Application of signed digraphs-based analysis for fault diagnosis of chemical process flowsheets. - Mano Ram Maurya; Raghunathan Rengaswamy; Venkat Venkatasubramanian (Eng. Appl. Artif. Intell., 2004)

A systematic framework for the design of reduced-order models for signal transduction pathways from a control theoretic perspective. - Mano Ram Maurya; Santhoji Katare; Priyan R. Patkar; Ann E. Rundell; Venkat Venkatasubramanian (Comput. Chem. Eng., 2006)

Fault diagnosis using dynamic trend analysis: A review and recent developments. - Mano Ram Maurya; Raghunathan Rengaswamy; Venkat Venkatasubramanian (Eng. Appl. Artif. Intell., 2007)

A framework for on-line trend extraction and fault diagnosis. - Mano Ram Maurya; Praveen K. Paritosh; Raghunathan Rengaswamy; Venkat Venkatasubramanian (Eng. Appl. Artif. Intell., 2010)

Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells. - Shakti Gupta; Mano Ram Maurya; Shankar Subramaniam (PLoS Comput. Biol., 2010)

Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism. - Shakti Gupta; Mano Ram Maurya; Alfred H. Merrill Jr.; Christopher K. Glass; Shankar Subramaniam (BMC Syst. Biol., 2011)

An information-theoretic algorithm to data-driven genetic pathway interaction network reconstruction of dynamic systems. - Farzaneh Farhangmehr; Daniel M. Tartakovsky; Parastou Sadatmousavi; Mano Ram Maurya; Shankar Subramaniam (BIBM, 2013)

A combined omics study on activated macrophages - enhanced role of STATs in apoptosis, immunity and lipid metabolism. - Ashok Reddy Dinasarapu; Shakti Gupta; Mano Ram Maurya; Eoin Fahy; Jun Min; Manish Sud; Merril J. Gersten; Christopher K. Glass; Shankar Subramaniam (Bioinform., 2013)

Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages. - Farzaneh Farhangmehr; Mano Ram Maurya; Daniel M. Tartakovsky; Shankar Subramaniam (BMC Syst. Biol., 2014)

Time-Varying Causal Inference From Phosphoproteomic Measurements in Macrophage Cells. - Maryam Masnadi-Shirazi; Mano Ram Maurya; Shankar Subramaniam (IEEE Trans. Biomed. Circuits Syst., 2014)

Doubly Penalized LASSO for Reconstruction of Biological Networks. - Behrang Asadi; Mano Ram Maurya; Daniel M. Tartakovsky; Shankar Subramaniam (Proc. IEEE, 2017)

Time varying causal network reconstruction of a mouse cell cycle. - Maryam Masnadi-Shirazi; Mano Ram Maurya; Gerald M. Pao; Eugene Ke; Inder M. Verma; Shankar Subramaniam (BMC Bioinform., 2019)

Topological and functional comparison of community detection algorithms in biological networks. - Sara Rahiminejad; Mano Ram Maurya; Shankar Subramaniam (BMC Bioinform., 2019)

Playbook workflow builder: Interactive construction of bioinformatics workflows. - Daniel J. B. Clarke; John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Anna I. Byrd; Mano Ram Maurya; Sumana Srinivasan; Keyang Yu; Varduhi Petrosyan; Matthew E. Roth; Miroslav Milinkov; Charles Hadley King; et al. (PLoS Comput. Biol., 2025)