Shahid M. Mukhtar headshot.

Shahid M. Mukhtar

Assistant Professor
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Campbell Hall 369
(205) 934-8335

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

Office Hours: By appointment


Dr. Mukhtar conducted his Ph.D. research on Arabidopsis transcriptional regulatory networks at the Max Planck Institute Cologne, Germany 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, at the University of North Carolina at Chapel Hill. He 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 & Center for Cancer Systems Biology, an affiliate of Harvard Medical School in Boston, MA. His four years long post-doc resulted in a first author publication in Science (The Arabidopsis-pathogens interactome; Mukhtar et al. Science 2011), as well as a number of co-authored high impact papers, including another large-scale network assembly (the Arabidopsis interactome map; Science 2011), global mapping of the G-protein interactions (Molecular Systems Biology 2011) and sequencing and assembly of 19 strains of pathogenic bacterium P. syringae using next-generation sequencing approaches (PLoS Pathogens 2011).

Research Opportunities
I am currently accepting graduate students to start in the next semester. UAB has both M.S. and Ph.D. programs in biology that are research focused. If you are interested in joining my lab, please explore the Shahid Mukhtar Lab and send me an email at This email address is being protected from spambots. You need JavaScript enabled to view it. that outlines your research interests, as well as your curriculum vitae.

Dr. 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. He 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. The Shahid Mukhtar Lab carries out a highly research-active program with graduate and undergraduate students working on a wide range of bioinformatics/genomics projects.

Research Interests

Genomics is the study of the entire genome, usually starting with whole genome sequencing. In the recent years, genomics and proteomics have become powerful tools for revealing gene function and genomic organization in large scale. Functional genomics relies on using the sequence data to explore how DNA and proteins work with each other and the environment to create complex, dynamic living systems.

The long-term goal of the Shahid Mukhtar Lab is to understand how macromolecular networks control biological processes and how environmental perturbations in such networks can explain diverse phenotypes. The current projects under investigation include:

  • Dynamics of Transcriptional Regulatory Networks in Plant Defense
  • Microbial Community Transcriptional Networks
  • Predictive Modelling to Identify Key Functionalities in Host-Pathogen Interactions
  • Exploring the Phytohormone-mediated Dynamic Properties of Network Modules
  • Systems Analyses to Identify Host Cell Metabolism Functional Modules.

For details about these projects, please check out the Shahid Mukhtar Lab.

Recent Courses

  • BY210: Genetics

BY210 provides an introduction to: (a) molecular genetic technologies, (b) principles and mechanisms of inheritance, (c) structure, action and regulation of genes, (d) applications of modern molecular genetic technology to human health and agriculture and (e) necessary background for upper-level courses in molecular genetics, cell biology and evolution.

  • BY434/634/734: Functional Genomics and Systems Biology

BY434/634/734 covers state-of-the-art, high-throughput, established and novel, experimental and computational approaches used in genome sequencing, transcriptomics, proteomics and metabolomics to obtain, integrate and analyze complex data. It is aimed to familiarize students with knowledge on experimental perturbation of genomes, gene regulatory networks, comparative genomics and evolution, as well as basic bioinformatics. This course is a combination of text-based lectures, computer exercises and discussions of the current literature relevant to Functional Genomics and Systems Biology.

  • BY499/789: Seminar in Genetics/Genomics

BY499/789 is designed to refine and extend students’ fluency (both verbal and written) in genetic concepts and techniques. Through the dissection of research papers on diverse genetics/genomics aspects, students learn how to critically think about experimental designs. Students also learn how to devise and propose hypothetical experiments to address unanswered questions in genetics/genomics. They can also appreciate the peer review process through critiquing the peer-reviewed papers.

  • BY397: Advanced Directed Reading

Dr. Shahid Mukhtar has been serving as a as a mentor for BY397 for reading and independent study in the areas of Genomics/Bioinformatics and computational modeling.

Graduate Students

Current Students
  • Ben Marsella, Lab Manager
  • Peter Blair, Ph.D. student
  • Yali Sun, Ph.D. student
  • Timothy C. (TC) Howton, Ph.D. student
  • John Lawson, M.S. student
  • Hayden Hamidi, M.S. student

Select Publications

  • 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.
  • Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Mukhtar MS, Law TF, Cherkis K, Roach J, Grant SR, Jones CD and Dangl JL, "Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates," PLoS Pathogens (2011) 10.1371/journal.ppat.1002132.
  • Mukhtar MS, Nishimura MT, Dangl JL, "NPR1 in Plant Defense: It's Not Over 'til It's Turned over," CELL 29 (2009):804-806.

Academic Distinctions and Professional Societies

  • American Phytopathological Society
  • American Society of Plant Biologists
  • International Society of Molecular Plant-Microbe Interactions

Student Groups

  • Phi Sigma
  • Alpha Epsilon Delta
  • Sigma Xi