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Shahid M Mukhtar, PhD

M. Shahid Mukhtar PhD Assistant Professor
Department of Biology
University of Alabama at Birmingham
1300 University Blvd.
CH464, Birmingham, AL 35294
Phone: (205) 934-8335 2

Research Interests:

Genomics and Bioinformatics are rapidly evolving disciplines of Biology generating an unprecedented amount of information about gene function and organization of the cell. My research focuses on the molecular mechanisms of host-pathogen interactions using genomics and systems level approaches. I am broadly interested in interdisciplinary research projects at the interface of genomics/systems biology of plant and human immunity using wet lab and computational approaches. Specifically, I aim to understand how macromolecular immune networks are organized in the cells and how these networks can be perturbed to cause diseases. To answer these questions, I work with two experimental systems: the model dicot plant Arabidopsis thaliana and human autoimmune diseases such as Rheumatoid Arthritis and Systemic Lupus Erythematosus.

My main interest is the computational modeling of gene regulatory networks, discovery of novel cis-regulatory motifs involved in plant and human immunity, in silico isolation of functional modules comprising transcription factors and cohorts of co-regulated genes, as well as providing empirical and experimental proofs of my computational/mathematical data in vivo. Moreover, I am also interested in generating large-scale immune interactome maps and understanding how pathogens perturb communications among key functional modules. The main projects that we are currently investigating are:

  1. Systems level approaches to generate host-pathogens protein-protein interaction networks using proteins from Arabidopsis as well as from diverse viral, bacterial, and oomycete pathogens.
  2. Generation of a large-scale Arabidopsis immune transcriptional regulatory network.
  3. Discovering the novel regulatory mechanisms of human Fc receptors in autoimmune diseases.

To achieve the above listed goals, I employ diverse cutting-edge technologies including high-throughput sequencing, transcriptomics, protein-protein interactions, degradomics, forward and reverse genetics, and bioinformatics. My work allows a global understanding of the molecular mechanisms involved in disease resistance and unraveling novel disease resistance signaling pathways to diverse pathogens

For more information about research, teaching and publications, please visit the Shahid Mukhtar Lab Website.


  • 2013
  • 2012
  • 2011
  • pre 2011
  1. Mukhtar MS* (2013) Stack the deck: Engineering Broad-spectrum disease resistance. Trends in Plant Science Sep;18(9):469-72. * Corresponding author
  2. Pajerowska-Mukhtar KM, Emerine DK and Mukhtar MS* (2013) Tell me more: NPRs' role in plant immunity. Trends in Plant Science Jul;18(7):402-11. * Corresponding author
  1. Duffee LE, Boatwright JL, Shockley JM, Mukhtar KPM, Mukhtar MS* (2012) Eukaryotic Endoplasmic Reticulum Stress-Sensing Mechanisms. Advances in Life Sciences DOI: 10.5923/j Volume 2, Number 7. * Corresponding author
  2. Baltrus DA, Nishimura MT, Biswas S, Mukhtar MS, Vicente J, Holub EB, Dangl JL (2012) The molecular basis of host specialization in bean pathovars of Pseudomonas syringae. Molecular Plant Microbe Interactions, (25):877-88.
  3. Moreno A*, Mukhtar MS*, Blanco F, Boatwright JL, Moreno I, Jordan MR, Chen Y, Brandizzi F, Dong X, Orellana A*, Pajerowska-Mukhtar KM* (2012) The IRE1 pathway of the unfolded protein response is activated by biotic stress and involves the splicing of bZIP60 mRNA in Arabidopsis. PLoS ONE 10.1371/journal.pone.0031944. *These authors contributed equally.
  1. Klopffleisch K, Phan N, et al. , Mukhtar MS*, Mudgil Y*, Pattathil S*, Schwarz J*, Seta S*, Tan M*, Temp U*, Trusov Y*, Urano D*, Welter B*, Yang J*, Panstruga R, Uhrig JF, Jones AM. (2011) The Arabidopsis G protein network: linking G protein signaling, cell wall carbohydrates and plant morphogenesis. Molecular Systems Biology 7:532. *These authors are listed alphabetically.
  2. Mukhtar MS*, Carvunis A-R*, Dreze M*, Epple P*, et al., Vidal M*, Beynon J*, Braun P* and Dangl JL* (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science, 333: 596-601.
  3. The Arabidopsis Interactome Mapping Consortium (2011) Evidence for Network Evolution in an Arabidopsis Interactome Map. Science, 333: 601-607. (The above two articles (6th and 7th) are featured in SCIENCE 333: 532-533, Nature Reviews Genetics 12, 586, on websites of NSF and American Society of Plant Biologists and several other news forums and press releases). doi: 10.1126/science.1203877
  4. Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Mukhtar MS, Law TF, Cherkis K, Roach J, Grant SR, Jones CD and Dangl JL (2011) Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLoS Pathogens 10.1371/journal.ppat.1002132.
  1. Mukhtar MS, Deslandes L, Auriac MC, Marco Y and Somssich IE (2008) The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum. The Plant Journal, 56:935-47.
  2. Pajerowska KM, Mukhtar MS, Guex N, Halim VA, Rosahl S, Somssich IE, Gebhardt C (2008) Natural variation of potato allene oxide synthase 2 causes differential levels of jasmonates and pathogen resistance in Arabidopsis. Planta, 228:293–306.
  3. Ulker B, Mukhtar MS and Somssich IE (2007) The WRKY70 transcription factor of Arabidopsis influences both the plant senescence and defense signaling pathways. Planta 226:125-137.
  4. Mukhtar MS, Rahman M and Zafar Y (2002) Assessment of genetic diversity among wheat (Triticum aestivum L.) cultivars using random amplified polymorphic DNA (RAPD) analysis. Euphytica 128: 417–425.
  5. Mukhtar MS, Khan TM and Khan AS (2000). Genetic Analysis of Yield and Yield Components in various Crosses of Cotton (Gossypium hirsutum). International J. of Agri. & Biology. 2-3 (258-260).
  6. Mansoor S, Mukhtar MS, Hussain M, Amin I, Zafar Y, Malik KA and Markham PG (2000) Widespread occurrence of cotton leaf curl virus on Radish in Pakistan. Plant Disease 84:809.
  7. Mukhtar MS, Khan TM, Khan AS, Khan MA and Khan MKR. (2000). Diallel Analysis of some Important Fibre Characteristics of Gossypium hirsutum. International J. of Agri. & Biology. 2-3 (261-263).