What is the Integrative Quantitative Biology Initiative?

QBI Director: Dr. Jacalyn Vogel

The Integrated Quantitative Biology Initiative (IQBI) is a multi-disciplinary research group, with faculty from McGill University (Biology, Chemistry, School of Computer Science and Physics) and the Université de Montréal. In June 2015, the IQBI was awarded a major research infrastructure grant from the Canadian Foundation for Innovation and Quebec valued at over $12,500,000 total from all partners. This investment recognizes McGill University's existing strength and outstanding promise for international leadership in
Quantitative Biology research.

News item: In June 2015, the Integrated Quantitative Biology Initiative (IQBI) was awarded a major research infrastructure grant from the Canadian Foundation for Innovation and Quebec valued at over $12,500,000 total from all partners. This investment recognizes McGill University's existing strength and outstanding promise for international leadership in Quantitative Biology research.

Media: Quantitative Biology comes to McGill - McGill Daily (March 2012)

Faculty Affiliation, Research Interests and Teaching

Mathieu Blanchette
School of Computer Science; McGill
Research interests:
Our group works on the development of algorithmic and machine learning approaches to problems arising in genomics and proteomics. We work with biologists and geneticists on the development of approaches for (i) genome sequencing and comparative genomics in plants and animals, (ii) the discovery of genetic and epigenetic factors affecting gene expression, and (iii) the identification of protein-protein interactions and the analysis of the complex networks they form.
QB Courses: BIOL 395/495

Gary Brouhard
Department of Biology and Associate Member, Physics; McGill
Research interests:
Dr. Brouhard's research interests are in the molecular basis of morphology, especially how the microtubule cytoskeleton determines the location of neurons in the brain. The Brouhard lab uses single-molecule biophysics, biochemistry, as well as work with model organisms to study how enzymes control the shape of microtubules.
QB Courses: BIOL 201, BIOL 395/495, BIOL 518.

Khanh Huy Bui
Department of Anatomy and Cell Biology; McGill
Research interests:
Our research focuses on elucidating the three-dimensional structure of the cilia and the underlying logistic system used to dynamically maintain and assemble the cilia. We aim to obtain high resolutions of various components of the cilia by cryo-electron microscopy and cryo-electron tomography. Together with complementary data, we will model the atomic structures of cilia components to get novel insights into the molecular mechanism of ciliary assembly. In addition, we will also use correlative light and electron microscopy to exploring the ciliary dynamics.

Gonzalo Cosa
Department of Chemistry; McGill
Research interests:
Research interests in the Cosa group involve the development of fluorescence-based methodologies to study complex biological systems. The integrating element in our research program is the exploitation of organic chemistry, biophysics, photophysics and microscopy towards imaging processes at the cellular or molecular level with enhanced sensitivity and specificity. Our interests/questions center on the role reactive oxygen species play in live cells, and on elucidating complex dynamics in self-assembled biological systems and biomaterials/nanomaterials. The tools we utilize in our research group span from the rational design and preparation of new fluorescent organic probes to the utilization and development of state-of-the-art single molecule fluorescence microscopy techniques.
QB Courses: BIOL 395/495

Damien D'amours
Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology; Université de Montréal
Research interests:
Our team studies the molecular and physical determinants of genome organization during mitosis. We combine classic genetic approaches with quantitative biochemistry to unravel how cells control genome/chromatin architecture to build mitotic chromosomes. Furthermore, we have a particular interest in the interplay between protein kinases, their substrates, and cell cycle checkpoints during cell division.
QB courses: BIOL 395/495

Allen J. Ehrlicher
Department of Bioengineering; McGill
Research interests:
Active mechanics of biological systems: Biological materials are unique in that they are able to convert chemical energy into active forces in precisely controlled ways. These active forces in biological interactions are as critical as the chemistry acting on biology. Our research strives to understand 1) how these forces change the material and biochemical properties of biological systems, particularly in the actin cytoskeleton, and 2) how we may capitalize on these unique mechanics to engineer new synthetic active biomimetic materials.

