864-889-0519 chg@clemson.edu
Shahid photo 4.15.2024

Dr. Shahid Mukhtar

Professor, Department of Genetics and Biochemistry

Email: mshahid@clemson.edu


Dr. Mukhtar completed his Ph.D. research on Arabidopsis transcriptional regulatory networks at the Max Planck Institute in Cologne, Germany. His postdoctoral research, conducted in the laboratory of Dr. Jeff Dangl at the University of North Carolina at Chapel Hill, focused on Arabidopsis-pathogens protein-protein interactions. Using genomics, bioinformatics, and systems-level analyses, he collaborated with the Dana Farber Cancer Institute & Center for Cancer Systems Biology to create the first large-scale Arabidopsis-pathogens protein-protein interaction network. This four-year post-doc led to a first-author publication in Science (The Arabidopsis-pathogens interactome; Mukhtar et al. Science 2011) and several co-authored papers, including the Arabidopsis interactome map, global mapping of G-protein interactions, and sequencing and assembly of 19 strains of the pathogenic bacterium P. syringae using next-generation sequencing approaches (Science 2011, Molecular Systems Biology 2011, PLoS Pathogens 2011).

As a prominent academic leader, he has a global impact through his role as the Director of The Multinational Arabidopsis Steering Committee (MASC), a collaborative effort involving 34 countries since its establishment in 1990. Serving as the Chair of the “Plant Immunity” subcommittee within MASC, he contributes to crafting annual reports and shaping the future of Arabidopsis immunity research. Additionally, He was actively involved in the Southern Section of the American Society of Plant Biologists (ss-ASPB) as Chair, Vice-Chair, Secretary/Treasurer, and Executive Member, organizing impactful conferences and symposia. In academia, he organizes workshops on “Systems Biology & Machine Learning” at the Plant & Animal Genome (PAG) meeting and introduced another on “Data Science” at PAG Australia. Dr. Mukhtar has an impressive history of mentoring students who have received numerous awards and scholarships, such as the Rising Star Award, NSF Graduate Research Scholar Program fellowship, Samuel Barker award, Ireland Research Travel Scholarship, Outstanding Student Development Award, Dean’s Outstanding Student Award and Dean’s scholarship. Additionally, his students have been honored with various awards for poster and oral presentations, regional, and national meetings/conferences. His excellence in teaching is evident through accolades such as the 2021 President’s Award for Excellence in Teaching and the CAS Dean’s Award for Excellence in Teaching. He is recently awarded the Odessa Woolfolk Community Service Award (2023)

Research Interests:

My research interests lie at the intersection of multiomics analyses, single-cell sequencing, large-scale protein-protein interactions (interactome), and GWAS, with a primary focus on addressing precision medicine and health disparity-related questions. Specifically, my research aims to harness the power of single-cell RNA sequencing (scRNA-seq), single-cell ATAC-seq (scATAC-seq), and spatial sequencing techniques to decipher cell type-specific gene regulatory networks and molecular signatures associated with disease states.

Selected Publications

List of peer-reviewed papers and books edited (last 5 years)


  1. Modeling Transcriptional Regulation (2021). Springer US (ISBN-13: 9781071615331)
  2. Protein-Protein Interaction (2023). Springer US (ISBN-13: 9781071633267)


