Mano Ram Maurya

Bioinformatics and Computational Systems Engineering & Biology

Please click tabs below to see all the publications.


Journals Papers:


A. Chemical Process Systems Engineering
  1. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “A Systematic Framework for the Development and Analysis of Signed Digraphs for Chemical Processes. 1. Algorithms and Analysis”, Ind. Eng. Chem. Res. 42(20), 4789-4810, 2003 [abstract/PDF].
  2. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “A Systematic Framework for the Development and Analysis of Signed Digraphs for Chemical Processes. 2. Control Loops and Flowsheet Analysis”, Ind. Eng. Chem. Res. 42(20), 4811-4827, 2003 [abstract/PDF].
  3. Dash, S., M. R. Maurya, R. Rengaswamy and V. Venkatasubramanian, “A Novel Interval-halving Framework for Automated Identification of Process Trends”, AIChEJ, 50(1), 149-162, 2004 [abstract/PDF].
  4. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “Application of Signed Digraphs-Based Analysis for Fault Diagnosis of Chemical Process Flowsheets”, Engineering Applications of Artificial Intelligence, 17(5), 501-518, 2004 [abstract/PDF] (won IFAC 2002 - 2005 paper prize).
  5. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “Fault Diagnosis by Qualitative Trend Analysis of the Principal Components”, Chemical Engineering Research and Design, 83(A9), 1122-1132, 2005 [abstract/PDF].
  6. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, "A Signed Directed Graph-based Systematic Framework for Steady-State Malfunction Diagnosis inside Control Loops", Chemical Engineering Science, 61(6), 1790-1810, 2006 [abstract/PDF].
  7. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, "Fault Diagnosis Using Dynamic Trend Analysis: A Review and Recent Developments", Engineering Applications of Artificial Intelligence, 20(2), 133-146, 2007 [abstract/PDF].
  8. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, "A Signed Directed Graph and Qualitative Trend Analysis-Based Framework for Incipient Fault Diagnosis", Chemical Engineering Research and Design, 85(A10), 1407-1422, 2007 [abstract/PDF].
  9. Maurya, M. R., P. K. Paritosh, R. Rengaswamy and V. Venkatasubramanian, "A Framework for On-Line Trend Extraction and Fault Diagnosis", Engineering Applications of Artificial Intelligence, 23(6), 950-960, 2010 [abstract/PDF].

B. Systems Biology (equal effort*)
  1. Bornheimer, S. J., M. R. Maurya, M. G. Farquhar and S. Subramaniam, “Computational modeling reveals how interplay between components of the GTPase cycle regulates signal transduction”, Proc. Natl. Acad. Sci. USA., 101(45), 15899-15904, 2004 [abstract/PDF].
  2. Maurya, M. R., S. J. Bornheimer, V. Venkatasubramanian and S. Subramaniam, "Reduced-Order Modeling of Biochemical Networks: Application to the GTPase-Cycle Signaling Module", IEE Proc. - Systems Biology, 152(4), 229-242, 2005 [abstract/PDF (IEEEXplore link)].
  3. Maurya, M. R., S. R. Katare, P. R. Patkar, A. Rundell and V. Venkatasubramanian, "A Systematic Framework for the Design of Reduced-Order Models for Signal Transduction Pathways from a Control Theoretic Perspective", Computers and Chemical Engineering, 30(3), 437-452, 2006 [abstract/PDF].
  4. Pradervand*, S., M. R. Maurya* and S. Subramaniam, “Identification of Signaling Components Required for the Prediction of Cytokine Release in RAW 264.7 Macrophages”, Genome Biology, 7(2), R11.1-R11.14, 2006 [abstract/PDF] .
  5. Maurya, M. R. and S. Subramaniam, "A Kinetic Model for Calcium Dynamics in RAW 264.7 Cells: 1. Mechanisms, Parameters and Sub-populational Variability", Biophysical Journal, 93(3), 709-728, 2007 [abstract/PDF].
  6. Maurya, M. R. and S. Subramaniam, "A Kinetic Model for Calcium Dynamics in RAW 264.7 Cells: 2. Knockdown Response and Long-Term Response", Biophysical Journal, 93(3), 729-740, 2007 [abstract/PDF].
  7. Maurya, M. R., S. J. Bornheimer, V. Venkatasubramanian and S. Subramaniam, "A Mixed-Integer Nonlinear Optimization Approach to Coarse-Graining Biochemical Networks", IET - Systems Biology, 3(1), 24-39, 2009 [abstract/PDF (IEEEXplore link)].
