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Course 20: Biological Engineering
IAP/Spring 2024


20.001 Introduction to Professional Success and Leadership in Biological Engineering
______

Undergrad (Fall)
Prereq: None
Units: 1-0-2 [P/D/F]
______
Interactive introduction to the discipline of Biological Engineering through presentations by alumni practitioners, with additional panels and discussions on skills for professional development. Presentations emphasize the roles of communication through writing and speaking, building and maintaining professional networks, and interpersonal and leadership skills in building successful careers. Provides practical advice about how to prepare for job searches and graduate or professional school applications from an informed viewpoint. Prepares students for UROPs, internships, and selection of BE electives. Subject can count toward the 6-unit discovery-focused credit limit for first-year students.  
P. Blainey, L. Griffith

20.005 Ethics for Engineers
______

Undergrad (Fall, Spring)
(Subject meets with 1.082[J], 2.900[J], 6.9320[J], 6.9321, 10.01[J], 16.676[J], 22.014[J])
Prereq: None
Units: 2-0-7
Lecture: M3-5 (66-156) or T3-5 (66-148) or W3-5 (66-148) or W EVE (7-9 PM) (66-148)
______
Explores how to be an ethical engineer. Students examine engineering case studies along with foundational ethical readings, and investigate which ethical approaches are best and how to apply them as engineers. Topics include justice, rights, cost-benefit analysis, safety, bias, genetic engineering, climate change, and the promise and peril of AI. Discussion-based. All sections cover the same core ethical frameworks, but some sections have a particular focus for engineering case studies, such as Computer Science or Bioengineering. Students are eligible to take any section of the course, regardless of their registered course number. The subject is taught in separate sections. For 20.005, students additionally undertake an ethical-technical analysis of a BE-related topic of their choosing.
P. Hansen, M. Hemann, D. Lauffenburger, K. Hansen
No required or recommended textbooks

20.010 Introduction to Experimentation in BE
______

Undergrad (Fall)
Prereq: None
Units: 1-0-2 [P/D/F]
______
Teaches students to ask research questions and use the steps in the experimental method to test hypotheses. Introduces best practices in basic data analysis and interpretation. Additional topics include exploring experimental failures, unexpected results, and troubleshooting. Goal is to prepare students for undergraduate research opportunities and laboratory-based coursework. This is a discussion-based subject and is dependent on group participation. Preference to first- and second-year students.
N. Lyell

20.020 Introduction to Biological Engineering Design Using Synthetic Biology
______

Undergrad (Spring)
Prereq: None
Units: 3-3-3
Lecture: TR2-5 (36-144)
______
Project-based introduction to the engineering of synthetic biological systems. Throughout the term, students develop projects that are responsive to real-world problems of their choosing, and whose solutions depend on biological technologies. Lectures, discussions, and studio exercises introduce components and control of prokaryotic and eukaryotic behavior; DNA synthesis, standards, and abstraction in biological engineering; and issues of human practice, including biological safety, security, ethics and ownership, sharing, and innovation. Students may have the option to continue projects for participation in the iGEM competition. Preference to first-year students.
J. Buck
No required or recommended textbooks

20.051 Introduction to NEET: Living Machines
______

Undergrad (Fall, Spring)
Prereq: Biology (GIR), Calculus II (GIR), Chemistry (GIR), and Physics I (GIR)
Units: 2-3-4
Lecture: WF4 (4-149) Lab: TBA
______
Focuses on physiomimetics: transforming therapeutic strategy and development. Overview of development of therapies for complex diseases, including disease mechanisms in heterogeneous patient populations, developing therapeutic strategies, modeling these in vitro, and testing the therapies. Explores the five essential technological contributions to this process: computational systems biology, synthetic biology, immuno-engineering, microphysiological systems devices/tissue engineering, and microfluidic device engineering for in vitro models and analysis. Introduces disease modeling, patient stratification, and drug development processes, includes extensive examples from industry, and provides context for choosing a concentration track in the Living Machines thread. Weekly lectures from experts in the field supplemented with structured, short projects in each topic area. Limited to 24; preference to students in the NEET Living Machines thread.
Fall: L. Griffith, M. Salek
Spring: L. Griffith, M. Salek
No required or recommended textbooks

20.054 NEET - Living Machines Research Immersion
______

Undergrad (Fall, Spring) Can be repeated for credit
Prereq: 20.051
Units arranged
Lecture: R10 (56-169)
______
A structured lab research experience in a specific Living Machines track. Students identify a project in a participating research lab, on a topic related to the five tracks in the NEET Living Machines program, propose a project related to the drug development theme, and prepare interim and final presentations and reports while conducting the project. Links to industry-sponsored research projects at MIT are encouraged. Project proposal must be submitted and approved in the term prior to enrollment. Limited to students in the NEET Living Machines thread.
Fall: L. Griffith, M. Salek
Spring: L. Griffith, M. Salek
No required or recommended textbooks

