Assistant Professor
Campbell Hall 369
(205) 934-8335

Research and Teaching Interests: Systems Biology, Functional Genomics, Bioinformatics, Plant Immune Networks

Shahid Mukhtar. Office Hours:
By appointment


Dr. Mukhtar conducted his PhD research on Arabidopsis transcriptional regulatory networks under the supervision of Dr. Imre Somssich. He was fortunate to continue his postdoctoral research in the laboratory of Dr. Jeff Dangl, a Howard Hughes Medical Institute investigator and a member of the National Academy of Sciences. Mukhtar employed genomics, bioinformatics, and computer-aided systems-level analyses to generate the first large-scale Arabidopsis-pathogens protein-protein interaction network in collaboration with the Dana Farber Cancer Institute and the Center for Cancer Systems Biology, an affiliate of Harvard Medical School in Boston, MA.

Research Opportunities

facebookI am currently accepting PhD students to start in Fall 2016. If you are interested in joining my lab, please send me an email that outlines your research interests, as well as your curriculum vitae. You can learn more about the lab on its Facebook page.
This research resulted in a first author publication in Science as well as a number of co-authored high impact papers, including another large-scale network assembly, global mapping of the G-protein interactions, and sequencing and assembly of 19 strains of pathogenic bacterium P. syringae using next-generation sequencing approaches.

The Shahid Mukhtar Lab at UAB carries out a highly research-active program with graduate and undergraduate students working on a wide range of bioinformatics/genomics projects. Dr. Mukhtar has fifteen years of training and experience in various aspects of life sciences such as genetics and genomics as well as in handling large datasets and employing computational tools to answer key questions in plant systems biology.

facebookDr. Mukhtar’s research at UAB focuses at the interface of bioinformatics and life sciences. He is broadly interested in interdisciplinary research projects focused on genomics/systems biology of host immunity using computational approaches. Specifically, he aims to understand how macromolecular networks are organized in the cells and how pathogen proteins perturb such networks to promote diseases.