  8. Gupta, S., M. R. Maurya, D. L. Stephens, E. A. Dennis and S. Subramaniam, "An Integrated Model of Eicosanoid Metabolism and Signaling Based on Lipidomics Flux Analysis", Biophysical Journal, 96(11):4542-51, 2009 [abstract/PDF].
  9. Gupta, S., M. R. Maurya and S. Subramaniam, "Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells", PLoS Comput Biol., 6(1), e1000654, 2010 [abstract/PDF (PLoS CB link)].
  10. Choi*, T. J., M. R. Maurya*, D. M. Tartakovsky and S. Subramaniam, “Stochastic Hybrid Modeling of Intracellular Calcium Dynamics”, J. Chem. Phys., 133(16), 165101, 2010.
  11. Dennis, E. A., R. A. Deems, R. Harkewicz, O. Quehenberger, H. A. Brown, S. B. Milne, D. S. Myers, C. K. Glass, G. Hardiman, D. Reichart, A. H. Merrill, M. C. Sullards, E. Wang, R. C. Murphy, C. R. H. Raetz, T. Garrett, Z. Guan, A. C. Ryan, D. W. Russell, J. G. McDonald, B. M. Thompson, W. A. Shaw, M. Sud, Y. Zhao, S. Gupta, M. R. Maurya, E. Fahy and S. Subramaniam, “A Mouse Macrophage Lipidome”, Journal of Biological Chemistry, 285(51), 39976-85, 2010.
  12. Gupta, S., M. R. Maurya, A. H. Merrill, Jr., C. K. Glass and S. Subramaniam, “Integration of Lipidomics and Transcriptomics Data Towards a Systems Biology Model of Sphingolipid Metabolism”, BMC Systems Biology, 5, 26, 2011.
  13. Subramaniam , S., E. Fahy, S. Gupta, M. Sud, R. W. Byrnes, D. R. Cotter, A. R. Dinasarapu and M. R. Maurya, “Bioinformatics and the Systems Biology of the Lipidome”, Chemical Reviews, 111(10), 6452-6490, 2011 (invited).
  14. DeAngelis, R.A., M. M. Markiewski, I. Kourtzelis, S. Rafail, M. R. Maurya, S. Gupta, S. Subramaniam and J. D. Lambris, A complement-IL-4 regulatory circuit controls liver regeneration, Journal of Immunology, 188(2), 641-648, 2012.
  15. Asadi*, B., M. R. Maurya*, D. M. Tartakovsky and S. Subramaniam, "Comparison of Statistical and Optimization-Based Methods for Data-Driven Network Reconstruction of Biochemical Systems", IET Systems Biology, 6(5), 155-163, 2012.
  16. Choi*, T. J., M. R. Maurya*, D. M. Tartakovsky and S. Subramaniam, "Stochastic Operator-Splitting Method for Reaction-Diffusion Systems", J. Chem. Phys., 137(18), 184102, 2012.
  17. M. R. Maurya, S. Gupta, X. Li, E. Fahy, A. R. Dinasarapu, M. Sud, H. A. Brown, C. K. Glass, R. C. Murphy, D. W. Russell, E. A. Dennis and S. Subramaniam, "Analysis of Inflammatory and Lipid Metabolic Networks across RAW264.7 and Thioglycolate-elicited Macrophages", Journal of Lipid Research, 54(9), 2525-2542, 2013.
  18. Dinasarapu, A. R., S. Gupta, M. R. Maurya, E. Fahy, J. Min, M. Sud, M. J. Gersten, C. K. Glass and S. Subramaniam, "A Combined Omics Study on Activated Macrophages - Enhanced role of STATs in Apoptosis, Immunity and Lipid Metabolism", Bioinformatics, 29(12), 2735-2743, 2013.
  19. Lemons, D., M. R. Maurya, S. Subramaniam and M. Mercola, "Developing microRNA Screening as a Functional Genomics Tool for Disease Research", Frontiers in Computational Physiology and Medicine, 4, Ar223.1-11, 2013 (invited, review paper).