20.101 Metakaryotic Biology and Epidemiology
______

Undergrad (Fall)
(Subject meets with 20.A02)
Prereq: None
Units: 2-0-4
______
Introduces non-eukaryotic, "metakaryotic" cells with hollow bell-shaped nuclei that serve as the stem cells of human fetal/juvenile growth and development as well as of tumors and atherosclerotic plaques. Studies the relationship of lifetime growth and mutations of metakaryotic stem cells to age-specific death rates. Considers the biological bases of treatment protocols found to kill metakaryotic cancer stem cells in vitro and in human pancreatic cancers in vivo.
W. Thilly

20.102 Metakaryotic Stem Cells in Carcinogenesis: Origins and Cures
______

Undergrad (Fall)
(Subject meets with 20.215)
Prereq: Biology (GIR), Calculus II (GIR), and Chemistry (GIR)
Units: 3-0-9
______
Metakaryotic stem cells of organogenesis, wound healing, and the pathogenic lesions of cancers and atherosclerotic plaques. Metakaryotic cell resistance to x-ray- and chemo-therapies. Common drug treatment protocols lethal to metakaryotic cancer stem cells in vivo first clinical trial against pancreatic cancer. Application of a hypermutable/mutator stem cell model to the age-specific mortality from clonal diseases, and the expected responses to metakaryocidal drugs in attempted cure and prevention of tumors or atherosclerotic plaques. Students taking 20.215 responsible for de novo computer modeling.
W. Thilly

20.104[J] Environmental Cancer Risks, Prevention, and Therapy
______

Undergrad (Spring)
(Same subject as 1.081[J])
Prereq: Biology (GIR), Calculus II (GIR), and Chemistry (GIR)
Units: 3-0-9
Lecture: TR1-2.30 (16-771)
______
Analysis of the history of cancer and vascular disease mortality rates in predominantly European- and African-American US cohorts, 1895-2016, to discover specific historical shifts. Explored in terms of contemporaneously changing environmental risk factors: air-, food- and water-borne chemicals; subclinical infections; diet and lifestyles. Special section on occupational risk factors. Considers the hypotheses that genetic and/or environmental factors affect metakaryotic stem cell mutation rates in fetuses and juveniles and/or their growth rates of preneoplastic in adults.
W. Thilly, R. McCunney
No required or recommended textbooks

20.106[J] Applied Microbiology
______

Undergrad (Fall)
Not offered regularly; consult department
(Same subject as 1.084[J])
Prereq: Biology (GIR) and Chemistry (GIR)
Units: 3-0-9
______
Introductory microbiology from a systems perspective - considers microbial diversity and the integration of data from a molecular, cellular, organismal, and ecological context to understand the interaction of microbial organisms with their environment. Special emphasis on specific viral, bacterial, and eukaryotic microorganisms and their interaction with animal hosts with focus on contemporary problems in areas such as vaccination, emerging disease, antimicrobial drug resistance, and toxicology.
J. Niles, K. Ribbeck

20.109 Laboratory Fundamentals in Biological Engineering
______

Undergrad (Fall, Spring) Institute Lab
Prereq: Biology (GIR), Chemistry (GIR), 6.100B, 18.03, and 20.110
Units: 2-8-5
Lecture: TR11 (4-237) Lab: TR1-5 (56-322) or WF1-5 (56-322)
______
Introduces experimental biochemical and molecular techniques from a quantitative engineering perspective. Experimental design, data analysis, and scientific communication form the underpinnings of this subject. In this, students complete discovery-based experimental modules drawn from current technologies and active research projects of BE faculty. Generally, topics include DNA engineering, in which students design, construct, and use genetic material; parts engineering, emphasizing protein design and quantitative assessment of protein performance; systems engineering, which considers genome-wide consequences of genetic perturbations; and biomaterials engineering, in which students use biologically-encoded devices to design and build materials. Enrollment limited; priority to Course 20 majors.
Fall: N. Lyell, J. Niles, B. Engelward, B.Meyer, J. Zhan, S. Clarke, C. Ricci-Tam
Spring: N. Lyell, A. Koehler, A. Belcher, B. Meyer, J. Zhan, S. Clarke, C. Ricci-Tam
No required or recommended textbooks

20.110[J] Thermodynamics of Biomolecular Systems
______

Undergrad (Fall) Rest Elec in Sci & Tech
(Same subject as 2.772[J])
Prereq: (Biology (GIR), Calculus II (GIR), Chemistry (GIR), and Physics I (GIR)) or permission of instructor
Units: 5-0-7
______
Equilibrium properties of macroscopic and microscopic systems. Basic thermodynamics: state of a system, state variables. Work, heat, first law of thermodynamics, thermochemistry. Second and third law of thermodynamics: entropy and its statistical basis, Gibbs function. Chemical equilibrium of reactions in gas and solution phase. Macromolecular structure and interactions in solution. Driving forces for molecular self-assembly. Binding cooperativity, solvation, titration of macromolecules.
M. Birnbaum, P. Blainey, S. Manalis

