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Research Projects in Bioengineering

Research projects with Professors Allen Ehrlicher, Adam Hendricks, Amine Kamen, Georgios Mitsis and Dan Nicolau are currently available.


Allen Ehrlicher

Project Title:
Biomimetic Hybrid Materials
Research Area:
Bioengineering, Mechanical Engineering, Materials
Start Date: Fall 2014 & Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Masters or Ph.D.
Contact Information:
ehrlicher [dot] lab [at] gmail [dot] com (Email) or Website

Position Description: Materials in nature display exceptionally rich mechanics; flexibility yet robustness, self-healing, strong and light-weight.  Moreover, animal cells are able to move, change shape, and exert forces on their environment. This project seeks to apply diverse engineering and materials design to create novel passive and active biomimetic materials with tunable stiffness.

Desired Skills: Core knowledge in biophysics, polymer physics, mechanical or chemical engineering, materials engineering, with a good grasp of biological materials. Most important is that applicants be highly self-motivated, and excel working in a diverse team
Documents Required: Transcripts (unofficial), current and complete CV, Sample publication (if available), one page personal statement of why you would like to do graduate research in our group, and two reference letters.


Project Title:
Cell Mechanics

Research Area:
Bioengineering, Mechanical Engineering, Materials

Start Date: Fall 2014 & Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Masters or Ph.D.
Contact Information: adam [dot] hendricks [at] mcgill [dot] ca (Email) or Website

Position Description: Cells are complex viscoelastic structures; changes in these mechanics are associated with a multitude of diseases, and may be a principle cause of pathology. In several related topics in cell mechanics, we will look at mechanical and motile changes as a result of mutations in key cytoskeleton proteins. Specific projects will include more details.

Desired Skills: Core knowledge in biophysics, polymer physics, mechanical or chemical engineering, materials engineering. Programming in MatLab. Most important is that applicants be highly self-motivated and excel working in a diverse team.
Documents Required: Transcripts (unofficial), current and complete CV, Sample publication (if available), one page personal statement of why you would like to do graduate research in our group, and two reference letters.


Adam Hendricks

Project Title:
Tuning of Cellular Mechanics by Dynamic Cytoskeletal Crosslinkers

Research Area:
Bioengineering, Cellular Biomechanics, Motor Proteins, Cytoskeleton

Start Date: Fall 2014, Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Ph.D.
Contact Information: adam [dot] hendricks [at] mcgill [dot] ca (Email) or Website

Position Description: To perform disparate structural and trafficking roles in the cell, cytoskeletal filaments are dynamically crosslinked to each other and the cell membrane allowing the cell to act as a solid or fluid depending on the time and length scale. These material properties are determined by the binding kinetics of proteins that dynamically crosslink the cytoskeletal network. We will perturb major crosslinking proteins including myosin II and alpha-actinin which crosslink actin filaments, myosin I which links actin to the plasma membrane, and cytoplasmic dynein which links microtubules to the plasma membrane. The resulting effects on the frequency-dependent response of the cell mechanics will be examined in living cells using advanced optical trapping methods. Mathematical models will be developed to describe the dynamic behavior of crosslinked cytoskeletal networks and directly compared to experimental results.

Desired Skills: This project encompasses approaches from physics, engineering, and cell biology. Prospective researchers should demonstrate excellence in one of these fields, and importantly an interest and ability to work across disciplines.

Documents Required: Transcripts (unofficial), CV, sample publication, personal statement describing research interests (1 page), and at least 2 reference letters.


Project Title:
Intracellular Transport Along Complex Cytoskeletal Networks

Research Area:
Bioengineering, Cellular Biomechanics, Motor Proteins, Cytoskeleton

Start Date: Fall 2014, Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Ph.D.
Contact Information: adam [dot] hendricks [at] mcgill [dot] ca (Email) or Website

Position Description: The dynamic nature of the cytoskeleton enables it to actively direct intracellular traffic by modulating the activity of motor proteins through its organization, post-translational modifications, and cytoskeletal-associated proteins. Using a combination of in vitro reconstitution and optical trapping in living cells, we will examine how the cytoskeleton’s organization regulates the function of microtubule motors. Does the dense actin network act to promote binding of the motors to microtubules by constraining diffusion? How does the degree of crosslinking affect transport? Do kinesin and dynein function more effectively on single or bundled microtubules? We will compare measurements of vesicular cargoes in living cells and on native cytoskeletal networks in vitro.