  20. Shibata, N., A. F. Carlin, N. J. Spann, K. Saijo, C. S. Morello, J. G. McDonald, C. Romanoski, M. R. Maurya, M. Kaikkonen, M. Lam, A. Crotti, D. Reichart, J. N. Fox, O. Quehenberger, C. R. Raetz, M. C. Sullards, R. C. Murphy, A. H. Merrill, Jr., H. A. Brown, E. A. Dennis, E. Fahy, S. Subramaniam, D.R. Cavener, D.H. Spector, D.W. Russell, C.K. Glass, "25-hydroxycholesterol activates the Integrated Stress Response to reprogram transcription and translation in macrophages", Journal of Biological Chemistry, 288(50), 35812-23, 2013.
  21. Kihara*, Y., S. Gupta*, M. R. Maurya, O. Quehenberger, A. Armando, C. K. Glass, E. A. Dennis and S. Subramaniam, "Modeling of Eicosanoid Fluxes in Macrophages Reveals Functional Coupling between Cyclooxygenases and Terminal synthases", Biophysical Journal, 106(4), 966-975, 2014.
  22. Masnadi-Shirazi*, M., M. R. Maurya* and S. Subramaniam, "Time-Varying Causal Inference from Phosphoproteomic Measurements in Macrophage Cells", IEEE Trans. Biomed. Circuits Syst., 8(1), 74-86, 2014.
  23. Farhangmehr*, F., M. R. Maurya*, D. M. Tartakovsky and S. Subramaniam, "Information Theoretic Approach to Complex Biological Network Reconstruction: Application to Cytokine Release in RAW 264.7 Macrophages", BMC Systems Biology, 8(1), 77, 2014.
  24. Rojas-Muñoz*, A., M. R. Maurya*, F. Lo and E. Willems, "Integrating Omics into the Cardiac Differentiation of Human Pluripotent Stem Cells", Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 6(4), 311-328, 2014 (review paper).
  25. Gorden, D. L., D. S. Myers, P. T. Ivanova, E. Fahy, M. R. Maurya, S. Gupta, J. Min, N. J. Spann, J. G. McDonald, S. L. Kelly, J. Duan, M. C. Sullards, T. J. Leiker, R. M. Barkley, O. Quehenberger, A. M. Armando, S. B. Milne, T. P. Mathews, M. D. Armstrong, C. Li, W. V. Melvin, R. H. Clements, M. K. Washington, A. M. Mendonsa, J. L. Witztum, Z. Guan, C. K. Glass, R. C. Murphy, E. A. Dennis, A. H. Merrill, Jr., D. W. Russell, S. Subramaniam and H. A. Brown, "Biomarkers of NAFLD Progression: A Lipidomics Approach to an Epidemic", Journal of Lipid Research, 56(3), 722-736, 2015.
  26. Zarrinpar, A., S. Gupta, M. R. Maurya, S. Subramaniam and R. Loomba, "Serum microRNAs Explain Discordance of Non-Alcoholic Fatty Liver Disease in Monozygotic and Dizygotic Twins: A Prospective Study", Gut, 65(9), 1546-54, 2016.
  27. Gupta, S., Y. Kihara, M. R. Maurya, P. C. Norris, E. A. Dennis and S. Subramaniam S., "Computational Modeling of Competitive Metabolism between omega-3- and omega-6-Polyunsaturated Fatty Acids in Inflammatory Macrophages", Journal of Physical Chemistry B, 120(33), 8346-8353, 2016.
  28. Min, J. S., R. A. DeAngelis, E. S. Reis, S. Gupta, M. R. Maurya, C. Evans, A. Das, C. Burant, J. D. Lambris and S. Subramaniam. "Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration", Journal of Immunology, 197(6), 2500-2508, 2016.
  29. Asadi*, B., M. R. Maurya*, D. M. Tartakovsky and S. Subramaniam, "Doubly Penalized LASSO for Reconstruction of Biological Networks", Special Issue, Proceedings of the IEEE "-Foundations & Applications of Science of Information", 105(2), 319-329, 2017.
  30. Ajami, N. E., S. Gupta, M. R. Maurya, P. Nguyen, J. Y. Li, J. Y-J. Shyy, Z. Chen, S. Chien and S. Subramaniam, "Systems Biology Analysis of Longitudinal Functional Response of Endothelial Cells to Shear Stress", Proc. Natl. Acad. Sci. USA, 2017, 114(41), 10990-10995.
  31. Li, Z., M. Martin, J. Zhang, H. Y. Huang, L. Bai, J. Kang, M. He, J. Li, M. R. Maurya, S. Gupta, G. Zhou, P. Sangwung, Y. J. Xu, T. Lei, H. D. Huang, M. Jain, M. K. Jain, S. Subramaniam, and J. Y. Shyy, "Kruppel-Like Factor 4 Regulation of Cholesterol-25-Hydroxylase and Liver X Receptor Mitigates Atherosclerosis Susceptibility", Circulation, 2017, 136(14), 1315-1330.
