Each student in the first year of the PhD program follows six curricular course (two weeks each, intensive). Four of these courses are mandatory and the two remaining requirements are electives from a selection of four courses, which may change from year to year.

After successfully completing the 1st year, students will prepare a thesis proposal and will start their research work. While conducting their research, students will also attend several doctoral seminars. The research work of each PhD student will be supervised by a thesis committee composed by professors and researchers both from MIT and the Portuguese participating institutions.

The development of the course curricula, the teaching methodologies and the evaluation process of the PhD course are conducted by a team of Portuguese and MIT faculty, coordinated by a Portuguese professor and an MIT professor.


Mandatory Courses

M1. Introduction to Technological Innovation
M2. Bioprocess Engineering
M3. Cell & Tissue Engineering
M4. Computational Biosystems Science & Engineering
M5. Laboratory rotation I
M6. Laboratory rotation II
M7. Bio-innovation teams with seminar


Elective Courses

E1. Biomedical Devices and Technologies
E2. Nanobiotechnology and Biomaterials
E3. Neuroscience: Molecular to Systems Neurobiology and Brain Diseases
E4. Principles and Practice of Drug Development


M1.  Introduction to Technical Innovation

1st Semester, 6 ECTS
Place: Lisbon, New University of Lisbon, Faculty of Economics (FEUNL)
Faculty leads: Charles Cooney (MIT)  / Luís Lages (UNL)

C. Cooney
(Co-Director, Sloan Program on the Pharmaceutical Industry (POPI)
Faculty Director, Deshpande Center for Technological Innovation)
L. Lages
(Associate Professor at Faculty of Economics, New University of Lisbon (UNL))

The course will consider the multiple stages of innovation in biomedical technologies: generation of ideas, nurturing these ideas through laboratory research and development, and into commercialization. Innovation is considered through the multiple lenses that include natural sciences, engineering, management sciences and business development. Identifying the best path for commercializing a breakthrough technology is an iterative process and requires creating a go-to-market strategy. Students are expected to put forth hypotheses, test them, then go back and revise them based on customer inputs and other data from the market place. This course is directly connected with the Bio-Teams module.

Main Topics

  • Product Identification and Design
  • Market Scanning and Data Collection
  • Market Selection and Product Development
  • IP & Licensing Strategy
  • Business model; Sales Systems and Project Management
  • Strategic management of technology and innovation, operations, staffing, funding, etc.
  • Creativity & Innovation in Problem Solving
  • Communication and Negotiation Skills
  • Growth and Future; Milestones

Learning outcomes

  • Capability of market scanning and collection of data with further analysis regarding a specific technology
  • Assessment of the current state of a technology and design a go-to-market strategy
  • Identification of the best path for commercializing a breakthrough technology
  • Development of communication and negotiation skills in innovation management


M2. Bioprocess Engineering

1st Semester, 6 ECTS
Place: Lisbon, New University of Lisbon, Faculty of Science and Technology (FCTUNL)
Faculty leads: Daniel Wang (MIT) / João Goulão Crespo (UNL)

D. Wang (Institute Professor of Chemical and Biochemical Engineering)
J.Crespo (Full Professor at Faculty of Science & Technology, New University of Lisbon)

The main objective of this course is to give the students a deep knowledge in the understanding of the bio-processes: how they operate and how they are designed.  Comprehensive operation of one-phase and multiphase bioreactors  culture media design,, process regime analysis, , application of design methods to scale-up & scale-down, modeling and control of bio-processes, down-stream and integrated processing are addressed.

Main Topics

  • Fundamentals on Growth and Metabolism
  • Transport Phenomenon
  • Media and Air Sterilization
  • Bioreactor Design
  • Scale-up and Scale-down
  • Downstream Processing
  • Measurement, Modelling, Monitoring & Control
  • Biological microreactors ;Fundamentals of animal cell culture;
  • Onset and dynamics of biofilms; Biocatalysis in non-aqueous media.