Paul Francois
Department of Physics and Associate Member, Biology; McGill
Research interests:
We study  theoretical aspects of biological phenomena, from gene networks dynamics to their evolution. We are especially interested in physical aspects of embryonic development (patterning, tissue mechanics), non linear dynamics in single cells (immune system, genetic oscillators, cells as control systems) and evolution of gene networks (computational evolution, connection to bifurcation theory). [Position Available >> view details]
QB Courses: BIOL 395/495, BIOL 551

Gregor Fussmann
Department of Biology; McGill and Director, Gault Nature Reserve
Research interests:
Community ecology, evolutionary ecology, aquatic ecology. Eco-evolutionary dynamics: evolutionary change in nature may be rapid and the distinction between ecological and evolutionary time scales is often arbitrary. To study eco-evolutionary dynamics people in my lab use aquatic model organisms and conduct controlled experiments in the laboratory and in the field. We believe that this approach, combined with mathematical modelling, will contribute to a better understanding of the dynamics of real ecosystems.
QB Courses: BIOL 206, BIOL 308, BIOL 331, BIOL 395/495, BIOL 432

Andrew Gonzalez
Department of Biology; McGill and Director, Quebec Centre for Biodiversity Science
Research interests:
Our lab is focused on the causes and consequences of biodiversity loss. As a corollary we hope to gain a better understanding of what it will take to slow extinction and mitigate its effects. In my lab we test and develop theory using simulation, experiments (field and lab) and large databases. Ongoing research projects focus on: adaptation to environmental change, population and community stability, biodiversity and ecosystem function, metapopulation and metacommunity dynamics in variable environments, and the impacts of economy on biodiversity loss.

Leon Glass
Department of Physiology; McGill
Research interests:
Leon Glass' research focuses on the applications of mathematics to study biological function and rhythms in the cardiovascular system, dynamics and control in genetic and neural networks, and visual perception. This involves developing nonlinear mathematical models for biological systems and studying the dynamics in these models using numerical and analytic methods. Particular problems involve mathematical methods for the interaction of nonlinear oscillators, the dynamics in large complex networks, and the role of spatial structure in determining the dynamics.
QB Courses: BIOL 309

Simon Gravel
Department of Human Genetics; McGill
Research interests:
History, biology, and disease all had a strong impact on today's human genomic diversity. We try to understand these effects by developing creative math and computational tools to interpret the latest generation of biological data. Recently, we have been working on reconstructing histories of populations with very diverse genetic heritage, including Hispanic/Latinos and African-Americans, and found that some nifty math tricks enabled us to track recent migration events very accurately. By developing detailed quantitative models of genomic diversity across human populations, we also test and improve our understanding of mutation, recombination, and selection processes that shape human evolution.

Frederic Guichard
Department of Biology; McGill and Co-Director Centre for Applied Mathematics in Bioscience And Medicine (CAMBAM)
Research interests:
Theoretical ecology and complex system theory applied to intertidal ecosystems and to marine reserve design. Emergence of large scale patterns and dynamics from local interactions among individuals. Multidisciplinary approach involving mathematical modeling, field experiments and remote sensing.
QB Courses: BIOL 308, BIOL 434, BIOL 395/49

Adam G. Hendricks
Department of Bioengineering; McGill
Research interests:
Many essential cellular functions including cell division, motility, protein synthesis, and intracellular transport are driven by motor proteins, a specialized set of enzymes that convert chemical energy into mechanical work. Two motor proteins, kinesin and cytoplasmic dynein, are responsible for the long-range transport of mRNA, proteins, organelles, and signaling molecules along the microtubule cytoskeleton. Active transport by kinesin and dynein is critical for the maintenance of biosynthetic, signaling, and degradative pathways in the cell. Long and highly-polarized cells like neurons are particularly sensitive, and accordingly mutations in kinesin or dynein cause neurodegenerative disease in mouse models and humans. Further, defects in intracellular transport have been linked to many neurodegenerative diseases including amyotrophic lateral sclerosis, Alzheimer’s disease, and Huntington’s disease.

In the complex cellular environment, kinesin and dynein are regulated by interactions with the cytoskeleton, other motor proteins, and binding partners. These interactions allow motors to perform complicated functions such as cell division and the targeted trafficking of intracellular cargoes. The Hendricks lab is focused on understanding how motor proteins function collectively, and how interactions among motor proteins and with the complex cellular environment modulate their behavior. We employ in vitro experiments that incorporate aspects of the cellular environment, high-resolution tracking and manipulation in living cells, and mathematical modeling to understand motor protein dynamics in the cell. In particular, we aim to develop methods to extend the application of single molecule techniques such as optical trapping, FRET, and subpixel resolution tracking to examine motor function in living cells.