  32. Miao, Y., N. E. Ajami, T.-S. Huang, F.-M. Lin, C.-H. Lou, Y.-T. Wang, S. Li, J. Kang, H. Munkacsi, M. R. Maurya, S. Gupta, S. Chien, S. Subramaniam and Z. Chen, "Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function", Nature Communications, 2018, 9(1), 292.
  33. Diez-Cuñado, M., K. Wei, P. J. Bushway, M. R. Maurya, R. Perera, S. Subramaniam, P. Ruiz-Lozano and M. Mercola, "MiRNAs that Induce Human Cardiomyocyte Proliferation Converge on the Hippo Pathway", Cell Reports, 2018, 23(7), 2168-2174.
  34. Aboulmouna, L., S. Gupta, M. R. Maurya, F. T. DeVilbiss, S. Subramaniam and D. Ramkrishna, "A Cybernetic Approach to Modeling Lipid Metabolism in Mammalian Cells", Processes, 2018, 6(8), 126.
  35. Rahiminejad, S., M. R. Maurya and S. Subramaniam, "Topological and Functional Comparison of Community Detection Algorithms in Biological Networks", BMC Bioinformatics, 2019, Accepted.
  36. Masnadi-Shirazi, M., M. R. Maurya, G. Pao, E. Ke, I. M. Verma, S. Subramaniam, "Time Varying Causal Network Reconstruction of a Mouse Cell Cycle", BMC Systems Biology, 2019, Accepted (being transferred to BMC Bioinformatics).

C. Submitted
  1. Ajami, N. E., M. R. Maurya, S. Gupta and S. Subramaniam, "DM-ChIP: An accessible online suite for the comparison of broad-peaked ChIP-seq data sets", BMC Bioinformatics, 2018, Submitted.
  2. Zarrinpar*, A., S. Gupta*, M. R. Maurya*, M. Downes, M. Valasek, D. A. Brenner, R. M. Evans, S. Subramaniam and R. Loomba, "Novel Association between Serum MicroRNA Profiling and Fibrosis in NAFLD: A Prospective Study", Hepatology Letters, 2017, Submitted.





Book chapters:

  1. Maurya, M. R., C. Benner, S. Pradervand, C. Glass and S. Subramaniam, "Systems Biology of Macrophages", Chapter 6 in Current Topics in Innate Immunity, Series: Advances in Experimental Medicine and Biology, Volume: 598, Editor: John D. Lambris, Publisher: Springer Science + Business Media, New York, ISBN-13: 978-0387717654, pp 62-79, 2007 (Invited).
  2. Maurya, M. R. and S. Subramaniam, "Computational Challenges in Systems Biology", Chapter 8 in Systems Biomedicine: Concepts and Perspectives, Editors: E. T. Liu and D. A. Lauffenburger, Publisher: Academic Press, San Diego, CA, USA, ISBN-13: 978-0123725509, pp 177-223, 2009 (Invited).
  3. Gupta*, S., A. R. Dinasarapu*, M. J. Gersten*, M. R. Maurya* and S. Subramaniam, "Omics Approaches to Macrophage Biology", Chapter 29 in Macrophages: Biology and Role in the Pathology of Diseases, Editors: Subhra K. Biswas and Alberto Mantovani, Publisher: Springer-Verlag, New York, NY, USA, ISBN-13: 978-1-4939-1310-7, pp 587-615, 2014 (Invited).


Refereed Publications in Conference Proceedings:

  1. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “Systematic Development and Application of Digraphs for Process Diagnosis and Hazards Analysis”, In the proceedings of the 4th IFAC Workshop on On-Line Fault Detection & Supervision in the Chemical Process Industries (CHEMFAS-4), Korea, June 7-8, pp 327-332, 2001.
  2. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “Incipient Fault Diagnosis of Tennessee Eastman Flowsheet using Signed Directed Graph and Trend Analysis”, In the supplementary proceedings of the 12th European Symposium on Computer Aided Process Engineering (ESCAPE-12), The Hague, The Netherlands, May 26-29, 2002.