Learning outcomes

  • Comprehensive understanding of growth kinetics and metabolism and transport phenomena in biological systems
  • Understanding the design of a bioreactor for a specific purpose and ability to apply the knowledge to novel situations
  • Definition of a downstream process with optimal design of the unit operations
  • Ability to monitor and define a control system based on measurement and modeling
  • General knowledge on animal cell culture reactors and systems, on biofilms and non-aqueous biocatalysis
  • Integration of the different stages of the design of a bioprocess in a more global perspective


M3. Cell & Tissue Engineering

1st Semester, 6 ECTS
Location: Lisbon, Instituto Superior Técnico (IST)
Faculty leads: Robert Langer (MIT) / Joaquim Cabral (IST) / Lino Ferreira (CNCUC)

R. Langer (Institute Professor of Chemical Engineering)
J. Cabral (Full Professor of Chemical and Biological Engineering at IST)
L. Ferreira (Assistant Researcher at Biocant CNCUC)

The main objectives of this course are to give to the students the fundamentals of cell biology and bioreactor technology for animal and human cell culture and processing, as well as integration with biomaterials for biomedical applications.

Main Topics

  • Cell development biology;
  • Animal cell culture
  • Stem cells for tissue engineering
  • Biomaterials and tissue engineering;
  • Biomaterials and delivery of growth factors and other molecules;
  • Patents;
  • Tailoring biomaterials for tissue engineering;
  • Biomedical applications;

Learning outcomes

  • Comprehensive understanding of Cell and Developmental Biology
  • Understanding of Animal Cell culture processes
  • Ability to understand Stem Cell Bioengineering processes and its applications to Tissue Engineering and Regenerative Medicine
  • Insight on biomaterial properties and integration of biomaterials on engineered tissues
  • Ability to tailor biomaterials for Tissue Engineering and Drug Delivery applications
  • Ability to integrate the knowledge on biomaterial fundamentals and Cell & Tissue Biology towards the development of Biomedical Applications


M4. Computational Biosystems Science and Engineering

1st Semester, 6 ECTS
Location: Braga, University of Minho (UMinho)
Faculty leads: Bruce Tidor (MIT) / Eugénio Ferreira (Univ. Minho)

B. Tidor (Associate Professor in the Biological Engineering Division and Department of Electrical Engineering & Computer Science)
E. Ferreira (Associate Professor at Minho University, School of Engineering Department of Biological Engineering)

This course provides an introduction to computational biology, emphasizing the fundamentals of nucleic acid and protein sequence and structural analysis. It also includes an introduction to the analysis of complex biological principles. Covers principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling. This course is based on a multi-disciplinary approach for obtaining, modeling, organizing and managing
large volumes of data, obtained experimentally or computationally. The central objective is to educate students in the techniques required to carry out research in this area.

Main Topics

  • Analysis of High-Throughput Data
  • Differential Equation Modeling
  • Sequence and Structural Bioinformatics
  • Biomolecular kinetics
  • Integrative Seminars

Learning outcomes

  • Ability to analyze DNA and proteins sequences using bioinformatics tools.
  • Ability to analyze biomolecular structures using modeling tools.
  • Application of ordinary differential equations in network modeling.
  • Ability to analyze omics high-throughput data using statistics and data mining approaches.
  • Comprehensive understanding of the theory and practice of biomolecular kinetics.
  • Integration of bioinformatics and systems biology concepts in particular biological cases.


M5. Laboratory rotation I

2nd Semester, 9 ECTS
The second semester will be used for 2 short laboratory introductions and placements (2 different laboratories), to be chosen by students and advisors according to the student’s professional interests. The students may want to stay in a totally different lab and in a research area from which they have none or little knowledge. This experience also helps students deciding if they want to proceed for the Doctoral program and about the research area they might want to pursue for their Ph.D. project. These short lab placements last for a total of 9 weeks (full-time). The short laboratory rotations research proposals come from within the research areas of the Program and from the participating institutions.

The main Learning outcomes are closely related with the research that the student will conduct in those lab placements:

  • Ability to learn and apply specific experimental and research lab techniques in Bio-Engineering.
  • Ability to correctly analyze the lab work results and make valuable information for future work/future publication.
  • Improvement of the problem-solving skills.
  • Gaining of communication, cooperation and research skills in a state-of-the-art research environment.


