Positions

Overview

  • 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).

    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.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2021 Network biology to uncover functional and structural properties of the plant immune systemCurrent Opinion in Plant Biology.  62. 2021
    2021 High Fructose Corn Syrup-Moderate Fat Diet Potentiates Anxio-Depressive Behavior and Alters Ventral Striatal Neuronal SignalingFrontiers in Neuroscience.  15. 2021
    2021 5′-Cap‒Dependent Translation as a Potent Therapeutic Target for Lethal Human Squamous Cell CarcinomaJournal of Investigative Dermatology.  141:742-753.e10. 2021
    2020 EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteomeMolecular Plant Pathology.  21:1257-1270. 2020
    2019 Direct regulation of the EFR-dependent immune response by arabidopsis TCP transcription factorsMolecular Plant-Microbe Interactions.  32:540-549. 2019
    2019 Systems biology and machine learning in plant–pathogen interactionsMolecular Plant-Microbe Interactions.  32:45-55. 2019
    2018 Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescencenpj Systems Biology and Applications.  4. 2018
    2018 Network biology discovers pathogen contact points in host protein-protein interactomesNature Communications.  9. 2018
    2018 Erratum to: An extracellular network of Arabidopsis leucine-rich repeat receptor kinases (Nature, (2018), 553, 7688, (342-346), 10.1038/nature25184)Nature.  561:E8. 2018
    2018 An extracellular network of Arabidopsis leucine-rich repeat receptor kinasesNature.  553:342-346. 2018
    2017 Identification of Norway Spruce MYB-bHLH-WDR Transcription Factor Complex Members Linked to Regulation of the Flavonoid PathwayFrontiers in Plant Science.  8. 2017
    2017 Mapping protein-protein interaction using high-throughput yeast 2-hybridMethods in Molecular Biology.  1610:217-230. 2017
    2016 Pathogen Tactics to Manipulate Plant Cell DeathCurrent Biology.  26:R608-R619. 2016
    2016 Making the right connections: Network biology and plant immune system dynamicsCurrent Plant Biology.  5:2-12. 2016
    2016 The roles of aquaporins in plant stress responsesJournal of Developmental Biology.  4. 2016
    2016 Intrinsically disordered proteins: Controlled chaos or random walkInternational Journal of Plant Biology.  6:52-57. 2016
    2015 Heterotrimeric G-proteins in Picea abies and their regulation in response to Heterobasidion annosum s.l. infectionBMC Plant Biology.  15. 2015
    2015 The Top 10 oomycete pathogens in molecular plant pathologyMolecular Plant Pathology.  16:413-434. 2015
    2014 Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of lifeCell Host and Microbe.  16:364-375. 2014
    2014 Getting to the edge: Protein dynamical networks as a new frontier in plant-microbe interactionsFrontiers in Plant Science.  5. 2014
    2014 Expression-based network biology identifies immune-related functional modules involved in plant defenseBMC Genomics.  15. 2014
    2012 The molecular basis of host specialization in bean pathovars of Pseudomonas syringaeMolecular Plant-Microbe Interactions.  25:877-888. 2012
    2011 Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesisMolecular Systems Biology.  7. 2011
    2009 NPR1 in Plant Defense: It's Not over 'til It's Turned overCell.  137:804-806. 2009
    2002 Assessment of genetic diversity among wheat (Triticum aestivum L.) cultivars from a range of localities across Pakistan using random amplified polymorphic DNA (RAPD) analysis 2002

    Research Overview

  • 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.

    Systems Biology, Functional Genomics, Bioinformatics, Plant Immune Networks
  • Teaching Activities