Desired Skills: This project encompasses approaches from physics, engineering, and cell biology. Prospective researchers should demonstrate excellence in one of these fields, and importantly an interest and ability to work across disciplines.
Documents Required: Transcripts (unofficial), CV, sample publication, personal statement describing research interests (1 page), and reference at least 2 letters.


Amine Kamen

Project Title:
Hepatitis C Vaccine Development
Research Area:
Cell Culture Engineering; Viral Vaccine Production
Start Date: January 2015
Deadline to Apply: September 2014
Graduate Program Level: Masters or Ph.D.
Contact Information:
Amine [dot] Kamen [at] McGill [dot] ca (Email)

Position Description: Recent data from collaborators indicate that very large amounts of virus stock can be produced in cell culture now making it feasible to develop a killed virus vaccine. An optimized and scalable process need to be developed and documented under GMP-guidelines for potential transfer to industrial manufacturer. Position at the post-graduate and graduate level will be considered.

Desired Skills:Biochemical engineering; Biological engineering; Process engineering; cell culture engineering, industrial virology and process analytical technologies.

Documents Required:CV, Statement of research Interest and list of publication.


Project Title:
Insect Cell Technology

Research Area:
Cell Culture Engineering, Viral Vector and Virus-like Production

Start Date: May 2015
Deadline to Apply: Not Specified
Graduate Program Level: Masters or Ph.D.

Contact Information: amine [dot] Kamen [at] mcgill [dot] ca (Email)

Position Description:The overall goal of a large-scale cell culture process is to maximize specific cell productivity while maintaining product quality attributes. One of the key methods to improve productivity is through the optimization of cell culture media and use of rational feeding strategies. By exploiting advanced analytical techniques to assess the entire metabolome of a cell culture during growth and productive infection phases it is expected to rationally re-design the media and tailor the process for high productivity. Position at the post-graduate and graduate level will be considered.

Desired Skills: Biochemical engineering; Biological engineering; Process engineering; cell culture engineering, Baculovirus design and engineering and process analytical technologies.
Documents Required: CV, Statement of research Interest and list of publication.


Project Title:
Viral Vector Production for Gene Delivery

Research Area:
Cell Culture Engineering, Viral Vector and Virus-like Production

Start Date: january 2015
Deadline to Apply: September 2014
Graduate Program Level: Masters or Ph.D

Contact Information: amine [dot] Kamen [at] mcgill [dot] ca (Email)

Position Description:Significant successes have been reported for cell and gene therapies for many chronic diseases including, Parkinson disease, congenital blindness and head and neck cancer The overall goal of a large-scale cell culture process is to maximize specific cell productivity while maintaining product quality attributes. This project will focus on alleviating the limitations for large scale production of Adeno-Associated Viral (AAV) vector, one of the successful delivery system used in these medical intervention. Position at the post-graduate and graduate level will be considered.

Desired Skills: Biochemical engineering; Biological engineering; Process engineering; cell culture engineering, Baculovirus design and engineering and process analytical technologies.

Documents Required: CV, Statement of research Interest and list of publication.


Project Title:
Hepatitis C Vaccine Development
Research Area:
Cell Culture Engineering; Viral Vaccine Production
Start Date: January 2015
Deadline to Apply: September 2014
Graduate Program Level: Masters or Ph.D.
Contact Information:
Amine [dot] Kamen [at] McGill [dot] ca (Email)

Position Description: Recent data from collaborators indicate that very large amounts of virus stock can be produced in cell culture now making it feasible to develop a killed virus vaccine. An optimized and scalable process need to be developed and documented under GMP-guidelines for potential transfer to industrial manufacturer. Position at the post-graduate and graduate level will be considered.

Desired Skills:Biochemical engineering; Biological engineering; Process engineering; cell culture engineering, industrial virology and process analytical technologies.
Documents Required:CV, Statement of research Interest and list of publication.