M6. Laboratory rotation II

2nd Semester, 9 ECTS
The second semester will be used for 2 short laboratory introductions and placements (2 different laboratories), to be chosen by students and advisors according to the student’s professional interests. The students may want to stay in a totally different lab and in a research area from which they have none or little knowledge. This experience also helps students deciding if they want to proceed for the Doctoral program and about the research area they might want to pursue for their Ph.D. project. These short lab placements last for a total of 9 weeks (full-time). The short laboratory rotations research proposals come from within the research areas of the Program and from the participating institutions.

The main Learning outcomes are closely related with the research that the student will conduct in those lab placements:

  • Ability to learn and apply specific experimental and research lab techniques in Bio-Engineering.
  • Ability to correctly analyze the lab work results and make valuable information for future work/future publication.
  • Improvement of the problem-solving skills.
  • Gaining of communication, cooperation and research skills in a state-of-the-art research environment.


M7. Bio-innovation teams with seminar

2nd Semester, 6 ECTS
This course is related to the innovation course that is held in the first semester. During the module, the students will work in teams and will spend a semester collaborating with researchers from the most important Portuguese research labs. Each team will work with a selected technology, and focus on building a go-to-market strategy for breakthroughs emerging from these pre-eminent labs. The teams will be guided by the labs' Principal Investigators. Additionally, collaborations with Schools of Management in the different Universities will be promoted such that each team has one catalyst with Management background (MBA student, PhD student or Professor). Throughout the semester, the students  will have formal classes, some of them with invited speakers, by videoconference (since all students are in different places in Portugal) and will also go on visits to selected companies or institutions and will also attend team meetings devoted to developing the project assigned to each team.

The main Learning outcomes that are expected from this course are:

  • Ability to do market research and technology based entrepreneurship
  • Ability to interact with venture capital firms, entrepreneurs and researchers from different companies/research labs/technology developers and establish communication lines
  • Ability to promote market-oriented projects in Bioengineering
  • Development of a Bio-teams culture in Portugal
  • Ability to promote the conversion of BioTechnologies developed in Portugal into Economic Value with the concept learning-by-doing
  • Ability to apply the subject concepts on building a go-to-market strategy on emerging technologies and possible applications

 

E1. Biomedical Devices & Technologies

1st Semester, 6 ECTS

Location: Lisboa, Instituto Superior Técnico (IST)
Faculty leads: Dava Newman (MIT)  / Jorge Martins and Miguel Tavares da Silva (IST)

D. Newman, (Full Professor at the MIT Department of Aeronautics & Astronautics, Engineering Systems Division, Harvard-MIT Health Sciences and Technology)
J. Martins (Assistant Professor at Instituto Superior Técnico; Department of Mechanical Engineering)
M. Silva (Assistant Professor at Instituto Superior Técnico; Department of Mechanical Engineering)

 

This course introduces students to current research issues in developing hybrid human-machine technologies for biomedical applications. Topics we will cover include human factors for these technologies, human augmentation, human rehabilitation and smart prostheses, wearable biomedical devices, nervous system modeling, and human-robotic interaction. The course (2 weeks) allows students to develop an understanding of the future potential and limitations of categories of medical devices and technologies. Topics include a mix of human augmentation technologies, rehabilitation technologies, brain-computer interface technologies, locomotion modeling, neural modeling and control technologies, and human-robotic technologies. Industry visits and hands-on laboratories are planned for the course.

Main Topics

  • Hybrid Human: Human Augmentation and Smart Suits
  • Active prosthetics
  • Surgical Robotics
  • Neural prostheses and neuromorphic control
  • Rehabilitation technologies
  • Human-robotic systems
  • Brain Computer Interface
  • Capsule endoscopy technologies for diagnosis and therapy
  • Human movement simulation and analysis using multibody dynamics methodologies.
  • Experimental techniques for movement acquisition and analysis in laboratorial environment
  • Learning outcomes:

  • General understanding of human physiology, biomechanics, and biomechanical control relevant to the development of these technologies
  • Understanding of the recent advances in active orthotic design to enhance locomotion and rehabilitation techniques for augmented gait
  • Introduction to surgical robotics, modeling and control in physical human-robot interaction
  • Identification of the essential elements of human-machine interfaces for medical device design and utilization
  • Ability to understand the functioning of e-textiles and their monitoring sensors and wireless communications concerning their applications
  • Ability to understand the modeling of neuromorphic control and the technologic knowledge behind neuro prostheses
  • General knowledge of brain-computer interface (BCI) as a device and capsule endoscopy technologies and applications
  • Capsule endoscopy technologies and application
  • Ability to acquire and analyze general human movements and the consequent application of such relevant biomechanical information to the design of medical devices and to the support of clinical decision