  • BY698 - Nonthesis Research (Summer Term 2021) 2021
  • BY798 - Nondissertation Research (Summer Term 2021) 2021
  • BY210 - Genetics (Spring Term 2021) 2021
  • BY501 - Genetics for Teachers (Spring Term 2021) 2021
  • BY798 - Nondissertation Research (Spring Term 2021) 2021
  • BY211 - Genetics for Honors-HON (Fall Term 2020) 2020
  • BY798 - Nondissertation Research (Fall Term 2020) 2020
  • BY798 - Nondissertation Research (Summer Term 2020) 2020
  • BY398 - Undergrad Research - RES (Spring Term 2020) 2020
  • BY798 - Nondissertation Research (Spring Term 2020) 2020
  • BY799 - Dissertation Research (Spring Term 2020) 2020
  • BY698 - Nonthesis Research (Fall Term 2019) 2019
  • BY798 - Nondissertation Research (Fall Term 2019) 2019
  • BY799 - Dissertation Research (Fall Term 2019) 2019
  • BY698 - Nonthesis Research (Summer Term 2019) 2019
  • BY799 - Dissertation Research (Summer Term 2019) 2019
  • BY210 - Genetics (Summer Term 2019) 2019
  • BY696 - Special Topics in Biology II (Summer Term 2019) 2019
  • BY210 - Genetics (Spring Term 2019) 2019
  • BY398 - Undergrad Research - RES (Spring Term 2019) 2019
  • BY501 - Genetics for Teachers (Spring Term 2019) 2019
  • BY698 - Nonthesis Research (Spring Term 2019) 2019
  • BY798 - Nondissertation Research (Spring Term 2019) 2019
  • BY799 - Dissertation Research (Spring Term 2019) 2019
  • BY398 - Undergrad Research - RES (Fall Term 2018) 2018
  • BY434 - Function Genomics Sys Bio (Fall Term 2018) 2018
  • BY634 - Function Genomics Sys Bio (Fall Term 2018) 2018
  • BY698 - Nonthesis Research (Fall Term 2018) 2018
  • BY734 - Function Genomics Sys Bio (Fall Term 2018) 2018
  • BY798 - Nondissertation Research (Fall Term 2018) 2018
  • BY799 - Dissertation Research (Fall Term 2018) 2018
  • BY698 - Nonthesis Research (Summer Term 2018) 2018
  • BY798 - Nondissertation Research (Summer Term 2018) 2018
  • BY799 - Dissertation Research (Summer Term 2018) 2018
  • BY210 - Genetics (Summer Term 2018) 2018
  • BY501 - Genetics for Teachers (Summer Term 2018) 2018
  • BY210 - Genetics (Spring Term 2018) 2018
  • BY398 - Undergrad Research - RES (Spring Term 2018) 2018
  • BY501 - Genetics for Teachers (Spring Term 2018) 2018
  • BY698 - Nonthesis Research (Spring Term 2018) 2018
  • BY798 - Nondissertation Research (Spring Term 2018) 2018
  • BY434 - Function Genomics Sys Bio (Fall Term 2017) 2017
  • BY634 - Function Genomics Sys Bio (Fall Term 2017) 2017
  • BY698 - Nonthesis Research (Fall Term 2017) 2017
  • BY734 - Function Genomics Sys Bio (Fall Term 2017) 2017
  • BY798 - Nondissertation Research (Fall Term 2017) 2017
  • BY696 - Special Topics in Biology II (Summer Term 2017) 2017
  • BY698 - Nonthesis Research (Summer Term 2017) 2017
  • BY798 - Nondissertation Research (Summer Term 2017) 2017
  • BY210 - Genetics (Summer Term 2017) 2017
  • BY698 - Nonthesis Research (Spring Term 2017) 2017
  • BY798 - Nondissertation Research (Spring Term 2017) 2017
  • BY698 - Nonthesis Research (Fall Term 2016) 2016
  • BY798 - Nondissertation Research (Fall Term 2016) 2016
  • BY210 - Genetics (Summer Term 2016) 2016
  • BY501 - Genetics for Teachers (Summer Term 2016) 2016
  • BY698 - Nonthesis Research (Summer Term 2016) 2016
  • BY699 - Thesis Research (Summer Term 2016) 2016
  • BY798 - Nondissertation Research (Summer Term 2016) 2016
  • BY210 - Genetics (Spring Term 2016) 2016
  • BY398 - Undergrad Research - RES (Spring Term 2016) 2016
  • BY501 - Genetics for Teachers (Spring Term 2016) 2016
  • BY698 - Nonthesis Research (Spring Term 2016) 2016
  • BY699 - Thesis Research (Spring Term 2016) 2016
  • BY798 - Nondissertation Research (Spring Term 2016) 2016
  • BY398 - Undergrad Research - RES (Fall Term 2015) 2015
  • BY434 - Function Genomics Sys Bio (Fall Term 2015) 2015
  • BY634 - Function Genomics Sys Bio (Fall Term 2015) 2015
  • BY698 - Nonthesis Research (Fall Term 2015) 2015
  • BY734 - Function Genomics Sys Bio (Fall Term 2015) 2015
  • BY798 - Nondissertation Research (Fall Term 2015) 2015
  • BY398 - Undergrad Research - RES (Summer Term 2015) 2015
  • BY698 - Nonthesis Research (Summer Term 2015) 2015
  • BY798 - Nondissertation Research (Summer Term 2015) 2015
  • BY210 - Genetics (Spring Term 2015) 2015
  • BY397 - Advanced Directed Readings (Spring Term 2015) 2015
  • BY398 - Undergrad Research - RES (Spring Term 2015) 2015
  • BY501 - Genetics for Teachers (Spring Term 2015) 2015
  • BY698 - Nonthesis Research (Spring Term 2015) 2015
  • BY798 - Nondissertation Research (Spring Term 2015) 2015
  • BY698 - Nonthesis Research (Fall Term 2014) 2014
  • BY699 - Thesis Research (Fall Term 2014) 2014
  • BY798 - Nondissertation Research (Fall Term 2014) 2014
  • BY398 - Undergrad Research - RES (Summer Term 2014) 2014
  • BY698 - Nonthesis Research (Summer Term 2014) 2014
  • BY798 - Nondissertation Research (Summer Term 2014) 2014
  • BY210 - Genetics (Spring Term 2014) 2014
  • BY699 - Thesis Research (Spring Term 2014) 2014
  • BY798 - Nondissertation Research (Spring Term 2014) 2014
  • BY434 - Function Genomics Sys Bio (Fall Term 2013) 2013
  • BY634 - Function Genomics Sys Bio (Fall Term 2013) 2013
  • BY698 - Nonthesis Research (Fall Term 2013) 2013
  • BY734 - Function Genomics Sys Bio (Fall Term 2013) 2013
  • BY210 - Genetics (Spring Term 2013) 2013
  • BY434 - Function Genomics Sys Bio (Fall Term 2012) 2012
  • BY634 - Function Genomics Sys Bio (Fall Term 2012) 2012
  • BY734 - Function Genomics Sys Bio (Fall Term 2012) 2012
  • BY499 - Biology Seminar (Spring Term 2012) 2012
  • BY689 - Seminar in Genetics (Spring Term 2012) 2012
  • BY789 - Seminar in Genetics (Spring Term 2012) 2012
  • BY434 - Function Genomics Sys Bio (Fall Term 2011) 2011
  • BY634 - Function Genomics Sys Bio (Fall Term 2011) 2011
  • BY734 - Function Genomics Sys Bio (Fall Term 2011) 2011
  • Education And Training

  • Doctor of Science or Mathematics in Genetics, 2005
  • Master of Sciences or Mathematics in Plant Genetics, University of Agriculture/Faisalabad 2000
  • Bachelor of Science or Mathematics in Plant Genetics, University of Agriculture/Faisalabad 1997
  • Full Name

  • Shahid Mukhtar