Dr Rima Chaudhuri

School of Life and Environmental Sciences

D17 - Charles Perkins Centre
The University of Sydney

Telephone 0286274078

Selected grants

2017

  • Identification of New Mechanisms in Insulin Resistance; Larance M, Chaudhuri R; National Health and Medical Research Council (NHMRC)/Project Grants.

2015

  • Probing the exercise biochemistry landscape for new therapeutic options for treating diabetes; James D, Chaudhuri R, Hoffman N; Diabetes Australia Research Trust (DART)/Research Grants.

Selected publications

Download citations: PDF RTF Endnote

Book Chapters

  • Chaudhuri, R., Yang, J. (2017). Cross-Species PTM Mapping from Phosphoproteomic Data. In Cathy H. Wu, Cecilia N. Arighi & Karen E. Ross (Eds.), Protein Bioinformatics: From Protein Modifications and Networks to Proteomics, (pp. 459-469). New York: Humana Press. [More Information]

Journals

  • Minard, A., Wong, M., Chaudhuri, R., Tan, S., Humphrey, S., Parker, B., Yang, J., Laybutt, D., Cooney, G., Coster, A., Stoeckli, J., James, D. (2016). Hyperactivation of the Insulin Signaling Pathway Improves Intracellular Proteostasis by Coordinately Up-regulating the Proteostatic Machinery in Adipocytes. Journal of Biological Chemistry, 291(49), 25629-25640. [More Information]
  • Davey, J., Watt, K., Parker, B., Chaudhuri, R., Ryall, J., Cunningham, L., Qian, H., Sartorelli, V., Sandri, M., Chamberlain, J., James, D., et al (2016). Integrated expression analysis of muscle hypertrophy identifies Asb2 as a negative regulator of muscle mass. JCI Insight, 1(5), 1-15. [More Information]
  • Kleinert, M., Parker, B., Chaudhuri, R., Fazakerley, D., Serup, A., Thomas, K., Krycer, J., Sylow Hansen, L., Fritzen, A., Hoffman, N., James, D., et al (2016). mTORC2 and AMPK differentially regulate muscle triglyceride content via Perilipin 3. Molecular Metabolism, 5(8), 646-655. [More Information]
  • Tonks, K., Coster, A., Christopher, M., Chaudhuri, R., Xu, A., Gagnon-Bartsch, J., Chisholm, D., James, D., Meikle, P., Greenfield, J., et al (2016). Skeletal Muscle and Plasma Lipidomic Signatures of Insulin Resistance and Overweight/Obesity in Humans. Obesity, 24(4), 908-916. [More Information]
  • Tam, C., Chaudhuri, R., Hutchison, A., Samocha-Bonet, D., Heilbronn, L. (2016). Skeletal muscle extracellular matrix remodeling after short-term overfeeding in healthy humans. Metabolism: Clinical and Experimental, 67, 26-30. [More Information]
  • Domanova, W., Krycer, J., Chaudhuri, R., Yang, P., Vafaee, F., Fazakerley, D., Humphrey, S., James, D., Kuncic, Z. (2016). Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies. PloS One, 11(6), 1-14. [More Information]
  • Chaudhuri, R., Khoo, P., Tonks, K., Junutula, J., Kolumam, G., Modrusan, Z., Samocha-Bonet, D., Meoli, C., Hocking, S., Fazakerley, D., Stockli, J., Yang, J., James, D., et al (2015). Cross-species gene expression analysis identifies a novel set of genes implicated in human insulin sensitivity. Npj Systems Biology And Applications, 1, 1-10. [More Information]
  • Rogers, S., McCloy, R., Parker, B., Chaudhuri, R., Gayevskiy, V., Hoffman, N., Watkins, D., Daly, R., James, D., Burgess, A. (2015). Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells. Data in Brief, 5, 45-52. [More Information]
  • Hoffman, N., Parker, B., Chaudhuri, R., Fisher-Wellman, K., Kleinert, M., Humphrey, S., Yang, P., Holliday, M., Trefely, S., Fazakerley, D., Stoeckli, J., Burchfield, J., James, D., et al (2015). Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates. Cell Metabolism, 22(5), 922-935. [More Information]
  • McCloy, R., Parker, B., Rogers, S., Chaudhuri, R., Gayevskiy, V., Hoffman, N., Ali, N., Watkins, N., Daly, R., James, D., et al (2015). Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Molecular and Cellular Proteomics, 14(8), 2194-2212. [More Information]