 

 

 

E2. Nanobiotechnology and Biomaterials

1st Semester, 6 ECTS
Location: Lisbon –Instituto Superior Técnico (IST) and Braga – University of Minho (UMinho)
Faculty leads: Paula Hammond (MIT) / João Conde (IST) / Rui Reis (UMinho)

P. Hammond, (Associate Professor at the MIT Department of Chemical Engineering)
João Pedro Conde (IST Department of Chemical and Biological Engineering; Associated Research Laboratory INESC-MN)
R. Reis (University of Minho Department of Polymer Engineering; Associated Research Laboratory Instituto de Biotecnologia e Bioengenharia)

This course is a broad survey course, aiming at providing a perspective of the novel developments of applications of micro and nanotechnology in bioengineering and materials science and engineering. The aim is to present a perspective that includes molecular biology, physical principles and engineering concepts.

Part 1: Nanobiotechnology

The objective of the Nanobiotechnology course is that the students understand in both breadth and depth the scientific and technological basis of Nanotechnology applied to Biomedical and BioEngineering. Application areas include: micro and nanofabrication, MEMS and NEMS, micro reactors, lab-on-a-chip systems, micro total analysis systems, carbon nanotubes, nanowires, atomic force microscopy, atomic and molecular manipulation, nanoparticles, (nano) biosensors, and biochips.

Main Topics

  • Emerging BioNano topics: synthetic biology, others
  • Microfluidics and Lab-on-a-chip systems
  • Cell-chips
  • Carbon nanostructures
  • DNA and protein nanostructures
  • Protein chips
  • Self-Assembly

Part 2: Biomaterials

The Biomaterials part of the course aims to introduce the principles and applications of materials science, engineering and biology related to Tissue Engineering.

Main Topics

  • Materials for Biomedical Applications
  • Degradable Biomaterials and Degradation Mechanisms
  • Biomineralization, Bioactivity and Biomimetics
  • Biocompatibility
  • Tissue Repair, Engineering and Regeneration
  • Surface Properties, Modification and Its Effects on Cell Behaviour
  • Smart Biomaterials and Carriers for the Controlled Release of Bioactive Agents
  • Biomaterials and Scaffolds for Tissue Regeneration: Applications and Industrial Situation

Learning outcomes

  • Understanding of the scientific and technological background of Nanotechnology
  • Ability to understand several applications of Nanotechnology to biological systems
  • Ability to know how to integrate nanostructures on biological systems and/or how to design them
  • Understanding the current state-of-the-art in Nanobiotechnology and its potential  future applications
  • Ability to understand the transport limitations at the micro/nano scale
  • Ability to design top-down and bottom-up nanofabricated structures for biotechnological applications
  • Ability to describe  the biomaterials properties used in biomedical applications and their most common features
  • Comprehensive understanding of degradation mechanisms of biomaterials
  • Ability to integrate and predict bioactivity and biocompatibility in biomedical applications
  • Understanding of tissue engineering fundamentals with a strong integration with the biomaterials properties
  • Ability to apply surface properties on a specific application
  • Ability to design a biomaterial application solution to a specific problem
  • General understanding on controlled-release processes of bio-agents
  • Ability to evaluate the current state-of-the-art in both research and industrial applications



E3. Neuroscience: Molecular to Systems Neurobiology and Brain Diseases

1st Semester, 6 ECTS
Location: Coimbra – Centre for NeuroScience and Cell Biology (CNC)  and Oeiras – Instituto Gulbenkian de Ciência (IGC)
Faculty leads: Susumu Tonegawa (MIT) / António Coutinho (GULBENKIAN) / Catarina Oliveira (CNC-Univ.Coimbra)

