 Disease modeling and its applications in model‐based drug R&D: The example of an integrated

model of hypertension, renal disease progression and therapeutic modulation of the reninangiotensin‐

aldosterone system (RAAS), at Innovation in Life Science & Healthcare, Bryn Mawr,

Oct 2009

 “Computation model for viral infection: small perturbations to large effects” at World

Congress in Nonlinear Analysis, Orlando, July 2008.

 “Dynamic regulation of Interferon beta in early viral infection” at Symposium on Modeling

Dendritic Cell Responses To Viral Infection, New York, Sept 2006.

Anamika Sarkar/Curriculum Vitae

5

 “Stochastic modeling and sensitivity analysis of signal transduction processes in T Cell

Dendritic Cell interactions”, at SIAM Conference on the Life Sciences, Portland, July 2004.

 “Understanding cell signaling processes by mathematical modeling: some applications and

limitations”, Bioengineering, University of California at San Diego, February 2004.

Invited Platform Presentations – continued…

 “Introduction and overview of systems biology: cellular modeling ‐ Part 1”, for lecture in a

seminar course CSE590 ‐ Modeling and Simulation in Systems Biology ‐ at Computer Science

Engineering Department, University of Washington, Seattle, Jan 2004.

 “Modeling and simulation of signal transduction process in T Cell, Dendritic Cell interactions”

at Annual Fall Meeting of Biomedical Society (BMES), Nashville, Oct 2003.

Conference Platform Presentations

 Anamika Sarkar, Estanis Nistal‐Villán, Antonio Borderia‐Giner, Ana Fernandez‐Sesma, Stuart

Sealfon, Adolfo García‐Sastre, Ravi Iyengar, “Regulation of Interferon β transcription during the

early phase of virus invasion”, Annual Fall Meeting of Biomedical Society (BMES), Los Angeles,

Sept 2007.

 Sarkar, A. and Jayaraman, G., “Nonlinear model of flow in a catheterized artery : steady

streaming effect”, 3rd World Congress in Biomechanics, Sapporo, Japan,1998.

 Sarkar, A. and Jayaraman, G., “Estimation of mean pressure in a catheterized stenosed artery:

steady streaming effect”, 24th National Conference of Fluid Mechanics and Fluid Power, Calcutta,

India, 1997.

 Sarkar, A., Jayaraman, G. and Iyengar, S. R. K. , “Effect of steady streaming in flow between a

clot model and a stenosis” 5th National Conference of Biomechanics, Chennai, India, 1996.

Conference Poster Presentations

 Anamika Sarkar, Melissa K. Hallow, Antoine Soubret, Gabriel Helmlinger, Ramesh Sarangapani,

Anna Georgieva, Multiscale disease model of heart failure and renal disease with therapeutic

application in drug R&D, BMES, Austin,TX, Oct 2010.

 Anamika Sarkar, Melissa Hallow, Ramesh Sarangapani, Jennifer Beh, Alan Charney, Hector De

Leon, Sergey Ermakov, Stuart Friedman, Anna Georgieva, Gabriel Helmlinger, Arthur Lo,

Ramprasad Ramakrishna, Manoj Rodrigo, Donald Stanski, and Jeff Trimmer, Of Mechanisms

Involved In GFR Decline and Albuminuria Using The RAAS Hypertension PhysioLab: A Systems

Biology Approach To Simulate Diabetic And Hypertensive Nephropathy, American Society of

Nephrology, San Diego, Oct 2009.

Anamika Sarkar/Curriculum Vitae

6

 Jennifer Beh, Hector De Leon, Sergey Ermakov, Stuart Friedman, Anna Georgieva, K. Melissa

Hallow, Gabriel Helmlinger, Arthur Lo, Ramprasad Ramakrishna, Mano Rodrigo, Ramesh

Sarangapan, Anamika Sarkar, Donald Stanski; Jeff Trimmer, Local generation of Ang I and Ang II in

the kidney do not contribute to systemic peptide levels in a dynamic model of systemic and tissue

renin‐angiotensin system (RAAS) kinetics, AAPS annual meeting, Los Angles, CA, Nov. 8 ‐12, 2009

Conference Poster Presentations – continued…

 Jennifer Beh, Hector De Leon, Sergey Ermakov, Stuart Friedman, Anna Georgieva, K. Melissa

Hallow, Gabriel Helmlinger, Arthur Lo, Ramprasad Ramakrishna, Mano Rodrigo, Ramesh

Sarangapan, Anamika Sarkar, Donald Stanski; Jeff Trimmer, Integrated model to simulate longterm

blood pressure (BP) control, hypertension development and the responses to

antihypertensive therapies: the renin angiotensin aldosterone (RAAS) Hypertension PhysioLab

Platform. American College of Clinical Pharmacology, San Antonio, Texas, Sep. 13‐15, 2009

 Anamika, Sarkar, Lipshtat, Azi, Berger, Seth and Ravi Iyengar, ”Role of cell shape on the local

propagation of cell signaling events”, Computational cell Biology Meeting, Cold Spring Harbor,

March 2007.

 Anamika Sarkar, Estanislao Nistal‐Villán, Antonio Borderia‐Giner, Ana Fernandez‐Sesma, Stuart

Sealfon, Adolfo García‐Sastre, Ravi Iyengar, “Regulation of Interferon  induction during the early

phase of viral infection”, Emerging Science of Emerging Pathogens: from atoms to the world, New

York, May 2007.