  1. Poudel, S., R.R. Vennam, L.V. Sankarapillai, J. Liu, K.J. Reddy, N.K. Wijewardane, M.S. Mukhtar, and R. Bheemanahalli, Negative Synergistic Effects of Drought and Heat During Flowering and Seed Setting in Soybean. bioRxiv, 2024.
  2. Liu, J., A. Majeed, N. Kumar, K.M. Pajerowska-Mukhtar, and M.S. Mukhtar, Single nuclei multiomics reveals the drought-driven gene regulatory atlas in Arabidopsis. bioRxiv, 2024.
  3. Gouli, S., A. Majeed, J. Liu, D. Mosely, M.S. Mukhtar, and J.H. Ham, Co-occurrence Networks and Topological Analyses Revealed Microbiome Structures in Soybean Roots from a Louisiana Soybean Field Severely Damaged by Prolonged High Temperatures and Drought Stress. bioRxiv, 2024.
  4. Bedgood, R., S. Almehmi, K. Chandran, J.M. Wyss, M.S. Mukhtar, and K.M. Pajerowska-Mukhtar, PlantGIFT: An effective teacher workshop model for translating experimental STEM research into hands-on classroom activities for middle and high school students. SSRN, 2024.
  5. Almehmi, S., R. Bedgood, K. Chandran, J.M. Wyss, K.M. Pajerowska-Mukhtar, and M.S. Mukhtar, PlantGIFT: An Effective Teacher Workshop Model for Increasing Plant-Based Laboratory Experiences in Secondary Science Classrooms. SSRN, 2024.
  6. Watkins, J.M., C. Montes, N.M. Clark, G. Song, C.C. Oliveira, B. Mishra, L. Brachova, C.M. Seifert, M.S. Mitchell, J. Yang, P.A. Braga Dos Reis, D. Urano, M.S. Muktar, J.W. Walley, and A.M. Jones, Phosphorylation dynamics in a flg22-induced, G-protein dependent network reveals the RGS1 phosphatase. Mol Cell Proteomics, 2023: p. 100705.
  7. Umfress, A., A. Chakraborti, S. Priya Sudarsana Devi, R. Adams, D. Epstein, A. Massicano, A. Sorace, S. Singh, M. Iqbal Hossian, S.A. Andrabi, D.K. Crossman, N. Kumar, M. Shahid Mukhtar, H. Luo, C. Simpson, K. Abell, M. Stokes, T. Wiederhold, C. Rosen, H. Lu, A. Natarajan, and J.A. Bibb, Cdk5 mediates rotational force-induced brain injury. Sci Rep, 2023. 13(1): p. 3394.
  8. Palmer, J.W., N. Kumar, L. An, A.C. White, M.S. Mukhtar, and H.L. Harris, Molecular heterogeneity of quiescent melanocyte stem cells revealed by single-cell RNA-sequencing. bioRxiv, 2023.
  9. Mishra, B., M. Athar, and M.S. Mukhtar, Integrative systems biology framework discovers common gene regulatory signatures in multiple mechanistically distinct inflammatory skin diseases. bioRxiv, 2023.
  10. Majeed, A. and S. Mukhtar, Protein-Protein Interaction Network Exploration Using Cytoscape. Methods Mol Biol, 2023. 2690: p. 419-427.
  11. Kumar, N. and S. Mukhtar, Building Protein-Protein Interaction Graph Database Using Neo4j. Methods Mol Biol, 2023. 2690: p. 469-479.
  12. Kumar, N. and M.S. Mukhtar, Ranking Plant Network Nodes Based on Their Centrality Measures. Entropy (Basel), 2023. 25(4).
  13. Kumar, N. and M.S. Mukhtar, Integrated Systems Biology Pipeline to Compare Co-Expression Networks in Plants and Elucidate Differential Regulators. Plants (Basel), 2023. 12(20).
  14. Kumar, N., B.K. Mishra, J. Liu, B. Mohan, D. Thingujam, K.M. Pajerowska-Mukhtar, and M.S. Mukhtar, Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators in Arabidopsis. Int J Mol Sci, 2023. 24(8).