  • Trefely, S., Khoo, P., Krycer, J., Chaudhuri, R., Fazakerley, D., Parker, B., Sultani, G., Lee, J., Stephan, J., Torres, E., James, D., Stoeckli, J., et al (2015). Kinome Screen Identifies PFKFB3 and Glucose Metabolism as Important Regulators of the Insulin/IGF-1 Signalling Pathway. The Journal of Biological Chemistry, 290(43), 25834-25846. [More Information]
  • Chaudhuri, R., Sadrieh, A., Hoffman, N., Parker, B., Humphrey, S., Stoeckli, J., Hill, A., James, D., Yang, J. (2015). PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modification. BMC Genomics, 16(1), 1-14. [More Information]
  • Fazakerley, D., Naghiloo, S., Chaudhuri, R., Koumanov, F., Burchfield, J., Thomas, K., Krycer, J., Prior, M., Parker, B., Murrow, B., Stoeckli, J., Meoli, C., James, D., et al (2015). Proteomic Analysis of GLUT4 Storage Vesicles Reveals Tumour Suppressor Candidate 5 (TUSC5) as a Novel Regulator of Insulin Action in Adipocytes. The Journal of Biological Chemistry, 290(39), 23528-23542. [More Information]
  • Parker, B., Yang, G., Humphrey, S., Chaudhuri, R., Ma, X., Peterman, S., James, D. (2015). Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry. Science Signaling, 8(380), 1-8. [More Information]
  • Li, J., Cantley, J., Burchfield, J., Meoli, C., Stockli, J., Whitworth, P., Pant, H., Chaudhuri, R., Groffen, A., Verhage, M., James, D. (2014). DOC2 isoforms play dual roles in insulin secretion and insulin-stimulated glucose uptake. Diabetologia, 57(10), 2173-2182. [More Information]
  • Chaudhuri, R., Carrillo, O., Laughton, C., Orozco, M. (2012). Application of drug-perturbed essential dynamics/molecular dynamics (ED/MD) to virtual screening and rational drug design. Journal of Chemical Theory and Computation, 8(7), 2204-2214. [More Information]
  • Chaudhuri, R., Lee, H., Truong, L., Torres, J., Patel, K., Johnson, M. (2012). Identification of non-macrocyclic small molecule inhibitors against the NS3/4A serine protease of hepatitis C virus through in silico screening. Journal of Chemical Information and Modeling, 52(8), 2245-2256. [More Information]
  • Lee, H., Torres, J., Truong, L., Chaudhuri, R., Mittal, A., Johnson, M. (2012). Reducing agents affect inhibitory activities of compounds: Results from multiple drug targets. Analytical Biochemistry, 423(1), 46-53. [More Information]
  • Chaudhuri, R., Tang, S., Zhao, G., Lu, H., Case, D., Johnson, M. (2011). Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: Inhibitor design implications. Journal of Molecular Biology, 414(2), 272-288. [More Information]
  • Ghosh, A., Takayama, J., Rao, K., Ratia, K., Chaudhuri, R., Mulhearn, D., Lee, H., Nichols, D., Baliji, S., Baker, S., et al (2010). Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: Design, synthesis, protein-ligand X-ray structure and biological evaluation. Journal of Medicinal Chemistry, 53(13), 4968-4979. [More Information]
  • Ghosh, A., Takayama, J., Aubin, Y., Ratia, K., Chaudhuri, R., Baez, Y., Sleeman, K., Coughlin, M., Nichols, D., Mulhearn, D., et al (2009). Structure-based design, synthesis, and biological evaluation of a series of novel and reversible inhibitors for the severe acute respiratory syndrome - Coronavirus papain-like protease. Journal of Medicinal Chemistry, 52(16), 5228-5240. [More Information]
  • Ratia, K., Pegan, S., Takayama, J., Sleeman, K., Coughlin, M., Baliji, S., Chaudhuri, R., fu, W., Prabhakar, B., Johnson, M., et al (2008). A new non-covalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105(42), 16119-16124. [More Information]

Patents

  • Orozco, M., Laughton, C., Carrillo, O., Chaudhuri, R. (2014). Method of exploring the flexibility of macromolecular targets and its use in rational drug design. Patent No. 14349068, 2012768828.
  • Ghosh, A., Takayama, J., Mesecar, A., Johnson, M., Ratia, K., Chaudhuri, R., Mulhearn, D. (2011). Compounds and Methods for Treating Respiratory Diseases. Patent No. 61090759.