Anmar Khadra
Department of Physiology (Centre for Nonlinear Dynamics); McGill
Research interests:
Understanding various aspects of physiological phenomena in immunology and endocrinology using computational models represents the core focus of my current work. These models provide important insights into the cellular and molecular processes occurring in these phenomena. Particularly, I’m interested in examining the role of immune cells, insulin-secreting beta cells and autoantibodies (via their interaction) in the progression of autoimmune Type 1 Diabetes, as well as analyzing the molecular mechanisms (which involve several receptors and ion channels) regulating neuronal synchrony/rhythmicity and hormone secretion. These projects are conducted in close collaboration with several, internationally renowned experimentalists. Beside their valuable relevance to physiology, such models also raise intriguing mathematical questions and generate very interesting problems that are either tackled numerically or theoretically using nonlinear stability analysis. For more details, please visit my website.
QB Course: MATH 437

Justin Kollman
Department of Biochemistry; University of Washington
Research interests:
We are examining the structures of the complex macromolecular machinery of cellular organization, with a focus on bacterial cytoskeletal systems and organelles. Our structural approach centers on cryo-electron microscopy of large macromolecular complexes, which we combine with X-ray crystallography of individual components. This integrative approach allows us to generate mechanistic insights over a broad range of size and resolution scales.
QB Courses: BIOL 395/495

Hans Larsson
Redpath Museum; McGill
Research interests:
Vertebrate palaeontology and developmental evolution. Palaeontological work focuses on terrestrial Mesozoic vertebrates in the Canadian arctic and explores signatures of ancient climate shifts in palaeo-faunas. Developmental evolution work addresses what developmental mechanisms (morphological and molecular) are responsible for changes in the evolution of vertebrate morphology.
QB courses: BIOL 395/495

Sabrina Leslie
Department of Physics; McGill
Research interests:
Dr. Leslie's research program strives to create a new mechanistic understanding of fast molecular searches, which underlie a host of key cellular processes. One class of fast molecular search processes, that remains largely uncharacterized due to limited analysis techniques, is the search that initiates DNA repair. The Leslie lab circumvents limitations in existing techniques by developing new single-molecule microscopy tools capable of simultaneously measuring: weak protein-DNA and DNA-DNA interactions; extended search trajectories of individual molecules over several seconds; millisecond-timescale interaction kinetics; and topologically complex or strained DNA substrates.
QB Courses: PHYS/BIOL 319; BIOL 395/495

Brian Leung
Department of Biology; McGill
Research interests:
Biological invasions, ecology of diseases, ecosystem management. Addressing environmental issues through the synthesis of models (mathematical, computational, and statistical) with empirical data (literature, field or lab studies). Creating models for ecological forecasting, given uncertainty and sparse data. Developing decision theory, using risk analysis.
QB Courses: BIOL 395/495, BIOL 373

Nicole Li
School of Communication Sciences and Disorders; Associate Member, Biomedical Engineering, Otolaryngology; McGill
Research interests:
Voice disorders affect one in ten children and adults at some point over their lifetime. Our laboratory integrates in vitro, in vivo and in silico (computational) approaches to study vocal fold biology and wound healing. The research goal is to generate a computational platform that can guide surgeons and speech pathologists in the best methods to repair voices that have been lost. Our lab uses agent-based modeling to simulate patient-specific vocal trauma and repair response in computers. Agent-based modeling with parallel computing and 3D visualization are exploited. We also use a systems biology approach to investigate individual genetic variance in soft tissue injury and treatment response.
Positions available: http://voice.lab.mcgill.ca/

Michael C. Mackey
Department of Physiology; McGill
Research interests:
Michael Mackey works in the field of biomathematics. His specific interests are focused on understanding the nature of periodic hematological diseases and building mathematical models for the regulation of hematopoietic cell proliferation and differentiation. The second area in which he works is the mathematical modelling of gene regulation and the dynamics of simple gene networks, including the effects of noise in modifying those dynamics.
QB Courses: MATH 437, PHYS 413