  3. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “Qualitative Trend Analysis of the Principal Components: Application to Fault Diagnosis”, In the proceedings of the 8th International Symposium on Process Systems Engineering (PSE-2003), P.R. China, January 5-10, pp 968-973, 2004.
  4. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “Consistent Malfunction Diagnosis Inside Control Loops using Signed Directed Graphs”, In the proceedings of the 13th European Symposium on Computer Aided Process Engineering (ESCAPE-13), Lappeenranta, Finland, June 1-4, pp 473-478, 2003.
  5. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “A Framework for On-line Trend Extraction and Fault Diagnosis”, In the proceedings of the International Symposium on Advanced Control of Chemical Processes (ADChEM-2003), Hong Kong, January 11-14, pp 423-428, 2004.
  6. Maurya, M. R., R. Rengaswamy and V. Venkatasubramanian, “Fault Diagnosis by Qualitative Trend Analysis of the Principal Components: Prospects and some new Results”, In the proceedings of the 5th IFAC symposium on Fault Detection, Supervision and Safety of Technical Processes (SAFEPROCESS-2003), Washington D.C., USA, June 9-11, pp 861-866, 2003.
  7. Maurya, M. R., S. J. Bornheimer, V. Venkatasubramanian and S. Subramaniam, “Reduced-Order Modeling of Biochemical Networks by Simultaneous Determination of Network Topology and Parameters”, In the proceedings of the Foundations of Systems Biology in Engineering (FOSBE 2005), University of California, Santa Barbara, August 7-10, pp 281-284, 2005.
  8. Srinivasan, R., M. R. Maurya and R. Rengaswamy, "Root Cause Analysis of Oscillating Control Loops", In the proceedings of the International Symposium on Advanced Control of Chemical Processes (ADChEM-2006), Gramado, Brazil, April 2-5, pp 1151-1156, 2006.
  9. Asadi*, B., M. R. Maurya*, D. M. Tartakovsky and S. Subramaniam, “Comparison of Statistical and Optimization-based Methods for Data-Driven Network Reconstruction of Biochemical Systems”, In the proceedings of the IASTED International Conference (CompBio 2010), Cambridge, MA, USA, Nov. 1-3, pp 587-592, 2010.


Posters and Papers Presented at Conferences and Meetings (*: speaker, §: equal effort):

  1. Maurya*, M. R., R. Rengaswamy and V. Venkatasubramanian, “Systematic Development of Digraphs and Application in Process Operations”, In AIChE Annual Meeting, 267b, Reno, NV, Nov. 4-9, 2001 [poster].
  2. Maurya*, M. R., R. Rengaswamy and V. Venkatasubramanian, “Signed Directed Graph and Trend Analysis-Based Framework for Incipient Fault Diagnosis- Application to Tennessee Eastman Case Study”, In AIChE Annual Meeting, 263h, Indianapolis, IN, Nov. 3-8, 2002.
  3. Maurya*, M. R., R. Rengaswamy and V. Venkatasubramanian, “Computational Aspects of Trend-Extraction and Trend-Based Similarity Estimation”, In AIChE Annual Meeting, 448e, San Francisco, CA, Nov. 16-21, 2003.
  4. Maurya*, M. R., S. R. Katare, P. R. Patkar, A. Rundell and V. Venkatasubramanian, “Control Theoretic Perspective of Mitogen Activated Protein Kinase Signalin  Pathways”, In AIChE Annual Meeting, 463e, San Francisco, CA, Nov. 16-21, 2003.
  5. Shimada, Y., C. Zhao*, F. Mu, M. R. Maurya and V. Venkatasubramanian, “A Design Rationale Centered Integrated Environment for Batch Process Design”, In AIChE Annual Meeting, 422d, San Francisco, CA, Nov. 16-21, 2003.
  6. Maurya, M. R., S. J. Bornheimer*, V. Venkatasubramanian and S. Subramaniam, “Reduced-Order Models of Biochemical Networks: GTPase Cycle as an Exemplar”, In Second RGS Protein Colloquium, Washington, D.C., April 17, 2004 [poster].
  7. Maurya*, M. R., S. J. Bornheimer, V. Venkatasubramanian and S. Subramaniam, “A Multidimensional Sensitivity Analysis Approach to Reduced-Order Modeling: GTPase Cycle as an Exemplar”, In AIChE Annual Meeting, 426b, Austin, TX, Nov. 7-12, 2004.
  8. Maurya*, M. R., "Computational Models for GTPase Cycle and Calcium Signaling", In AIChE Annual Meeting, 293bd, Austin, TX, Nov. 7-12, 2004 [poster].