 Sonali Patil, Ganesh Viswanathan, Anamika Sarkar, Jianzhong Hu, Avi Ma’ayan, Myung‐June

Park, Fernand Hayot, James Wetmur, Adolfo Garcia‐Sastre, Ravi Iyengar and Stuart Sealfon,

Bioinformatics‐based Dendritic Cell Signaling Network and Modeling, Infection and Immunity,

New York, September 2006

 Sarkar, A., Meila, M., Franza, B.R., Mathematical Modeling of T‐cell and Dendritic cell

interaction: Signals from very low number of molecules, Computational Physiology: From

Genome to Physiome, San Diego, March 2005.

 Pettigrew, Michel F. Sarkar, Anamika , Kellen, M. and Li, Z., Mathematical models and

stochastic simulation of T Cell activation by Antigen Presenting Cells (APC), SIAM Workshop on

Computational Models and Simulation for Intra‐cellular Processes (CM02), Washington, D.C.,

October 2002.

 Sarkar, A., Pettigrew, Michel F., Keane, J., Crowther,G., P. Loriaux and Franza, B., A Model for a

Network of T‐cell Signaling in Presence of Antigen Presenting Cell ,Annual meeting of American

Society for Cell Biology, San Francisco, December 2002.

 Sarkar, A. and Jayaraman, G,, “Dispersion in a Catheterized Artery”, Annual Fall Meeting of

Biomedical Engineering Society (BMES), Seattle, October 2000.

Anamika Sarkar/Curriculum Vitae

7

Awards and Fellowships

Recipient of travel award from Department of Energy for attending and chairing a session

at SIAM Conference on the Life Sciences at Portland.

2004

Recipient of post doctoral Fellowship of Pacific Northwest National Laboratory (PNNL)

and University of Washington (UW) Joint Program in Cell.

2002

Recipient of travel grant from both Japanese and Indian Governments for attending

3rd World Congress in Biomechanics at Sapporo, Japan

1998

Recipient of Dr M G Deshpande Memorial Prize for best paper, from Academic and

Research Organisation, presented at

24th National Conference of Fluid Mechanics and Fluid Power, Calcutta, India.

1997

Senior Research Fellowship from the Indian Government 1996‐1999

Junior Research Fellowship from the Indian Government

Software Skills

MATLAB and R, SimBiology, Ingenuity, worked in PC and Linux environment

1994‐1999

Teaching Experiences

TA for pre‐PhD core course “Systems Biomedicine” at Pharmacology and Systems

Therapeutics, Mt. Sinai School of Medicine, New York

Oct 2007

Mentored Alina Peterson, a rotation PhD student in Ravi Iyengar’s lab, Mt. Sinai School of

Medicine, New York.

Jan 2007 ‐

Mar 2007

Mentored René van Ee, from Leiden University Medical Center, Amsterdam, as a part of

the International Exchange Program between Universities.

Dec 2004

Mentored Afshin M. Hossain, Bioengineering undergraduate as part of the Work Study

program at University of Washington, Seattle.

2003‐2004

Taught biological modelling to High‐School students of Ballard High School, Seattle, as

part of an outreach program at UW/CSI, Seattle.

Summer of

2002 & 2003

TA for pre‐PhD course Bioengineering 589 “Bioengineering Principles of Physiology” at

Bioengineering, University of Washington, Seattle

Winter 2002

TA for pre‐PhD course Bioengineering 550 “Biological Mass Transport” at Bioengineering,

University of Washington, Seattle

Spring 2001

Mentored Gregory F. Byrd “Validation of 3‐D morphometric and topologic data in the

heart” for submitting thesis to School of Medicine, University of Washington, Seattle, for

ISMS (The Independent study in Medical Science) requirement.

2001 ‐2002

Classroom Tutorials for under‐graduate and post‐graduate students in Indian Institute of

Technology Delhi, India for courses ‐Differential Equations, Boundary Value Problems,

Numerical Analysis, Complex Analysis, Mathematical Modeling

1995‐2000

Anamika Sarkar/Curriculum Vitae

8

Organizational Experiences :

Co‐organizer for the Track Session “Modeling Non‐linear Dynamics of Natural Systems” at

World Congress of Nonlinear Analysis at Orlando,

July 2008

Organized Minisymposium titled “Mathematical Modeling of Cellular Dynamics” at SIAM

Conference on the Life Sciences at Portland.

July 2004

Professional Affiliations:

 Member of American Association for Advancement of Science (AAAS)

 Member of Biomedical Engineering Society (BMES)

 Member of Society for Industrial and Applied Mathematics (SIAM)

 Member of Mathematical Society, Indian Institute Technology Delhi, New Delhi, India

University and Academic Services:

Reviewed manuscripts for the journals

Physics of Fluids

Annals of Biomedical Engineering

Mathematical Biosciences

IEE Systems Biology

Applied Mathematics and Computation

Selected as review panel for improvement of Nature 2009‐2010

Selected as postdoctoral representative for the Members of Student Affairs Committee of

Bioengineering department, University of Washington, Seattle.

2001‐2004

Secretary of BEPA (Bioengineering Postdoctoral Association), University of Washington,

Seattle.

2001

Organising member for Summer Workshop on “Computational Modeling” hosted by NSR,

UW Seattle.

Developed teaching materials and conducted classes, especially on

Electrophysiological problems.

Aug 2000

and 2001

Organised MQWEST (Math Quiz) at a local school level while at Indian Institute

Technology Delhi, New Delhi, India.

1998

Vice‐president Mathematical Society, Indian Institute Technology Delhi, New Delhi, India. 1996‐1997