Asad Abidi received the BSc degree in Electrical Engineering from Imperial College, London, in 1976, and the Ph.D. from the University of California, Berkeley, in 1982. He worked at Bell Laboratories, Murray Hill until 1985, and then joined the faculty of the University of California, Los Angeles, where he is Distinguished Chancellor’s Professor of Electrical Engineering. With his students, he has developed many of the radio circuits and architectures that enable today’s mobile devices. Among other awards, Professor Abidi has received the 2008 IEEE Donald O. Pederson Award in Solid-State Circuits and the Best Paper Award from the IEEE Journal of Solid-State Circuits in 2012. The University of California, Berkeley’s Department of EECS recognized him as a Distinguished Alumnus in 2015. He was elected Fellow of IEEE in 1996, Member of the US National Academy of Engineering, and Fellow of TWAS, the world academy of sciences. Professor Abidi holds the Abdus Salam Chair at the SBASSE School of Science & Engineering, LUMS, Lahore.

Genetics and genomics are rapidly evolving fields that use technological innovations to understand biological processes in a unique way. This workshop aims to foster scientific exchange and synergies across genetics and genomics by bringing together leading and emerging scientists to discuss the classical concepts and the most recent advances in these areas. During this workshop, participants will learn how to employ forward and reverse genetic approaches to design genetic screens for discovering new genes and understanding cellular function. Using model systems, such as Arabidopsis and Drosophila, the participants will learn how newly discovered genes are characterized using various functional genomics approaches. Moreover, the participants will be introduced to various gene-editing approaches, in particular, CRISPR-Cas methodology, to study the function of various genes, focusing on the human genome. An important highlight of the workshop will be hands-on experience in: 

(i) imaging using confocal microscopy,
(ii) analysis of gene expression using real-time PCR,
(iii) genetic studies in Arabidopsis & Drosophila, and finally
(iv) a workflow of CRISPR-Cas9 based gene editing.

Speakers:

Khurram Bashir (PhD)
Plant Biotechnology/Molecular Biology

Dr Khurram's research focuses on plant’s response to different abiotic stresses, such as mineral deficiency and drought stress. It involves identifying and characterizing the molecular function of individual genes using combinations of biotechnological tools and employing several approaches such as the development and characterization of transgenic crops which are tolerant or sensitive to these stresses. It also includes utilizing different plant metabolites to mitigate abiotic stress responses in plants. 

Muhammad Shoaib (PhD)
Chromatin function and Genome Integrity

Dr Shoaib’s research focuses on understanding the role of chromatin-centered molecular pathways that govern key cellular processes including DNA replication, transcription, and DNA damage response. Perturbation of these pathways is linked to the onset and progression of different diseases, in particular, cancer. He employs a highly interdisciplinary approach and relies on both conventional molecular & cellular biology techniques and high-throughput genomics & proteomics technologies such as ChIPseq, RNAseq, Mass Spec, etc., and subsequent bioinformatics analysis. Using Systems Biology approaches, he is keen on integrating the high throughput biological data to build next-generation multiscale in-silico networks of Epigenetic and DNA damage response factors to develop next-generation precision cancer therapies.

Muhammad Tariq (PhD)
Epigenetics

Dr Tariq is interested in understanding how cell fates are established and how they are maintained during our development. His laboratory works on Polycomb (PcG) and Trithorax group (TrxG) genes which are involved in maintaining epigenetic states of gene expression. Defects in gene regulation by these groups of proteins are linked to different types of cancers. Establishing the molecular link between PcG/TrxG and cell signalling pathways is a major long-term goal of the epigenetics lab.

Zaigham Shahzad (PhD)
Plant genetics and epigenetics

Dr. Shahzad is interested in understanding how variation in plant genomes and epigenomes translate to phenotypic variation. This involves developing high-throughput phenotyping, next generation sequencing, and genetic and epigenetic association mapping methods. The long-term aim of the lab is to employ genome and epigenome editing approaches to improve crop production in normal and stressed environments. 

For more information and registration, log on to: https://sbasse.lums.edu.pk/genetics-and-genomics

For any query please reach out to:
Ms. Iqra Manzoor Qadir  |  iqra.manzoor@lums.edu.pk

Final Defense Committee Members:

1. Dr. Basit Shafiq (Chair & Associate Professor, External Thesis Committee Member)

Syed Babar Ali School of Science and Engineering, Department of Computer Science, Lahore University of Management Sciences (LUMS), Pakistan.

2. Dr. Shamshad Zarina (Visiting Professor, External Thesis Committee Member)

Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Pakistan.