  15. Kashyap, M.P., B. Mishra, R. Sinha, L. Jin, N. Kumar, K.F. Goliwas, J. Deshane, B.E. Elewski, C.A. Elmets, M. Athar, M.S. Mukhtar, and R. C., NK and NKT cells in the pathogenesis of Hidradenitis suppurativa: Novel therapeutic strategy through targeting of CD2. bioRxiv, 2023.
  16. Jin, L., M.P. Kashyap, Y. Chen, J. Khan, Y. Guo, J.Q. Chen, M.B. Lee, Z. Weng, A. Oak, P. Patcha, T. Mayo, R. Sinha, V. Atigadda, S.M. Mukhtar, J.S. Deshane, C. Raman, C. Elston, B.E. Elewski, C.A. Elmets, and M. Athar, Mechanism underlying follicular hyperproliferation and oncogenesis in hidradenitis suppurativa. iScience, 2023. 26(6): p. 106896.
  17. Hussain, A., A.A. Khan, M.Q. Aslam, A. Nazar, N. Zaman, A. Amin, M.A. Mahmood, M.S. Mukhtar, H.B. Rahman, M. Farooq, M. Saeed, I. Amin, and S. Mansoor, Comparative Analysis, Diversification and Functional Validation of Plant Nucleotide-Binding Site Domain Genes. bioRxiv, 2023.
  18. Hasan, M., N. Kumar, A. Majeed, A. Ahmad, and S. Mukhtar, Protein-Protein Interaction Network Analysis Using NetworkX. Methods Mol Biol, 2023. 2690: p. 457-467.
  19. Gupta, P., B. Herring, N. Kumar, K. Telange, S.S. Garcia-Buntley, T.W. Caceres, S. Colantonio, F. Williams, P. Kurup, A.M. Carter, D. Lin, H. Chen, B. Rose, R. Jaskula-Sztul, M.S. Mukhtar, S. Reddy, and J.A. Bibb, A Potential Instigator of an Aggressive Phenotype in Cdk5-dependent Medullary Thyroid Carcinoma. bioRxiv, 2023.
  20. Fakhar, A.Z., J. Liu, K.M. Pajerowska-Mukhtar, and M.S. Mukhtar, The Lost and Found: Unraveling the Functions of Orphan Genes. J Dev Biol, 2023. 11(2).
  21. Fakhar, A.Z., J. Liu, K.M. Pajerowska-Mukhtar, and M.S. Mukhtar, The ORFans’ tale: new insights in plant biology. Trends Plant Sci, 2023. 28(12): p. 1379-1390.
  22. Wang, W., J. Liu, B. Mishra, M.S. Mukhtar, and J.M. McDowell, Sparking a sulfur war between plants and pathogens. Trends Plant Sci, 2022.
  23. Srivastava, R.K., P. Guroji, L. Jin, M.S. Mukhtar, and M. Athar, Combined inhibition of BET bromodomain and mTORC1/2 provides therapeutic advantage for rhabdomyosarcoma by switching cell death mechanism. Mol Carcinog, 2022.
  24. Mishra, B., N. Kumar, and M. Shahid Mukhtar, A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets. Comput Struct Biotechnol J, 2022. 20: p. 2001-2012.
  25. Liu, J., A. Majeed, and M.S. Mukhtar, Rooting through single-cell sequencing in phloem pole cells. Commun Biol, 2022. 5(1): p. 1194.
  26. Liu, J., A.Z. Fakhar, K.M. Pajerowska-Mukhtar, and M.S. Mukhtar, A TIReless battle: TIR domains in plant-pathogen interactions. Trends Plant Sci, 2022. 27(5): p. 426-429.
  27. Kumar, N., B. Mishra, and M.S. Mukhtar, A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions. STAR Protoc, 2022. 3(3): p. 101608.
  28. Kashyap, M.P., J. Khan, R. Sinha, L. Jin, V. Atigadda, J.S. Deshane, A.R. Ahmed, A. Kilic, C. Raman, M.S. Mukhtar, C.A. Elmets, and M. Athar, Advances in molecular pathogenesis of hidradenitis suppurativa: Dysregulated keratins and ECM signaling. Semin Cell Dev Biol, 2022.
  29. Hussain, A., J. Liu, B. Mohan, A. Burhan, Z. Nasim, R. Bano, A. Ameen, M. Zaynab, M.S. Mukhtar, and K.M. Pajerowska-Mukhtar, A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants. Sci Rep, 2022. 12(1): p. 12328.
  30. Hussain, A., N. Asif, A.R. Pirzada, A. Noureen, J. Shaukat, A. Burhan, M. Zaynab, E. Ali, K. Imran, A. Ameen, M.A. Mahmood, A. Nazar, and M.S. Mukhtar, Genome wide study of cysteine rich receptor like proteins in Gossypium sp. Sci Rep, 2022. 12(1): p. 4885.
