Dr Deena Gendoo BSc, MRes, PhD

Dr Deena Gendoo

Institute of Cancer and Genomic Sciences
Senior Lecturer in Computational Biology & Bioinformatics

Contact details

Address
Centre for Computational Biology
Institute of Cancer and Genomic Sciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT

Dr Deena Gendoo is a Senior Lecturer in Computational Biology at the Institute of Cancer and Genomic Sciences. Dr Gendoo obtained her PhD in 2012 at McGill University in Canada, and completed her postdoctorate fellowship at the Princess Margaret Cancer Centre in Canada. Over the course of her career, she has developed extensive expertise in bioinformatics and computational biology, applied to cancer research and neurodegenerative diseases.

Dr Gendoo’s interdisciplinary background and expertise, in both biology and computer science, provide her with unique perspectives to embark on future research directions that bridge the disciplines of transcriptomics, pharmacogenomics, and structural bioinformatics. Her research program focuses on translational bioinformatics and integrative approaches towards characterization of preclinical disease models (organoids, xenografts, GEMMs) and their application in personalized therapy. One of her research axes focuses on elucidating the molecular pathogenesis of in vitro and in vivo pre-clinical disease models (xenografts, organoids, GEMMs), and developing reliable and quantifiable frameworks for matching model systems to their human counterparts. In tandem, Dr Gendoo will also focus on developing translational and pharmacogenomics approaches that harness these disease models for therapeutics. 

Dr Gendoo was awarded several competitive international fellowships that have supported her research directions, including a Marie Curie Fellowship in the UK, and a Brain Canada-CIBC Brain Cancer Research Training Award in Canada. She received multiple travel awards to present her work in international conferences and workshops, including prestigious and competitive speaker invitations from the Keystone Symposia (USA). She was invited to give an oral presentation of her work on drug inference at the Keystone Symposium on “Genomics and Personalized Medicine” in February 2016. Dr Gendoo also presented her work on the comparison of the genomic landscape of pancreatic tumours, xenografts, and organoids at the Keystone Symposium entitled “Engineered Cells and Tissues as Platforms for Discovery and Therapy”, held in Boston, USA in March 2017.

Dr Gendoo has a strong track record of publications, with 20 publications and an H index of 11. She has published in specialized and high-impact journals within bioinformatics, and developed new software packages to enable reproducible research in bioinformatics. Her work is published in leading impact journals in biomedical research (Cancer Research), and bioinformatics (Oxford Bioinformatics, Plos Computational Biology).

Qualifications

  • PhD in Biology (with graduate specialization in Bioinformatics), McGill University, Canada, 2012
  • MRes in Advanced Genetic Analysis, University of Leeds, United Kingdom, 2007
  • BSc (Hons), American University in Cairo, Egypt, 2006

Biography

Dr Deena Gendoo earned her PhD in Biology, with graduate specialization in Bioinformatics, at McGill University in Montreal, Canada. As part of her PhD, she was also a trainee of the McGill Centre for Bioinformatics, and of the CIHR Systems Biology Training Program. Her research focused on the bioinformatic sequence and structural analysis of amyloidogenicity in prions and other proteins. Prior to her PhD, Dr Gendoo was a Marie Curie Early Student Training Research Fellow at the University of Leeds, where she pursued a Master of Research (MRes) in Advanced Genetic Analysis. Her fellowship allowed her to focus on bioinformatics projects involving transcriptomic analysis and drug design.

Dr Gendoo pursued her postdoctorate fellowship focusing on cancer bioinformatics, at the Princess Margaret Cancer Centre in Toronto, Canada. Her work encompassed molecular subtyping and omics profiling across different cancer types, and drug repurposing and drug inference for cancer. She was one of a small but select number of awardees across Canada for the Brain Canada-CIBC Brain Cancer Research Training Awards to support her postdoctorate fellowship. Towards the end of her fellowship, Dr Gendoo developed an avid interest in pre-clinical disease models, which is now one of her research axes at the University of Birmingham.

Teaching

MSc in Genomic Medicine:

  • Bioinformatics, Interpretation, Statistics and Data Quality Assurance in Genomic Analysis
  • Advanced Bioinformatics 

MSc in Bioinformatics:

  • Genomics & Next Generation Sequencing

Research

One of Dr Gendoo's research axes focuses characterizing the molecular pathogenesis of in vitro and in vivo pre-clinical disease models (xenografts, organoids, GEMMs), and developing reliable and quantifiable frameworks for these matching these models to their human counterparts using bioinformatics and multi-omics profiling. In tandem, Dr Gendoo is focused on developing translational and pharmacogenomics approaches that harness these disease models for therapeutics. 

Both axes combine a variety of ‘omics’ approaches, including transcriptomics and next-gen sequencing, pharamacogenomics, and structural bioinformatics, towards development of an integrative pipeline for the molecular and biological characterization of model systems, and the development of potential therapeutics against these systems. 

Collaborations with clinicians, basic researchers, bioinformaticians, and computer scientists are always welcome.