Stephen Michnick
Department of Biochemistry; Université de Montréal
Research interests:
We are interested in two broad questions: 1) How do cells make decisions about their fate based on their interpretation of external signals and internal queues and 2) How have macromolecular complexes evolved to regulate cell fate decisions. We use a variety of techniques to achieve our aims, including cell-based assays to study the dynamics, topological organization and of protein-protein interactions, quantitative single cell time-lapsed imaging of protein, RNA and DNA dynamics, protein analysis by mass-spectrometry, and a variety of computational and modeling approaches.
QB courses: BIOL 395/49; PHYS/BIOL 319

Georgios D. Mitsis
Department of Biolengineering; McGill
Research interests:
Our group is interested in developing algorithms for the identification of nonlinear and nonstarionary dynamic systems, a category which subsumes the vast majority of biological/ physiological systems. We are specifically interested in data-driven models (e.g. Volterra-type models) that place minimal assumptions on the structure of the system and we are applying principles from machine/ statistical learning, such as neural networks and Bayesian estimation, in order to achieve more efficient estimation and perform model order selection. Applications of interest include cerebral hemodynamics and blood flow autoregulation, functional neuroimaging and resting-state networks analysis, glucose metabolism and control, as well as computational oncology.

Anthony Mittermaier
Department of Chemistry; McGill
Research interests:
The Mittermaier lab studies the molecular basis of protein function, particularly in the context of drug design. They use Nuclear Magnetic Resonance spectroscopy to characterize protein structure and dynamics, as well as calorimetry to measure the heat flow associated with protein folding and binding. The combination of these two techniques yields descriptions of protein behaviour that are atomically precise and thermodynamically rigorous.
QB courses: BIOL 395/495; CHEM 514

Nicolas Moitessier
Department of Chemistry; McGill
Research interests:
Interfacing and applying computational and medicinal chemistry for the development of pharmaceuticals
QB courses: BIOL 395/495; CHEM 211, 212, 503 and 504

Marlene Oeffinger
Institut de recherches cliniques de Montréal (IRCM); Université de Montréal
Research Interests
Regulation and dynamics of RNA maturation pathways. The main focus of our lab is to determine the temporal and spatial assembly and coordination of RNA maturation factors, as well as to identify the underlying control mechanisms that drive the processing, modification and assembly of different RNAs. We combine proteomic, RNomic, biochemical and computational approaches to build a dynamic picture of RNA maturation pathways in different cellular contexts and organisms (yeast, human and flies) to yield important information on how RNA maturation is linked to other cellular processes including cell division, development as well as onset of various diseases.

Sebastian Pechmann
Department of Biochemistry; Université de Montréal
Research Interests
Our research integrates computation and experiment to understand how the cell as a system maintains protein homeostasis. We develop computational approaches for the analysis and integration of sequence, structural and systems biology data to decipher biological design principles and regulatory mechanisms that support proteome integrity. We then iterate through model refinement, targeted experimental perturbation, and biochemical validation to derive a systems level understanding of successful protein homeostasis in health, and origins of its failure in diseases linked to protein misfolding.
QB courses: BIOL 395/495

Rodrigo Reyes-Lamothe
Department of Biology; McGill
Research interests:
Dr. Reyes studies the biology of chromosomes using fluorescent microscopy single-molecule techniques in living cells. The aim of his work is to providing insight on the stoichiometry, architecture, dynamics and heterogeneity of various multi-component molecular machines that participate in the replication, repair and segregation of chromosomes. His group develops chemical and genetic probes to report on the metabolism of cells, genetic tools for precise manipulation of cell physiology, and microscopy techniques for detection of weak fluorescent signal and image analysis.
QB courses: BIOL 301, BIOL 395/495

Derek Ruths
School of Computer Science; McGill
Research interests:
I'm interested in characterizing and modelling the dynamics of biochemical and social networks. The fact that experimental data in molecular biology can be quite noisy makes inferring accurate models of biochemical networks very challenging. In my lab, we're building modeling methods for signaling and transcriptional dynamics that are resilient to the noise inherent in the experimental results used to train them.
QB courses: BIOL 395/495; COMP 364

Jon Sakata
Department of Biology; McGill
Research interests:
Our lab studies the mechanisms underlying the learning and control of birdsong. Much of our research aims to understand the computational processes underlying decisions about vocal motor sequencing. For this we utilize Markov, mixed effects, and multivariate linear models to reveal how sensory feedback, social interactions, and age influence the sequencing of acoustic elements. We also use machine learning, cluster analysis, and a variety of other analytical tools to examine the learning and plasticity of vocal communication and decipher information encoded in neurophysiological activity.