  9. Maurya*, M. R., S. J. Bornheimer, V. Venkatasubramanian and S. Subramaniam, “Model-Reduction by Simultaneous Determination of Network Topology and Parameters: Application to Modules in Biochemical Networks”, In AIChE Annual Meeting, 381a, Cincinnati, OH, Oct. 31 - Nov. 4, 2005.
  10. Pradervand, S., M. R. Maurya* and S. Subramaniam, “Identification of Important Signaling Proteins and Stimulants for the Production of Cytokines in RAW 264.7 Macrophages”, In AIChE Annual Meeting, 304g, Cincinnati, OH, Oct. 31 - Nov. 4, 2005.
  11. Maurya*, M. R. and S. Subramaniam, “Modeling of Heterotrimeric G-Protein Mediated Calcium Response in RAW 264.7 Macrophage Cells”, In AIChE Annual Meeting, 506g, Cincinnati, OH, Oct. 31 - Nov. 4, 2005.
  12. Maurya*, M. R. and S. Subramaniam, "Optimization as a Tool for Predictive Modeling of Biological Systems and Mining of Large-Scale Data Sets", In AIChE Annual Meeting, 4bl, Cincinnati, OH, Oct. 31 - Nov. 4, 2005 [poster].
  13. Lo*, F., S. Subramaniam, M. Mercola, R. Guzzo, A. Foley, M. R. Maurya, "Reconstruction of Pathways Leading to Cardiomyocyte Differentiation from ESCs", Presented by Frederick Lo. In The Stem Cell Meeting on the Mesa, La Jolla, CA, Oct. 20, 2006 [poster].
  14. Gupta*, S., M. R. Maurya, A. Maer and S. Subramaniam, "Integrated Modeling of Lipids Metabolism and Signaling Pathways", In AIChE Annual Meeting, 242g, Salt Lake City, UT, Nov. 4 - 9, 2007.
  15. Gupta*, S., M. R. Maurya and S. Subramaniam, "Reconstruction of Phosphoproteins Signaling Network In Raw 264.7 Macrophages", In AIChE Annual Meeting, 572u, Philadelphia, PA, Nov. 16 - 21, 2008 [poster].
  16. Choi*, T., M. R. Maurya, D. M. Tartakovsky and Shankar Subramaniam, "Stochastic Simulation of Cytosolic Calcium Dynamics", In AIChE Annual Meeting, 151b, Nashville, TN, Nov. 8 - 13, 2009.
  17. Gupta*, S., M. R. Maurya and S. Subramaniam, "Modeling of Sphingolipids Metabolism in Mouse Macrophage RAW 264.7 Cells", In AIChE Annual Meeting, 173f, Nashville, TN, Nov. 8 - 13, 2009.
  18. Maurya*, M. R. and S. Subramaniam, "Sensitivity Analysis of a Model of Calcium Dynamics Reveals Hot-Spots of Signaling", In AIChE Annual Meeting, 636d, Nashville, TN, Nov. 8 - 13, 2009.
  19. Sud*, M., D. Cotter, E. Fahy*, R. Byrnes, S. Gupta, S. Li, M. R. Maurya, Y. Zhao, S. Subramaniam, H. A. Brown, C. K. Glass, A. H. Merrill, Jr., R. C. Murphy, C. R. H. Raetz, D. W. Russell, E. A. Dennis, "LIPID Metabolites And Pathways Strategy (LIPID MAPS)", In LIPID MAPS Annual Meeting, Poster No. 18, La Jolla, CA, May 06 - 07, 2009 [poster].
  20. Sud*, M., E. Fahy, Y. Zhao, D. Cotter, R. Byrnes, S. Gupta, S. Li , M. R. Maurya, S. Subramaniam, H. A. Brown, C. K. Glass, A. H. Merrill, Jr., R. C. Murphy, C. R. H. Raetz, D. W. Russell, E. A. Dennis, "Integrated Lipids, Genes, and Pathways Data across Timecourse Experiments for RAW 264.7 Cells Treated with Kdo2-lipid A", In LIPID MAPS Annual Meeting, Poster No. 19, La Jolla, CA, May 06 - 07, 2009 [poster].
  21. Byrnes*, R., D. Cotter, E. Fahy, S. Gupta, S. Li, M. R. Maurya, M. Sud*, S. Subramaniam, "LIPID MAPS Methodologies for Pathway Construction and Analysis", In LIPID MAPS Annual Meeting, Poster No. 46, La Jolla, CA, May 03 - 04, 2010 [poster].