2017

  • Chaudhuri, R., Yang, J. (2017). Cross-Species PTM Mapping from Phosphoproteomic Data. In Cathy H. Wu, Cecilia N. Arighi & Karen E. Ross (Eds.), Protein Bioinformatics: From Protein Modifications and Networks to Proteomics, (pp. 459-469). New York: Humana Press. [More Information]

2016

  • Minard, A., Wong, M., Chaudhuri, R., Tan, S., Humphrey, S., Parker, B., Yang, J., Laybutt, D., Cooney, G., Coster, A., Stoeckli, J., James, D. (2016). Hyperactivation of the Insulin Signaling Pathway Improves Intracellular Proteostasis by Coordinately Up-regulating the Proteostatic Machinery in Adipocytes. Journal of Biological Chemistry, 291(49), 25629-25640. [More Information]
  • Davey, J., Watt, K., Parker, B., Chaudhuri, R., Ryall, J., Cunningham, L., Qian, H., Sartorelli, V., Sandri, M., Chamberlain, J., James, D., et al (2016). Integrated expression analysis of muscle hypertrophy identifies Asb2 as a negative regulator of muscle mass. JCI Insight, 1(5), 1-15. [More Information]
  • Kleinert, M., Parker, B., Chaudhuri, R., Fazakerley, D., Serup, A., Thomas, K., Krycer, J., Sylow Hansen, L., Fritzen, A., Hoffman, N., James, D., et al (2016). mTORC2 and AMPK differentially regulate muscle triglyceride content via Perilipin 3. Molecular Metabolism, 5(8), 646-655. [More Information]
  • Tonks, K., Coster, A., Christopher, M., Chaudhuri, R., Xu, A., Gagnon-Bartsch, J., Chisholm, D., James, D., Meikle, P., Greenfield, J., et al (2016). Skeletal Muscle and Plasma Lipidomic Signatures of Insulin Resistance and Overweight/Obesity in Humans. Obesity, 24(4), 908-916. [More Information]
  • Tam, C., Chaudhuri, R., Hutchison, A., Samocha-Bonet, D., Heilbronn, L. (2016). Skeletal muscle extracellular matrix remodeling after short-term overfeeding in healthy humans. Metabolism: Clinical and Experimental, 67, 26-30. [More Information]
  • Domanova, W., Krycer, J., Chaudhuri, R., Yang, P., Vafaee, F., Fazakerley, D., Humphrey, S., James, D., Kuncic, Z. (2016). Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies. PloS One, 11(6), 1-14. [More Information]

2015

  • Chaudhuri, R., Khoo, P., Tonks, K., Junutula, J., Kolumam, G., Modrusan, Z., Samocha-Bonet, D., Meoli, C., Hocking, S., Fazakerley, D., Stockli, J., Yang, J., James, D., et al (2015). Cross-species gene expression analysis identifies a novel set of genes implicated in human insulin sensitivity. Npj Systems Biology And Applications, 1, 1-10. [More Information]
  • Rogers, S., McCloy, R., Parker, B., Chaudhuri, R., Gayevskiy, V., Hoffman, N., Watkins, D., Daly, R., James, D., Burgess, A. (2015). Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells. Data in Brief, 5, 45-52. [More Information]
  • Hoffman, N., Parker, B., Chaudhuri, R., Fisher-Wellman, K., Kleinert, M., Humphrey, S., Yang, P., Holliday, M., Trefely, S., Fazakerley, D., Stoeckli, J., Burchfield, J., James, D., et al (2015). Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates. Cell Metabolism, 22(5), 922-935. [More Information]
  • McCloy, R., Parker, B., Rogers, S., Chaudhuri, R., Gayevskiy, V., Hoffman, N., Ali, N., Watkins, N., Daly, R., James, D., et al (2015). Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Molecular and Cellular Proteomics, 14(8), 2194-2212. [More Information]
  • Trefely, S., Khoo, P., Krycer, J., Chaudhuri, R., Fazakerley, D., Parker, B., Sultani, G., Lee, J., Stephan, J., Torres, E., James, D., Stoeckli, J., et al (2015). Kinome Screen Identifies PFKFB3 and Glucose Metabolism as Important Regulators of the Insulin/IGF-1 Signalling Pathway. The Journal of Biological Chemistry, 290(43), 25834-25846. [More Information]
  • Chaudhuri, R., Sadrieh, A., Hoffman, N., Parker, B., Humphrey, S., Stoeckli, J., Hill, A., James, D., Yang, J. (2015). PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modification. BMC Genomics, 16(1), 1-14. [More Information]
  • Fazakerley, D., Naghiloo, S., Chaudhuri, R., Koumanov, F., Burchfield, J., Thomas, K., Krycer, J., Prior, M., Parker, B., Murrow, B., Stoeckli, J., Meoli, C., James, D., et al (2015). Proteomic Analysis of GLUT4 Storage Vesicles Reveals Tumour Suppressor Candidate 5 (TUSC5) as a Novel Regulator of Insulin Action in Adipocytes. The Journal of Biological Chemistry, 290(39), 23528-23542. [More Information]
  • Parker, B., Yang, G., Humphrey, S., Chaudhuri, R., Ma, X., Peterman, S., James, D. (2015). Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry. Science Signaling, 8(380), 1-8. [More Information]