Georgios Mitsis

Project Title:
Modeling of Cerebral Hemodynamics and Autoregulation

Research Area:
Bioengineering, Biosignal Processing, Cerebrovascular Physiology, Functional Neuroimaging

Start Date:  Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Masters or Ph.D.

Contact Information:
georgios [dot] mitsis [at] McGill [dot] ca (Email)

Position Description: The ability of the brain to maintain a relatively constant blood flow in response to arterial pressure perturbations is extremely important and achieved by the synergy of multiple homeostatic mechanisms. We use advanced systems identification methods, focusing on multivariate, nonlinear and nonstationary approaches, as well as multimodal experimental data (Doppler ultrasound, fMRI) to obtain detailed quantitative descriptions of this ability (dynamic cerebral autoregulation) in health and disease. We are also interested in modeling the BOLD hemodynamic response function using multimodal experimental data (fMRI, simultaneous EEG-fMRI).

Desired Skills: Core knowledge in Electrical Engineering/ Biomedical Engineering/ Bioengineering. Signal and image processing, time series analysis, systems modeling/ identification, knowledge in cerebrovascular physiology/ neuroimaging, self-motivated, ability to work in a diverse team.

Documents Required: Transcripts (unofficial), CV including names of 2 referees or 2 reference letters if available, sample publication(s) - if available, research statement.


Project Title:
Physiological Factors in Resting-State Network Analyses

Research Area:
Bioengineering, Biosignal Processing, Cerebrovascular Physiology, Functional Neuroimaging

Start Date:  Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Masters or Ph.D.

Contact Information:
georgios [dot] mitsis [at] McGill [dot] ca (Email)

Position Description: The observation that spontaneous brain activity is not random noise, but is specifically organized in the resting human brain, termed resting state networks (RSNs), has generated a new exciting avenue of neuroimaging research, as it suggests that it is not necessary to use externally induced experimental protocols to drive brain activity. Functional connectivity RSN measures hold great promise as potential biomarkers; however, in order to realize this potential, the nature of RSNs has to be better elucidated. The objective of this project is to better understand the emergence of functional brain networks and their properties over multiple time scales by using forward models that link neural activity to the corresponding neuroimaging signals (fMRI, EEG or MEG) in order to generate realistic simulations and extract relevant functional connectivity measures and comparing them to experimental data. We are also interested in the effect of physiological fluctuations (heart rate, respiration, arterial CO2) on RSN properties and particularly on their nonstationary characteristics.

Desired Skills: Core knowledge in Electrical Engineering/ Biomedical Engineering/ Bioengineering. Signal and image processing, time series analysis, systems modeling/ identification, knowledge in cerebrovascular physiology/ neuroimaging, self-motivated, ability to work in a diverse team.

Documents Required: Transcripts (unofficial), CV including names of 2 referees or 2 reference letters if available, sample publication(s) - if available, research statement.


Project Title:
Tumor-Specific Growth Prediction and Optimal Therapy Design

Research Area:
Bioengineering, Time Series Modeling, Computational Oncology, Automatic Control

Start Date:  Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Masters or Ph.D.

Contact Information:
georgios [dot] mitsis [at] McGill [dot] ca (Email)

Position Description: This project concerns the development of deterministic and stochastic mathematical models that describe the dynamic evolution of cancerous tumours, as well as the effect of therapy using pharmacokinetic/pharmacodynamic models. It also concerns the use of optimal and adaptive control strategies to design optimal therapies that utilize the aforementioned models, taking into account drug toxicity and the emergence of drug resistance. An important aim is the validation of these models and evaluation of optimally designed therapies in animal models (double transgenic mice) using experimental from our experimental collaborators (Laboratory of Tumour Virology, University of Cyprus, Dr. K. Strati). We also aim to combine macroscopic growth data with transcriptomic data from the same set of mice in order to develop multiscale models of tumor growth.

Desired Skills: Core knowledge in Electrical Engineering/ Biomedical Engineering/ Bioengineering. Time series analysis, systems modeling/ identification, knowledge in cancer biology/ systems biology/ bioinformatics, self-motivated, ability to work in a diverse team.

Documents Required: Transcripts (unofficial), CV including names of 2 referees or 2 reference letters if available, sample publication(s) - if available, research statement.