Jackie Vogel
Department of Biology and Associate Member, Computer Science, Goodman Cancer Research Centre, McGill; Coordinator of the QB Option
Research interests:
The mitotic spindle plays an essential role in the transmission of genetic information during cell division in all eukaryotic cells. Our research focuses on spindle assembly and mitotic control mechanisms. We use budding yeast as a model for the detailed analysis of these evolutionarily conserved processes, using high-resolution microscopy, biochemistry, molecular genetics, and the analysis of relevant genetic networks and protein structure-function relationships using genomic and bioinformatics methods.
QB courses: BIOL 395/495, 518, 551

Jérôme Waldispühl
School of Computer Science; McGill
Research interests:
Prediction, evolution, dynamics of molecular structures. Our group works in the computational structural biology area broadly defined. We develop theoretical models and algorithms to decipher the relationship between RNA and protein sequences and structures. Predicting molecular structures is not a finality but a means to understand the genetic code and biological systems.
QB courses: BIOL 395/495; COMP 462/561, COMP 761

Alanna Watt
Department of Biology; McGill
Research interests:
Dr. Watt is interested in brain development, and how early patterned network activity is involved in the development of neuronal circuits. Using techniques including electrophysiology, two-photon and confocal imaging, the Watt lab studies how network activity plays a role in sculpting the developing cerebellum.
QB courses: BIOL 306, BIOL 395/495

Stephanie Weber
Department of Biology; McGill
Research interests:
Cells are crowded with macromolecules that form highly organized yet dynamic structures. While advances in fluorescence microscopy enable us to visualize this spatiotemporal heterogeneity, the mechanisms underlying intracellular organization remain largely unknown. The Weber lab uses quantitative live-cell imaging and physical modeling to understand how biological systems establish and dynamically regulate spatial order in the cell and ultimately how these processes affect the growth, size and health of the whole organism.
QB courses: BIOL 313

Tamara Western
Department of Biology; McGill
Research interests:
Correct growth and development in plants is inextricably linked with the characteristics of their cell walls. Dr. Western's research focuses on the mechanisms of cell wall production and modification using a combination of genetics and cell biology. She also addresses the ramifications of changes in cell wall properties on plant development through morphological and biomechanical studies.
QB courses: BIOL 202, BIOL 395/495

Paul Wiseman
Departments of Chemistry and Physics; McGill
Research interests:
Biophysical technique development involving fluorescence fluctuation and correlation analysis and applications to study the molecular regulation of cell adhesion, migration and cell signalling in mammalian cells and neurons. Also applications of single molecule tracking methods and nanoparticles to study protein receptor distributions and transport and nonlinear microscopy methods for imaging extra cellular matrix within intact tissue.
QB Courses: BIOL 395/495, CHEM 514

Sarah Woolley
Department of Biology; McGill
Research interests:
Our lab studies the neural basis of vocal production and perception in songbirds. Using a combination of behavioural analysis, neurophysiological recording and computational modelling we investigate the role of basal ganglia circuits in modulating aspects of song production, particularly song variability and plasticity. In addition, we use these tools to look at the role of auditory and prefrontal-like circuits in auditory decision-making and individual recognition in females.

Yu (Brandon) Xia
Departments of Bioengineering; McGill
Research interests:
My research focuses on computational structural and systems biology. I develop computer models of complex biomolecular systems such as proteins and protein networks, and use such models to elucidate the general principles governing the structure, function, and evolution of these biomolecular systems. My research combines the data-driven approach of integrated probabilistic modeling of diverse genome-wide information, together with the principle-driven approach of biophysical modeling and mechanistic simulation of complex systems.

Daniel Zenklusen
Department of Biochemistry; Université de Montréal
Research interests:
Analysis of gene expression using single molecule approaches. We use imaging techniques to study the mechanisms and kinetics of different processes along the gene expression pathway in yeast and higher eukaryotes. In particular, we combine single cell-single molecule techniques and quantitative analysis methods with mathematical modeling to gain better understanding of the general rules governing the expression of genes in complex systems.
QB Courses: BIOL 395/4

Last update: Oct. 20, 2016
Carole Verdone-Smith, Department of Biology, McGill University