Shahid Mukhtar and two grad students. Dr. Mukhtar and two graduate students in the Shahid Mukhtar Lab. Proteins are the key components of plant cellular machinery, and many cellular functions are executed by proteins modules embedded in Protein-Protein and Protein-DNA interaction networks. On the contrary, pathogens have evolved sophisticated mechanisms to manipulate the intracellular networks of their hosts to their advantage. Specifically, both inter- and intracellular pathogens deploy virulence effector proteins (called effectors) into host cells that drastically rewire cellular pathways to modulate immune responses and maintain infectivity. The long-term goal of the Shahid Mukhtar Lab is to understand how macromolecular networks control biological processes and how pathogen-mediated perturbations in such networks can explain disease-related genotype-phenotype relationships. To achieve this, we utilize two experimental systems: the model dicot plant Arabidopsis thaliana and human autoimmune diseases. The current projects under investigation include:
  • Generation of a Large-Scale Arabidopsis-Pathogens Protein-Protein Interaction Network: Despite the progress of understanding phytopathogenic microbes and plant infectious diseases, the arms race between hosts and pathogens fuels further scientific research. Within the past decades, the molecular approaches to solve these crises entailed reductionism that seeks to explain a biological system through the summation of its isolated parts. While conceptual origins of systems biology date back almost 100 years, a shift from the reductionist approach to a more inclusive and integrative one started to occur at dawn of this millennium. It also seeks to uncover the unpredictable and predictable intricacies of many different causal relations within diverse biological components. A major aim of systems biology is to create interactome maps as they facilitate studies of biological processes and systems. The interactome seeks to map a universe of molecular interactions that could portray key information towards understanding both healthy and disease phenotypes. For this reason it is referred to as the gateway to systems biology. Currently, we are constructing a large-scale Arabidopsis network using effectors from viral, bacterial, and oomycete pathogens.
  • Dynamics of Transcriptional Regulatory Networks in Plant Defense: In any eukaryotic cell, thousands of genes and their products orchestrate their transcriptional activities to create cellular functions, phenotypic plasticity, and organismal fecundity. Functional modules embedded within protein-DNA interactions networks execute diverse cellular functions. The dichotomous (deterministic or stochastic) nature of network modules is beneficial to cells or organisms for adaptation to physiological perturbations, environmental cues, or pathological signals. As with any host–pathogen conflict, plants and their pathogens are in an evolutionary “arms race” in which the host mounts defenses and the pathogen develops new strategies to thwart the defensive mechanisms, which in turn forces the host to adapt. Currently, we are developing a platform by integrating existing and novel computational tools and algorithms that can be exploited to predict, model and determine the dynamics of plant immune regulatory networks.
  • Discovering the novel regulatory mechanisms of human Fc receptors in autoimmune diseases: Failure of an organism to recognize its own constituent parts as self enables the production of autoantibodies, which attack its own cells, tissues, and/or organs. This causes inflammation and damage and leads to autoimmune disorders such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). The fragment crystallizable receptor IIb (FcγRIIb) expression levels have been linked, by genetic studies in the human population, to the onset of autoimmune diseases. The overriding goals of this research project are: (a) genomics of FCGR2B copy number variation (CNV), (b) determining the mechanisms that influence FcγRIIb expression, and (c) signaling partners of FcγRIIb under steady and signal competent states.
Follow the linked course names to see sample syllabi which describe course aims, learning objectives, requirements, and schedules. These are samples only. The instructor may make changes to these syllabi in future courses.
Shahid Mukhtar Lab 2015Current students:
Download a list of past graduate students.
  • Tully JP, Hill AE, Ahmed HA, Whitley R, Skjellum A, Mukhtar MS*, "Expression-based network biology identifies immune-related functional modules involved in plant defense," BMC Genomics 15 (2014): 421. *Corresponding author
  • Weßling R, Epple P, Altmann S, He Y, Yang L, Henz SR, McDonald N, Wiley K, Bader KC, Gläßer C, Mukhtar MS, et al., "Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life," Cell Host & Microbe 16 (no. 3, September 10, 2014, doi: 10.1016/j.chom.2014.08.004): 364-75.
  • Garbutt CG, Bangalore PV, Kannar P and Mukhtar MS*, "Getting to the Edge: Protein dynamical networks as a new frontier in plant-microbe interactions," Frontiers in Plant Science (2014, doi: 10.3389/fpls.2014.00312). *Corresponding author
  • Mukhtar MS*, Carvunis A-R*, Dreze M*, Epple P*, et al., Vidal M*, Beynon J*, Braun P* and Dangl JL*, "Independently evolved virulence effectors converge onto hubs in a plant immune system network," SCIENCE 333 (2011): 596-601.
  • The Arabidopsis Interactome Mapping Consortium, "Evidence for Network Evolution in an Arabidopsis Interactome Map," SCIENCE 333 (2011): 601-7.
  • Mukhtar MS*, "Engineering NLR immune receptors for broad-spectrum disease resistance," Trends in Plant Science 18 (2013): 469-72. *Corresponding author
  • Pajerowska-Mukhtar KM, Emerine DK, Mukhtar MS*, "Tell me more: NPRs’ role in plant immunity," Trends in Plant Science 18 (2013): 402-11. *Corresponding author
  • Moreno A*, Mukhtar MS*, Blanco F, Boatwright JL, Moreno I, Jordan MR, Chen Y, Brandizzi F, Dong X, Orellana A*, Pajerowska-Mukhtar KM*, "The IRE1 pathway of the unfolded protein response is activated by biotic stress and involves the splicing of bZIP60 mRNA in Arabidopsis," PLoS ONE (2012, 10.1371/journal.pone.0031944). *These authors contributed equally.
  • 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, "The Arabidopsis G protein network: linking G protein signaling, cell wall carbohydrates and plant morphogenesis," Molecular Systems Biology 7 (2011): 53. *These authors are listed alphabetically.
  • American Phytopathological Society
  • American Society of Plant Biologists
  • International Society of Molecular Plant-Microbe Interactions
  • Phi Sigma
  • Alpha Epsilon Delta
  • Sigma Xi