3. Dr. Shaper Mirza (Associate Professor, Thesis Committee Member)

Syed Babar Ali School of Science and Engineering, Department of Life Sciences, Lahore University of Management Sciences (LUMS), Pakistan.

4. Dr. Muhammad Tariq (Associate Professor, Thesis Committee Member)

Syed Babar Ali School of Science and Engineering, Department of Life Sciences, Lahore University of Management Sciences (LUMS), Pakistan.

5. Dr. Safee Ullah Chaudhary (Associate Professor, PhD Supervisor)

Syed Babar Ali School of Science and Engineering, Department of Life Sciences, Lahore University of Management Sciences (LUMS), Pakistan.

Publications:

1. Basharat, Abdul Rehman, Kanzal Iman, Muhammad Farhan Khalid, Zohra Anwar, Rashid Hussain, Humnah Gohar Kabir, Maria Tahreem et al. "SPECTRUM–A MATLAB toolbox for proteoform identification from top-down proteomics data." Scientific reports 9, no. 1 (2019): 1-14.

2. Khalid, Muhammad Farhan, Kanzal Iman, Amna Ghafoor, Mujtaba Saboor, Ahsan Ali, Urwa Muaz, Abdul Rehman Basharat et al. "PERCEPTRON: An open-source GPU-accelerated proteoform identification pipeline for top-down proteomics." Nucleic Acids Research (2021).

3. Kanzal Iman, Kyung-Hoon Kwon, Sung Hwan Kim, Kyu Hwan Park, Manhoi Hur, Yong Seong Cho, Hyun Sik Kim et al. “De novo-based Complementary Ion Search (COINS) Algorithm for Enhanced Proteoform Identification and Characterization in Top-Down Proteomics.” Proteomics. (In Review)

4. Ashraf, Muhammad Usman, Kanzal Iman, Muhammad Farhan Khalid, Hafiz Muhammad Salman, Talha Shafi, Momal Rafi, Nida Javaid et al. "Evolution of efficacious pangenotypic hepatitis C virus therapies." Medicinal research reviews 39, no. 3 (2019): 1091-1136.

5. Kanzal Iman, Muhammad Usman Mirza, Fazila Sadia, Matheus Froeyen, Safee Ullah Chaudhary. “An integrative pharmacophore-based screening, covalent docking, molecular dynamics and MM-GBSA approach reveals a covalent inhibitor for targeting drug-resistant Genotype 3 variants of Hepatitis C Viral NS3/4A serine protease”. PLOS ONE. (In Review)

6. Ambreen Sabir, Zainab Nasir, Zonaira Khalid, Hafiz Muhammad Salman, Muhammad Farhan Khalid, Muhammad Burhan Khalid, Fatima Arshad, Kanzal Iman et al. “Profiling microbial and heavy metal contamination of Hudiara drain and its adjoining areas in Lahore, Pakistan.” Chemosphere. (In Review)

Specialization of cells needs maintenance of cell type specific gene expression patterns established during cell fate determination. The Trithorax group (trxG) proteins counteract repressive effect of Polycomb group (PcG) complexes and maintain transcriptional memory of active states of key developmental genes. Although, chromatin structure and modifications appear to play a fundamental role in this process, it is not clear how trxG prevents PcG-silencing at target genes. Recently, our lab employed a whole genome RNAi approach to identify novel trxG-like factors involved in maintaining gene activity. In this study, a hitherto unknown role for Drosophila Mask is described which emerged as one of the candidate trxG genes in RNAi screen. This study provides evidence that trxG mediated gene activation requires Mask. The genome-wide binding profile of Mask correlates with known Trithorax binding sites across Drosophila genome. The potential role of Mask in gene activation is substantiated by its overlap with H3K27ac, a hallmark of gene activation deposited by trxG protein CBP. Notably, Mask positively regulates H3K27ac levels and biochemically interacts with CBP. In addition, Mask predominantly associates with actively transcribed genes and its depletion results in downregulation of trxG targets. Importantly, mask mutant strongly suppresses extra sex comb phenotype in Pc mutants, and enhances trx mutant phenotype. Together, this data provides physiological relevance of Mask linked to trxG and explains in detail a previously unknown role for Mask in maintenance of gene activation by trxG.