2014

  • Li, J., Cantley, J., Burchfield, J., Meoli, C., Stockli, J., Whitworth, P., Pant, H., Chaudhuri, R., Groffen, A., Verhage, M., James, D. (2014). DOC2 isoforms play dual roles in insulin secretion and insulin-stimulated glucose uptake. Diabetologia, 57(10), 2173-2182. [More Information]
  • Orozco, M., Laughton, C., Carrillo, O., Chaudhuri, R. (2014). Method of exploring the flexibility of macromolecular targets and its use in rational drug design. Patent No. 14349068, 2012768828.

2012

  • Chaudhuri, R., Carrillo, O., Laughton, C., Orozco, M. (2012). Application of drug-perturbed essential dynamics/molecular dynamics (ED/MD) to virtual screening and rational drug design. Journal of Chemical Theory and Computation, 8(7), 2204-2214. [More Information]
  • Chaudhuri, R., Lee, H., Truong, L., Torres, J., Patel, K., Johnson, M. (2012). Identification of non-macrocyclic small molecule inhibitors against the NS3/4A serine protease of hepatitis C virus through in silico screening. Journal of Chemical Information and Modeling, 52(8), 2245-2256. [More Information]
  • Lee, H., Torres, J., Truong, L., Chaudhuri, R., Mittal, A., Johnson, M. (2012). Reducing agents affect inhibitory activities of compounds: Results from multiple drug targets. Analytical Biochemistry, 423(1), 46-53. [More Information]

2011

  • Chaudhuri, R., Tang, S., Zhao, G., Lu, H., Case, D., Johnson, M. (2011). Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: Inhibitor design implications. Journal of Molecular Biology, 414(2), 272-288. [More Information]
  • Ghosh, A., Takayama, J., Mesecar, A., Johnson, M., Ratia, K., Chaudhuri, R., Mulhearn, D. (2011). Compounds and Methods for Treating Respiratory Diseases. Patent No. 61090759.

2010

  • Ghosh, A., Takayama, J., Rao, K., Ratia, K., Chaudhuri, R., Mulhearn, D., Lee, H., Nichols, D., Baliji, S., Baker, S., et al (2010). Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: Design, synthesis, protein-ligand X-ray structure and biological evaluation. Journal of Medicinal Chemistry, 53(13), 4968-4979. [More Information]

2009

  • Ghosh, A., Takayama, J., Aubin, Y., Ratia, K., Chaudhuri, R., Baez, Y., Sleeman, K., Coughlin, M., Nichols, D., Mulhearn, D., et al (2009). Structure-based design, synthesis, and biological evaluation of a series of novel and reversible inhibitors for the severe acute respiratory syndrome - Coronavirus papain-like protease. Journal of Medicinal Chemistry, 52(16), 5228-5240. [More Information]

2008

  • Ratia, K., Pegan, S., Takayama, J., Sleeman, K., Coughlin, M., Baliji, S., Chaudhuri, R., fu, W., Prabhakar, B., Johnson, M., et al (2008). A new non-covalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105(42), 16119-16124. [More Information]

To update your profile click here. For support on your academic profile contact .