S. Tonegawa, (MIT Department of Biology; Director, Picower Institute for Learning and Memory)
Elly Nedivi, (MIT Department of Brain and Cognitive Sciences)
A. Coutinho (Gulbenkian Institute of Sciences)
Zach Mainen (Gulbenkian Institute of Sciences)
C. Oliveira, (Center for Neuroscience and Cell Biology (CNC),University of Coimbra, Portugal )
Rodrigo Cunha (Center for Neuroscience and Cell Biology (CNC),University of Coimbra, Portugal )

This course will be taught in a condensed form during 2 weeks, corresponding to 2 Parts. Part 1 will be taught by faculty from the CNC coordinated by Catarina Oliveira and Rodrigo Cunha, with participation of faculty from other Portuguese institutions. Part 2 will be taught by MIT faculty and IGC, Oeiras, coordinated by Zach Mainen and Elly Nedivi.

Part 1: The Brain as an Information Processing and Control Device

The first part of the course will lay the foundation for a basic understanding of how the brain is put together and works to process sensory input and produce motor output at the systems and cellular level. The goal is to set a common baseline for students coming from diverse educational backgrounds.

Main Topics

  • Anatomy and Function
  • Cell biology of the neuron
  • Physiology
  • Development
  • Synaptic Plasticity

Part 2: Tinkering with Brain Function

The second part of the course is designed to expose students to hot topics that are at the forefront of modern neuroscience and introduce them to some of the innovative technologies that are being applied to investigate these topics. This week the last session of each day will include 2 paper presentations and a discussion prepared by the students, which will constitute the basis of their evaluation.

Main Topics

  • Modulators of Plasticity
  • Engineering Genes and Genetic therapies
  • Visualizing modules, cells, and molecules: uses for studies of function and pathology
  • Growth factors
  • Stem cells

Learning outcomes of the course as a whole

  • Comprehensive knowledge of the anatomy and function of the human brain including sensor and motor systems
  • Ability to understand the molecular cell biology of neurons including development, physiology, signal processing (receiving & transmission) and propagation
  • General understanding of synaptic plasticity
  • Integration of drug development studies with neuroscience research areas
  • Ability to understand the importance of genetic technologies in neuroscience and how they are used in applications
  • General understanding of circuit analysis and tetrode electrophysics
  • Ability to describe the methods on cell and functional imaging and how to apply the concepts/methods to a particular research subject


E4. Principles and Practice of Drug Development

1st Semester, 6 ECTS
Location: Coimbra, Centre for Neuroscience and Cell Biology (CNC)
Faculty leads: Thomas Allen & Stan Finkelstein (MIT) / Conceição Lima & João Moreira (CNC)

T. Allen (MIT Sloan School of Management; Engineering Systems Division)
S. Finkelstein, (Harvard-MIT Health Sciences and Technology, Engineering Systems Division)
C. Lima, (University of Coimbra Department of Biochemistry; Associate Research Laboratory CNC)
J. Moreira (University of Coimbra, Faculty of Pharmacy; Associate Research Laboratory CNC)

This course deals with the description and critical assessments of the major issues and stages of developing a pharmaceutical or bio-pharmaceutical: drug discovery, preclinical development, clinical investigation, manufacturing and regulatory issues considered for small and large molecules, as well as economical and financial considerations of the drug development process.  Moreover, multidisciplinary perspectives from Faculty in clinical, life and management sciences are expected to be involved, as well as industrial guests.

Main Topics

  • The Pharmaceutical Industry and the Drug Development Process
  • Basic Science – Discovery Innovation, Emerging Technology, Toxicology
  • Business of Biotechnology
  • Management of Scientific and Clinical Decisions
  • FDA Process and Insurance Coverage of Drugs
  • Drug Delivery
  • Value of Pharmaceuticals
  • Manufacturing
  • Synthetic Biology
  • Special Topics

Learning outcomes

  • Comprehensive knowledge of the pharmaceutical industry in a global perspective and the drug development process
  • Understanding of the basic scientific concepts behind the drug development process and the stages behind it
  • Ability to make management and clinical decisions on a certain stage of the development process
  • Ability to recognize the clinical development and clinical trials as very important part of the process
  • Understanding  the role of regulatory institutions and agencies, regarding the complete drug development process implementation and its legal issues
  • Ability to understand how the drug delivery is made and how to measure the value of pharmaceuticals
  • General understanding of drug manufacturing processes based on case studies in industrial environment and applied to the development of a potential new drug