Our Research Center
The Laboratory of Integrative Multi-Omics Research in the Department of Pharmacology is engaged in cutting-edge research that aims to integrate large-scale data derived from varied bio-analytical technology platforms including next-generation sequencing (NGS), mass spectrometry (MS), magnetic resonance spectroscopy (MRS), among others.
The lab focuses on questions related to cancer biology, specifically understanding the etiology of pediatric malignancies, their diagnosis and progression and, their heterogeneous response to pharmacotherapeutics. We develop novel methods for modeling the emergence of biological phenotypes following measurements of their genomes, transcriptomes, and proteomes over a period of time or course of pharmacological intervention. The -omics technologies employed in our lab are listed below.
Genomics - via DNA-seq, aCGH, WGS, WES
Epigenomics - via ChIP-seq, DNA methylation
Transcriptomics - via microarrays, RNA sequencing of bulk sample or single cells
Proteomics - via mass spectrometry
Targeted and untargeted metabolomics - via magnetic resonance and/or mass spectrometry
The Karakach lab is made up of students and researchers of various disciplines, skills, and educational backgrounds. Meet the team below.
Tobias K. Karakach, Ph.D.
Assistant Professor, Faculty of Medicine,
Department of Pharmacology
Dr. Karakach obtained an MSc. degree in Analytical Chemistry with a concentration in Chemometrics from Dalhousie University, Halifax NS Canada and a Ph.D., also from Dalhousie Chemistry, with a concentration on Bioinformatics for Functional Genomics. After his post-doc work at the National Research Council of Canada, he accepted a Research Officer (RO) position at the same institution and focused his research on developing computational methods to analyze data derived from bioanalytical technologies such as Magnetic Resonance, Mass spectrometry, hyperspectral imaging, fluorescence, Infrared, and other vibrational spectroscopic tools applied to questions from diverse fields ranging from biomedical research to metrology.
In 2017, Tobias moved to the Vlaams Institute voor Biotechnologie (VIB) in Leuven, Belgium, and took up a position as a Bioinformatics Staff Scientist at the laboratory for Angiogenesis and Vascular metabolism. During this time, he expanded his repertoire of bioinformatics skills to single-cell transcriptomics by RNA-seq (scRNA-seq), genomics (DNAseq, aCGH, WGS, WES), and epigenomics (ChIPseq, DNA methylation) data analysis and, added invaluable biological knowledge to his computational expertise.
He is currently an Assistant Professor in the Department of Pharmacology at Dalhousie University and holds a cross-appointment in the Department of Biochemistry and Medical Genetics at the University of Manitoba.
Karla Valenzuela, Ph.D.
Karla comes all the way from the land of wines, Chile, where she obtained a bachelor's degree in medical technology. In 2013, she came to Dalhousie where she did her master's and Ph.D. in the Microbiology and Immunology department. After many years of studying intracellular bacterial pathogens, Karla switched gears and joined the Karakach lab as a post-doctoral fellow to study cancer biology focusing on Wilm’s tumours.
Karla is the leader of our functional biology pillar where she uses her expertise in molecular and cell biology to set up the empirical measurements and train students. Importantly, Karla has founded the birthday committee ensuring our blood sugar levels are high year-round!
Ibrahim Ahmed, Ph.D.
Reynolds Post-Doctoral Fellow
Ibrahim Ahmed is a post-doctoral fellow in the Karakach lab. Ibrahim completed his Ph.D. from the South African National Bioinformatics Institute, University of the Western Cape. Ibrahim's research interest focuses on the integration of data analysis and statistical methods into unified well-defined work-flow. These methods include: data pre‑treatment and normalization, dimensionality reduction, clustering, differential and enrichment analysis, pathway mapping, trajectory inference, survival analysis, predictive modelling with machine learning, and more. Ibrahim worked as a senior lecturer at the department of computer science University of the Western Cape. In addition to a postdoctoral fellow and bioinformatics trainee in the South African National Bioinformatics Institute.
Seketoulie Keretsu, Ph.D.
Seke received his Ph.D degree in bioinformatics from Chosun University, South Korea. Thereafter, he joined the Cancer Mutation Research Centre at Chosun University as a post-doctoral researcher. His prior works were focused on the identification and design of novel inhibitors that target medically important proteins using Computer-Aided Drug Design methods. As a graduate student at Tezpur University in India, Seke used data mining techniques to predict protein complexes in protein-protein interaction networks. Currently, Seke is a post-doctoral research fellow at the Karakach lab and the Gujar lab, gearing to use computational techniques to answer obscure biological questions with an immunological context.
Nithya Ramakrishnan, Ph.D.
Nithya is a joint Post-doctoral Fellow in the labs of Tobias and Shashi Gujar. She completed her PhD from the Indian Institute of Technology Delhi. Nithyas' research interests span machine learning, Information theory and Bioinformatics. She has worked on genetic and epigenetic data analyses in cancer, probabilistic modeling of epigenetic inheritance and Cancer prediction based on DNA Methylation distribution. Prior to her research career, Nithya gained about 13 years of programming/software development experience in the software industry. Nithya is also a trained Carnatic vocalist and violinist.
Maddison Hodgins, B.Sc.
Masters (Pharmacology) Candidate
Maddy graduated with a degree in undergraduate Medical Sciences from Dalhousie University in 2021. She is currently completing a Master’s degree in the Department of Pharmacology at Dalhousie. Her research involves the use of multi-omics measurements to identify a panel of molecular markers for frailty in a mouse model.
Masters (Computational Biology & Bioinformatic) Candidate
Fabian is currently in his last year of his Double Major in Chemistry and Computer Science. Over the summer he had the opportunity to gain experience in the Bioinformatics field while working on DNA Methylation data from Wilm's Tumor patients. Currently, Fabian is continuing this research but also focusing on his honours project concerning DNA methylation during different embryonic developmental stages.
B.Sc. Honors (Medical Sciences) Candidate
Hannah is an undergraduate student in her fourth year of Medical Sciences at Dalhousie University. Throughout the summer of 2021, she received the Faculty of Medicine Summer Research Scholarship where she completed metabolomics research in the Karakach Lab. She is currently performing research in the lab through her experiential learning research class. Her research involves using multi-omics methods to identify frailty biomarkers in mouse kidneys.
B.Sc. Honors (Medical Sciences) Candidate
Mahan is a fourth-year medical sciences student at Dalhousie university. He initially joined the lab as an experiential learning student working on analyzing next-generation sequencing (NGS) data, performing quality control, mapping, visualization, and differential expression analysis. He is now doing his honors focusing on activity-based proteomics.
Lucien Cayer, M.Sc.
Ph.D. Candidate, Sessional Instructor
Lucien completed a BSc at the University of Winnipeg where he majored in Chemistry. He then did a second degree in Human Nutritional Sciences at the University of Manitoba. During this time, he began research on lipids, with a focus on oxylipins. He then completed a MSc in Human Nutritional Sciences at the University of Manitoba, studying the impact to oxylipins from the food toxin 2-MCPD. He is currently a PhD student and Sessional Instructor in Human Nutritional Sciences at the University of Manitoba, where his research aims are to develop computational modelling procedures for oxylipins.