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
- 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).
- 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)
- 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)
- 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.
- Sarkar, Anamika, Lipshtat, Azi, Berger, Seth and Iyengar, Ravi, (2007) Local propagation of signal transduction: role of cell shape (submitted).
- 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 .
- 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.
- Jayaraman, G. and Sarkar, A., (2005) “Nonlinear analysis of arterial blood flow – steady streaming effect”, Nonlinear Analysis: Theory, Methods & Applications, 63, 880-890.
- 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.
- 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.
- Sarkar, A. and Jayaraman, G., (2002) The effect of wall absorption on dispersion in annular flows, Acta Mechanica, 158, No:122, 105-119.
- 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.
- 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”, 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.
- 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
|
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
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