Interestingly, Mask is known to interact with a histone kinase, Ballchen (Ball), via a muscle sarcomere structural protein known as Obscurin. Recently, our lab also discovered that Ball substantially co-localizes with H3K27ac at trxG target loci and is required to maintain gene activation in Drosophila. In this study, a previously unknown interaction between Ball and CBP is identified. Analysis of genome-wide binding profile of Ball and CBP reveals major overlap and their co-localization at actively transcribed genes. Importantly, Ball biochemically interacts with CBP and depletion of Ball results in drastic reduction in H3K27ac similar to mask knockdown. Ball also shows significant overlap with Mask binding on chromatin. Together, these results demonstrate a previously unknown synergy between Ball, Mask and CBP that reveals a potentially new pathway required to maintain gene activation during development.   

Publications:

1. Shaukat, A., Khan, M.H.F., Akhtar, J., Haseeb, M.A., Mazhar, K., Umer, Z. and Tariq, M. (2022) Genome-wide binding of Drosophila Mask reveals its role in maintenance of gene activation by Trithorax group. bioRxiv.

2. Shaukat, A., Khan, M.H.F., Ahmad, H., Umer, Z. and Tariq, M. (2021) Interplay Between BALL and CREB Binding Protein Maintains H3K27 Acetylation on Active Genes in Drosophila. Frontiers in Cell and Developmental Biology.

3. Khan, M.H.F., Akhtar, J., Umer, Z., Shaheen, N., Shaukat, A., Munir, M.S., Mithani, A., Anwar, S. and Tariq, M. (2021) Kinome-wide RNAi screen uncovers role of Ballchen in maintenance of gene activation by trithorax group in Drosophila. Frontiers in Cell and Developmental Biology, 9, 458.

Dr. Zaigham completed his PhD and MS  from  Montpellier SupAgro in France in 2010 and  2007 respectively. He has worked as postdoc in his alma mater, followed by research stints at the Glasgow University and since 2020, at the John Innes Centre which is a world renowned Centre in plant and microbial sciences. 

Dr. Zaigham is an established researcher in DNA methylation, evolutionary biology and the translation of genetic code to phenotype, especially in plants. He has several revolutionary discoveries to his credit, an article under review in The Cell which is one of the most prestigious journal in all of sciences and at least two published articles in Nature Communications. He was also the speaker for The Great French Advances in Biology Prize Lecture in 2007, where he spoke about “How plants perceive and respond to flooding”. Dr. Zaigham’s presence in Biology and SBASSE will strengthen its emphasis on plants and agriculture.

Dr. Iqbal is working as a Lead Machine Learning Scientist at Cajal Neuro, Seattle, WA where he's developing a scalable AI system to discover novel solutions for neurodegenerative disorders. In addition, he also serves as a Visiting Research Scientist at UNI | ETH Zurich, Switzerland as well as a Scientific Advisor in tech startups LAAM and Wizlabs in Lahore, PK. Prior to that, Asim worked as a Machine Learning Researcher at Google[x], IBM Research, Allen Institute, and MIT. With a background in Electrical Engineering, Dr. Iqbal holds a Master's and Ph.D. in Machine Learning and Computational Neuroscience from UNI | ETH Zurich as well as a Postdoctorate from Center for Intelligent Systems, EPFL, CH. His research expertise lies in building neuro-inspired deep neural networks, domain adaptation, and deep reinforcement learning.

Dr. Perrimon has 30 years of experience in the fields of developmental genetics, signal transduction and genomics. By developing, improving, and applying a number of genetic techniques (germline clones, FLP/FRT, Gal4/UAS, CRISPR, etc.), he identified many key components of the Receptor Tyrosine Kinases, JAK/STAT, Wnt, Hedgehog, and Notch signaling pathways. His group established high-throughput genome-wide RNAi screens and pooled CRISPR screens to systematically interrogate the entire Drosophila genome in various cell-based assays. In 2003, he created the Drosophila RNAi Screening Center (DRSC) at Harvard Medical School to make this technology available to the community. In addition, in 2008, he initiated the Transgenic RNAi Project (TRiP) to generate transgenic RNAi lines for the community using optimized shRNA vectors that his lab developed, and more recently transgenic gRNA lines for CRISPR loss of function and gain of function screens. Currently, his lab is applying large-scale RNAi and proteomic methods to obtain a global understanding to the structure of a number of signaling pathways and their cross-talks. In addition, he is studying the roles of signaling pathways in homeostasis and tissue remodeling in Drosophila muscles and gut stem cells, as well as hormonal systems involved in inter-organ communication. Since 2015, he has been the PI of the Drosophila database FlyBase. Dr. Perrimon has trained more than 115 students and postdoctoral fellows, most of whom currently hold academic positions.