  22. DeAngelis*, R. A., M. M. Markiewski, M. R. Maurya, S. Gupta, S. Subramaniam, and J. D. Lambris, “A Complement-IL-4 Regulatory Circuit Controls Liver Regeneration”, In XXIII International Complement Conference, New York, NY (Molecular Immunology, 47(13), 2227-2227 (Abstract No. 173)), Pergamon-Elsevier Science Ltd, Oxford, UK. Aug 1-5, 2010.
  23. Maurya*, M. R. and S. Subramaniam, “On the Incorporation of Direction and Magnitude in Statistical Correlation: Application to Gene-Microarray Data”, In AIChE Annual Meeting, 693f, Salt lake City, UT, Nov. 7 - 12, 2010.
  24. Maurya*, M. R., T Choi, D. M. Tartakovsky and Shankar Subramaniam, “Timescale Analysis of Cytosolic Calcium Dynamics”, In AIChE Annual Meeting, 155d, Salt lake City, UT, Nov. 7 - 12, 2010.
  25. Gupta, S., M. R. Maurya* and S. Subramaniam, “Matrix and Optimization Approach to Kinetic Modeling of Lipid Pathways”, In AIChE Annual Meeting, 568o, Salt lake City, UT, Nov. 7 - 12, 2010 [poster].
  26. Maurya*, M. R., S. Gupta and S. Subramaniam, “F-Test in k-Fold Cross Validation and Its Application to the Discovery of Biological Networks”, In AIChE Annual Meeting, 597b, Salt lake City, UT, Nov. 7 - 12, 2010.
  27. Choi*, T., M. R. Maurya, D. M. Tartakovsky and Shankar Subramaniam, “Stochastic Operator Splitting Method for Biological Systems”, In AIChE Annual Meeting, 243f, Minneapolis, Oct. 16 - 21, 2011.
  28. Maurya*, M. R., S. Gupta, E. Fahy, A. R. Dinasarapu, X. Li, M. Sud and S. Subramaniam, “Comparative Analysis of Transcriptome and Lipidome of RAW 264.7 and Primary Macrophages”, In AIChE Annual Meeting, 306f, Minneapolis, Oct. 16 - 21, 2011.
  29. Asadi*, B., M. R. Maurya, D. M. Tartakovsky and Shankar Subramaniam, “Data-Driven Network Reconstruction of Biological Systems: Comparison of Statistical and Optimization-Based Methods”, In AIChE Annual Meeting, 764b, Minneapolis, Oct. 16 - 21, 2011.
  30. Maurya*, M. R., S. Gupta, A. R. Dinasarapu, E. Fahy, M. Sud and S. Subramaniam, "Integrated Transcriptomic and Lipidomic Study of Macrophage Response to Liver X Receptor Ligand 25-Hydroxy-Cholesterol", In AIChE Annual Meeting, 760g, Pittsburgh, PA, Oct. 28 - Nov. 2, 2012.
  31. Asadi*,§, B., M. R. Maurya§, D. M. Tartakovsky and S. Subramaniam, "Doubly Penalized Approach for Reconstructing Biological Networks", In AIChE Annual Meeting, 497h, Pittsburgh, PA, Oct. 28 - Nov. 2, 2012.
  32. Gupta*, S., Y. Kihara, M. R. Maurya, O. Quehenberger, A. Armando, C. K. Glass, E. A. Dennis and S. Subramaniam, "Integration of Transcriptomic Data in Kinetic Modeling of Eicosanoids Fluxes Reveals Functional Coupling between Cyclooxygenases and Terminal Synthases", In Biomedical Engineering Society Annual Meeting, P-Fri-B-10, Atlanta, GA, Oct. 24 - 27, 2012.
  33. Maurya*,§, M. R., A. R. Dinasarapu§, S. Gupta§, E. Fahy, M. Sud and S. Subramaniam, "An Integrated Transcriptomic and Lipidomic Study of Oxidized Lipid Activated RAW 264.7 Macrophages", In BMES Annual Meeting, P-Fri-B-21 ("Genomics, Transcriptomics and Proteomics"), Seattle, WA, Sept 25-28, 2013 [poster].