  31. Goliwas, K.F., M.P. Kashyap, J. Khan, R. Sinha, Z. Weng, A.S.W. Oak, L. Jin, V. Atigadda, M.B. Lee, C.A. Elmets, M.S. Mukhtar, C. Raman, J.S. Deshane, and M. Athar, Ex Vivo Culture Models of Hidradenitis Suppurativa for Defining Molecular Pathogenesis and Treatment Efficacy of Novel Drugs. Inflammation, 2022. 45(3): p. 1388-1401.
  32. Chehade, S.B., G.B.H. Green, C.D. Graham, A. Chakraborti, B. Vashai, A. Moon, M.B. Williams, B. Vickers, T. Berryhill, W. Van Der Pol, L. Wilson, M.L. Powell, D.L. Smith, Jr., S. Barnes, C. Morrow, M.S. Mukhtar, G.D. Kennedy, J.A. Bibb, and S.A. Watts, A modified standard American diet induces physiological parameters associated with metabolic syndrome in C57BL/6J mice. Front Nutr, 2022. 9: p. 929446.
  33. Yoshino, Y., B. Roy, N. Kumar, M. Shahid Mukhtar, and Y. Dwivedi, Molecular pathology associated with altered synaptic transcriptome in the dorsolateral prefrontal cortex of depressed subjects. Transl Psychiatry, 2021. 11(1): p. 73.
  34. Srivastava, R.K., B. Mishra, S. Muzaffar, M.S. Gorbatyuk, A. Agarwal, M.S. Mukhtar, and M. Athar, Dynamic Regulation of the Nexus Between Stress Granules, Roquin, and Regnase-1 Underlies the Molecular Pathogenesis of Warfare Vesicants. Front Immunol, 2021. 12: p. 809365.
  35. Srivastava, R.K., J. Khan, A. Arumugam, S. Muzaffar, P. Guroji, M.S. Gorbatyuk, C.A. Elmets, A.T. Slominski, M.S. Mukhtar, and M. Athar, 5′-CapDependent Translation as a Potent Therapeutic Target for Lethal Human Squamous Cell Carcinoma. J Invest Dermatol, 2021. 141(4): p. 742-753 e10.
  36. Mishra, B., N. Kumar, and M.S. Mukhtar, Network biology to uncover functional and structural properties of the plant immune system. Curr Opin Plant Biol, 2021. 62: p. 102057.
  37. Mishra, B., M. Athar, and M.S. Mukhtar, Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity. Sci Rep, 2021. 11(1): p. 7373.
  38. Kumar, N., B. Mishra, M. Athar, and S. Mukhtar, Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC. Methods Mol Biol, 2021. 2328: p. 171-182.
  39. Chakraborti, A., C. Graham, S. Chehade, B. Vashi, A. Umfress, P. Kurup, B. Vickers, H.A. Chen, R. Telange, T. Berryhill, W. Van Der Pol, M. Powell, S. Barnes, C. Morrow, D.L. Smith, Jr., M.S. Mukhtar, S. Watts, G. Kennedy, and J. Bibb, High Fructose Corn Syrup-Moderate Fat Diet Potentiates Anxio-Depressive Behavior and Alters Ventral Striatal Neuronal Signaling. Front Neurosci, 2021. 15: p. 669410.
  40. Carter, A.M., N. Kumar, B. Herring, C. Tan, R. Guenter, R. Telange, W. Howse, F. Viol, T.R. McCaw, H.H. Bickerton, P. Gupta, F. Gillardon, E.A. Woltering, D. Dhall, J. Totenhagen, R.R. Banerjee, E.M. Kurian, S. Reddy, H. Chen, J. Schrader, J. Bart Rose, M.S. Mukhtar, and J.A. Bibb, Cdk5 drives formation of heterogeneous pancreatic neuroendocrine tumors. Oncogenesis, 2021. 10(12): p. 83.
  41. Zaidi, S.S., R.Z. Naqvi, M. Asif, S. Strickler, S. Shakir, M. Shafiq, A.M. Khan, I. Amin, B. Mishra, M.S. Mukhtar, B.E. Scheffler, J.A. Scheffler, L.A. Mueller, and S. Mansoor, Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum). Plant Biotechnol J, 2020. 18(3): p. 691-706.