Dan Nicolau

Project Title:

Classification of Biological Nano-Objects According to Their Spatial Properties

Research Area:

Bioengineering, nanotechnology, image recognition, molecular surfaces

Start Date: Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Masters or Ph.D.
Contact Information:
dan_nicolau [at] yahoo [dot] com (Email) or Phone: 514.398.7138

Position Description:

The spatial recognition of objects, from airplanes to human faces, is of ever-increasing interest in the present much more interconnected and crowded world. While this problem is tackled in real life by a myriad of image analysis and recognition algorithms as implemented in dedicated software, a similar problem is optimally solved by the ‘image recognition’ between biomolecules – the cornerstone of all biological processes. However, and despite their theoretical similarity, presently highly sophisticated, but separate, specialised programs are used for image recognition and classification applications for the macro-world, e.g., biometrics, and nano-world, e.g., drug discovery. A more complex problem than the ‘simple’ classification of objects is their classification in pairs or groups according to interactions between them, or other members of a different class. One of the major problems related to the progress of nanotechnology is the uncertainty related to the effects of nanomaterials on humans, food and environment, which is –essentially- a problem related to the appropriate classification of objects according to their interaction. The project will involve the use of existing in-house developed software for building images of biomolecules, followed by the development of an interface between structural databases, image building for the bio-objects present in these databases, and the archiving, classification and access to a database of molecular images.

Additional information: Plos One

Desired Skills: Core knowledge in Biomedical Engineering/ Bioengineering/Biochemistry/ Molecular Biology and good programming skills. Ability to work in a diverse team.

Documents Required: Transcripts (unofficial), CV including names of 2 referees or 2 reference letters if available, sample publication(s) - if available, research statement.


Project Title:

Biocomputation with Individual or Small Populations of ‘Smart’ Biological Agents

Research Area:

Bioengineering, nanotechnology, image recognition, molecular surfaces

Start Date: Winter 2015
Deadline to Apply: Rolling
Graduate Program Level: Masters or Ph.D.
Contact Information:
dan_nicolau [at] yahoo [dot] com (Email) or Phone: 514.398.7138

Position Description:

Many mathematical and real-life problems cannot, or are very difficult to be solved by the present computers which process the information sequentially and with extreme precision. Among these problems one can mention travel and production scheduling, class time tables, and cryptography. Despite this difficulty, these problems are solved easily by individual biological agents, from microorganisms to humans, who do not process the information sequentially, but in parallel, and who trade precision for heuristic decision making. Alternatively, some mathematical and real-life problems that cannot be solved by the present computers are also difficult to solve by individuals, due to the limited capacity of an individual to process the information in parallel, but can be solved heuristically by groups of individuals operating together either explicitly or tacitly. Among these problems one can mention behaviour of groups in panic situations, solving complex traffic problems, hierarchical self-organisation of groups in conflictual situations. To this end, the project aims to assess the individual and collective ‘computational power’ of individual biological agents in optimally partitioning the available space and taking optimal decisions. The possible applications range from medical to new algorithms and computer paradigms.

The project involves either experiments, such as observing the ‘intelligent’ behaviour of microorganisms facing space confinement via their movement in microfabricated networks; or the modelling and simulation of their behaviour; or a combination of both. The ‘smart’ biological agent of choice is a fungus, which has been demonstrated as using intelligent algorithms for searching labyrinths.

Additional information: www.youtube.com/user/BionanoinfoLiverpool?ob=0&feature=results_main

Desired Skills:The project can be approached, depending on the student’s strengths, either from an experimental, or a simulation perspective.

For the former, Core knowledge in biology, in particular microbiology and fabrication, in particular micro/nanofabrication are required. Experimental tasks comprise the fabrication of simple microfluidics structures; growth of microorganisms in microfluidics structures; observation and recording of microorganisms behavior.

For the latter, good programming skills are paramount. Simulation tasks comprise the translation of microorganisms behavior in logic rules and simple algorithms; and the simulation of microorganisms behavior in complex structures.

Documents Required: Transcripts (unofficial), CV including names of 2 referees or 2 reference letters if available, sample publication(s) - if available, research statement.