LinkedIn

Publications

A full list of publications can be found on Google Scholar 

Selected publications:

  • Deena M.A. Gendoo et al. Whole Genomes Define Concordance of Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer. Plos Computational Biology, 2019, doi: doi.org/10.1371/journal.pcbi.1006596 
  • Dong-Yu Wang, Deena Gendoo, Yaacov Ben David, James Woodgett, Eldad Zacksenhaus. A subgroup of microRNAs defines Pten-deficient, triple-negative breast cancer patients with poorest prognosis and alterations in RB1, MYC and Wnt signalling, Accepted, Breast Cancer Research, 2019
  • Deena M.A. Gendoo. Michael Zon, Vandana Sandhu, Venkata Manem, Natchar Ratanasirigulchai, Gregory Chen, Levi Waldron, Benjamin Haibe-Kains. MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature. Under Review, Scientific Reports
  • Gregory M Chen, Lavanya Kannan, Ludwig Geistlinger, Victor Kofia, Zhaleh Safikhani, Deena M.A. Gendoo, Giovanni Parmigiani, Michael J Birrer, Benjamin Haibe-Kains, Levi Waldron. Consensus on Molecular Subtypes of High-grade Serous Ovarian Carcinoma. Clin Cancer Res. 2018 July doi: 10.1158/1078-0432.CCR-18-0784   
  • Nehme El-Hachem*, Deena M.A. Gendoo*, Laleh Ghoraie*, Zhaleh Safikhani, Petr Smirnov, Ruther Isserlin, Gary D. Bader, Anna Goldbenberg, Benjamin Haibe-Kains. Integrative pharmacogenomics to infer large-scale drug taxonomy. Cancer Research, 2017 Jun 1;77(11):3057-3069   *Co-first authors
  • Jennifer Haynes, Trevor D. McKee, Andrew Haller, Yadong Wang, Cherry Leung, Deena M.A. Gendoo, Evelyne Lima-Fernandes, Antonija Kreso, Robin Wolman, Eva Szentgyorgyi, Douglass C. Vines, Benjamin Haibe-Kains, Bradly Wouters, Ur Metser, David Jaffray, Myles Smith, Catherine A. O'Brien. Administration of Hypoxia-Activated Prodrug Evofosfamide after Coneventional Adjuvant Therapy Enhances Therapeutic Outcome and Targets Cancer-Initiating Cells in Preclinical Models of Colorectal Cancer. Clin Cancer Res. 2018 May 1;24(9):2116-2127
  • Deena M.A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schröder, and Benjamin Haibe-Kains. Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. Oxford Bioinformatics, 2016.
  • Torchia et al., Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell 2016;30(6): 891-908 
  • Yujing J. Heng, et al. The molecular basis of breast cancer pathologic phenotypes. The Journal of Pathology, 2016.  Doi: 10.1002/path.4847
  • P Smirnov, Z Safikhani, N El-Hachem, D Wang, A She, C Olsen, M. Freeman, H Selby, D Gendoo, P Grossman, A Beck, H Aerts, M Lupien, A Goldenberg, B Haibe-Kains. PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Oxford Bioinformatics, 2016
  • Lavanya Kannan, Marcel Ramos, Angela Re, Nehme El-Hachem,Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero,Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedin C. Culhane, Benjamin Haibe-Kains and Levi Waldron. Public data and open source tools for multi-assay genomic investigation of disease. Briefings in Bioinformatics, 2015.
  • Gendoo DM, Smirnov P, Lupien M, Haibe-Kains B. Personalized diagnosis of medulloblastoma subtypes across patients and model systems. Genomics. 2015;106(2):96-106. 
  • Turcotte M, Spring K, Pommey S, Chouinard G, Cousineau I, George J, Chen GM, Gendoo DM, Haibe-Kains B, Karn T, Rahimi K, Le Page C, Provencher D, Mes-Masson AM, Stagg J. CD73 is associated with poor prognosis in high-grade serous ovarian cancer. Cancer Res. 2015.
  • Wang X, Dubuc AM, Ramaswamy V, Mack S, Gendoo DM, Remke M, et al. Medulloblastoma subgroups remain stable across primary and metastatic compartments. Acta Neuropathol. 2015;129(3):449-57.
  • Kime L, Vincent HA, Gendoo DM, Jourdan SS, Fishwick CW, Callaghan AJ, et al. The first small-molecule inhibitors of members of the ribonuclease E family. Sci Rep. 2015;5:8028.
  • Harbi D, Parthiban M, Gendoo DM, Ehsani S, Kumar M, Schmitt-Ulms G, et al. PrionHome: a database of prions and other sequences relevant to prion phenomena. PLoS One. 2012;7(2):e31785.
  • Gendoo DM, Harrison PM. The landscape of the prion protein's structural response to mutation revealed by principal component analysis of multiple NMR ensembles. PLoS Comput Biol. 2012;8(8):e1002646.  
  • Gendoo DM, Harrison PM. Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids. PLoS One. 2011;6(11):e27342.
  • Gendoo DM, Harrison PM. Discordant and chameleon sequences: their distribution and implications for amyloidogenicity. Protein Sci. 2011;20(3):567-79.

View all publications in research portal