  34. Gupta*, S., A. R. Dinasarapu, M. R. Maurya, E. Fahy, J. Min, M. Sud, M. J. Gersten, C. K. Glass and S. Subramaniam, "Intricate Interplay Between TLR4 and Purinergic Receptor Signaling in Activated Macrophages", In BMES Annual Meeting, P-Fri-B-7 ("Genomics, Transcriptomics and Proteomics"), Seattle, WA, Sept 25-28, 2013 [poster].
  35. Asadi*, B., M. R. Maurya, D. M. Tartakovsky and S. Subramaniam, "Data-Driven Reconstruction of Biological Networks Using a Nonlinear Model Formulation", In AIChE Annual Meeting, 680a, San Francisco, CA, Nov. 3 - Nov. 8, 2013.
  36. Masnadi-Shirazi, M., M. R. Maurya* and S. Subramaniam, "Causal Inference of Time-Varying Signaling Networks Using Dynamic Data", In AIChE Annual Meeting, 601e, Atlanta, GA, Nov. 16 - Nov. 21, 2014 [poster].
  37. DeVilbiss*, F. T., D. Jayachandran, M. R. Maurya, S. Gupta, S. Subramaniam and D. Ramkrishna, "Predicting Gene Expression Data from Changes in Eicosanoid Metabolite Levels in RAW 264.7 Macrophages Using Cybernetic Variables", In AIChE Annual Meeting, 332g, Atlanta, GA, Nov. 16 - Nov. 21, 2014.
  38. DeVilbiss*, F. T., M. R. Maurya, S. Gupta, A. Mandli, S. Subramaniam and D. Ramkrishna, "Prediction of Gene Expression Using Goal-Directed Metabolic Models", In AIChE Annual Meeting, 72e, Salt Lake City, UT, Nov. 8 - Nov. 13, 2015.
  39. Maurya*, M.R., L. Szpankowski, L. S. B. Goldstein and S. Subramaniam, "Dynamic Modeling of Molecular Motor Association with Axonal Amyloid Precursor Protein Vesicles", In AIChE Annual Meeting, 72h, Salt Lake City, UT, Nov. 8 - Nov. 13, 2015.
  40. Gupta*, S., Y. Kihara, M. R. Maurya, P. C. Norris, E. A. Dennis and S. Subramaniam, "A systems Biology Approach to Metabolic Antagonism Between Omega-3 and Omega-6 Fatty Acids During Macrophage Inflammatory Response", In Biomedical Engineering Society Annual Meeting, P-Th-109, Tampa, FL, Oct. 7-10, 2015.
  41. Maurya*, M. R., E. Fahy, S. Gupta, J. Min, S. Subramaniam and LIPID MAPS Consortium, "Lipidomic and Transcriptomic Biomarkers for Diagnosis of Nonalcoholic Fatty Liver Diseases", In AIChE Annual Meeting, 228dr, San Francisco, CA, Nov. 13 - Nov. 18, 2016 [poster].
  42. DeVilbiss*, F. T., M. R. Maurya, S. Gupta, S. Subramaniam and D. Ramkrishna, "Deductive Determination of Dynamic Cellular Objectives from Biological Data", In AIChE Annual Meeting, 740g, San Francisco, CA, Nov. 13 - Nov. 18, 2016.
  43. Masnadi-Shirazi, M., M. R. Maurya, G. Pao, E. Ke, I. M. Verma, S. Subramaniam, "Time Varying Causal Network Reconstruction of Mouse Cell Cycle using Temporal Gene Expression Data", In Biomedical Engineering Society Annual Meeting, 653, Phoenix, AZ, Oct. 11-14, 2017.
  44. Aboulmouna, L., F. T. DeVilbiss, M. R. Maurya, S. Gupta, S. Subramaniam and D. Ramkrishna, "A Cybernetic Approach to Modeling Lipid Metabolism in Mammalian Cells", In AIChE Annual Meeting, 732c, Minneapolis, MN, Oct. 29 - Nov. 03, 2017.
  45. Subramaniam, S. and M. R. Maurya*, "Computational Challenges in Systems Biology", In AIChE Annual Meeting, 89c, Pittsburgh, PA, Oct. 28 - Nov. 02, 2018.
  46. Aboulmouna, L., S. Gupta, M. R. Maurya, F. T. DeVilbiss, S. Subramaniam and D. Ramkrishna, "Application of Cybernetic Control Variables in the Modeling of Lipid Metabolism in Mammalian Systems", In AIChE Annual Meeting, 188dk, Pittsburgh, PA, Oct. 28 - Nov. 02, 2018.