  42. Parry, G., N.J. Provart, S.M. Brady, B. Uzilday, and C. Multinational Arabidopsis Steering, Current status of the multinational Arabidopsis community. Plant Direct, 2020. 4(7): p. e00248.
  43. Kumar, N., B. Mishra, A. Mehmood, A. Mohammad, and M.S. Mukhtar, Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis. iScience, 2020. 23(9): p. 101526.
  44. Kashyap, M.P., R. Sinha, M.S. Mukhtar, and M. Athar, Epigenetic regulation in the pathogenesis of non-melanoma skin cancer. Semin Cancer Biol, 2020.
  45. Hussain, A., M. Farooq, R.Z. Naqvi, I. Amin, K. Pervaiz, M. Saeed, M. Asif, M.S. Mukhtar, and S. Mansoor, Genome-wide identification and classification of resistance genes predicted several decoy domains in Gossypium sp. Plant Gene, 2020. 24: p. 100250.
  46. Gonzalez-Fuente, M., S. Carrere, D. Monachello, B.G. Marsella, A.C. Cazale, C. Zischek, R.M. Mitra, N. Reze, L. Cottret, M.S. Mukhtar, C. Lurin, L.D. Noel, and N. Peeters, EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. Mol Plant Pathol, 2020. 21(10): p. 1257-1270.
  47. Carter, A.M., C. Tan, K. Pozo, R. Telange, R. Molinaro, A. Guo, E. De Rosa, J.O. Martinez, S. Zhang, N. Kumar, M. Takahashi, T. Wiederhold, H.K. Ghayee, S.C. Oltmann, K. Pacak, E.A. Woltering, K.J. Hatanpaa, F.E. Nwariaku, E.G. Grubbs, A.J. Gill, B. Robinson, F. Gillardon, S. Reddy, R. Jaskula-Sztul, J.A. Mobley, M.S. Mukhtar, E. Tasciotti, H. Chen, and J.A. Bibb, Phosphoprotein-based biomarkers as predictors for cancer therapy. Proc Natl Acad Sci U S A, 2020. 117(31): p. 18401-18411.
  48. Spears, B.J., T.C. Howton, F. Gao, C.M. Garner, M.S. Mukhtar, and W. Gassmann, Direct Regulation of the EFR-Dependent Immune Response by Arabidopsis TCP Transcription Factors. Mol Plant Microbe Interact, 2019. 32(5): p. 540-549.
  49. Naqvi, R.Z., S.S. Zaidi, M.S. Mukhtar, I. Amin, B. Mishra, S. Strickler, L.A. Mueller, M. Asif, and S. Mansoor, Transcriptomic analysis of cultivated cotton Gossypium hirsutum provides insights into host responses upon whitefly-mediated transmission of cotton leaf curl disease. PLoS One, 2019. 14(2): p. e0210011.
  50. Mott, G.A., E. Smakowska-Luzan, A. Pasha, K. Parys, T.C. Howton, J. Neuhold, A. Lehner, K. Grunwald, P. Stolt-Bergner, N.J. Provart, M.S. Mukhtar, D. Desveaux, D.S. Guttman, and Y. Belkhadir, Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases. Sci Data, 2019. 6: p. 190025.
  51. Mishra, B., N. Kumar, and M.S. Mukhtar, Systems Biology and Machine Learning in Plant-Pathogen Interactions. Mol Plant Microbe Interact, 2019. 32(1): p. 45-55.
  52. Li, C., B. Mishra, M. Kashyap, Z. Weng, S.A. Andrabi, S.M. Mukhtar, A.L. Kim, D.R. Bickers, L. Kopelovich, and M. Athar, Patched1 haploinsufficiency severely impacts intermediary metabolism in the skin of Ptch1(+/-)/ODC transgenic mice. Sci Rep, 2019. 9(1): p. 13072.

Honors and Awards

2023                     Odessa Woolfolk Community Service Award

2021                     President’s Award for Excellence in Teaching

2021                     Dean’s Award for Excellence in Teaching

2019                       Nominated for Best Graduate Mentor

2018                       Nominated for Best Graduate Mentor


Google Scholar – Shahid Mukhtar (https://scholar.google.com/citations?user=eCi_q_8AAAAJ&hl=en)