20.129[J] Biological Circuit Engineering Laboratory
______

Undergrad (Spring) Institute Lab
(Same subject as 6.4880[J])
Prereq: Biology (GIR) and Calculus II (GIR)
Units: 2-8-2
Lecture: MW12 (4-163) Lab: MW1-5 (26-035)
______
Students assemble individual genes and regulatory elements into larger-scale circuits; they experimentally characterize these circuits in yeast cells using quantitative techniques, including flow cytometry, and model their results computationally. Emphasizes concepts and techniques to perform independent experimental and computational synthetic biology research. Discusses current literature and ongoing research in the field of synthetic biology. Instruction and practice in oral and written communication provided. Enrollment limited.
J. Niles, R. Weiss, J. Buck
No required or recommended textbooks

20.200 Biological Engineering Seminar
______

Graduate (Fall, Spring) Can be repeated for credit
Prereq: Permission of instructor
Units: 1-0-2 [P/D/F]
Lecture: F12 (32-155)
______
Weekly one-hour seminars covering graduate student research and presentations by invited speakers.
Fall: B. Bryson, B. Engelward
Spring: B. Bryson, B. Engelward
No required or recommended textbooks

20.201 Fundamentals of Drug Development
______

Graduate (Fall, Spring)
Prereq: Permission of instructor
Units: 4-0-8
Lecture: MW1.30-3 (56-614) Recitation: F1.30 (56-614)
______
Team-based exploration of the scientific basis for developing new drugs. First portion of term covers fundamentals of target identification, drug discovery, pharmacokinetics, pharmacodynamics, regulatory policy, and intellectual property. Industry experts and academic entrepreneurs then present case studies of specific drugs, drug classes, and therapeutic targets. In a term-long project, student teams develop novel therapeutics to solve major unmet medical needs, with a trajectory to a "start-up" company. Culminates with team presentations to a panel of industry and scientific leaders.
Fall: P. C. Dedon, R. Sasisakharan
Spring: P. C. Dedon, R. Sasisekharan
No required or recommended textbooks

20.202 In vivo Models: Principles and Practices
______

Graduate (Spring)
Not offered regularly; consult department
Prereq: Permission of instructor
Units: 1-1-4
______
Selected aspects of anatomy, histology, immuno-cytochemistry, in situ hybridization, physiology, and cell biology of mammalian organisms and their pathogens. Subject material integrated with principles of toxicology, in vivo genetic engineering, and molecular biology. A lab/demonstration period each week involves experiments in anatomy (in vivo), physiology, and microscopy to augment the lectures. Offered first half of spring term.
J. Fox

20.203[J] Neurotechnology in Action
______

Graduate (Spring)
(Same subject as 9.123[J])
Prereq: Permission of instructor
Units: 3-6-3
Lecture: TR2.30-4 (46-4062)
______
Offers a fast-paced introduction to numerous laboratory methods at the forefront of modern neurobiology. Comprises a sequence of modules focusing on neurotechnologies that are developed and used by MIT research groups. Each module consists of a background lecture and 1-2 days of firsthand laboratory experience. Topics typically include optical imaging, optogenetics, high throughput neurobiology, MRI/fMRI, advanced electrophysiology, viral and genetic tools, and connectomics.
A. Jasanoff, E. Boyden, M. Jonas, E.Boyden
No required or recommended textbooks

20.205[J] Principles and Applications of Genetic Engineering for Biotechnology and Neuroscience
______

Undergrad (Spring)
(Same subject as 9.26[J])
Prereq: Biology (GIR)
Units: 3-0-9
Lecture: F1-4 (4-146)
______
Covers principles underlying current and future genetic engineering approaches, ranging from single cellular organisms to whole animals. Focuses on development and invention of technologies for engineering biological systems at the genomic level, and applications of engineered biological systems for medical and biotechnological needs, with particular emphasis on genetic manipulation of the nervous system. Design projects by students.
F. Zhang
No textbook information available

20.213 Genome Stability and Engineering in the Context of Diseases, Drugs, and Public Health
______

Undergrad (Spring); second half of term
Prereq: 5.07, 7.05, or permission of instructor
Units: 4-0-5
Begins Apr 1. Lecture: MW9-11 (56-167)
______
Studies how DNA damage leads to diseases, and how DNA repair modulates cancer risk and treatment. Also covers how DNA repair impacts genetic engineering, whether by targeted gene therapy or CRISPR-mediated genetic changes. Students gain a public health perspective by examining how DNA-damaging agents in our environment can lead to downstream cancer. Explores the underlying chemical, molecular and biochemical processes of DNA damage and repair, and their implications for disease susceptibility and treatment.
B. P. Engelward
No textbook information available

20.215 Macroepidemiology, Population Genetics, and Stem Cell Biology of Human Clonal Diseases
______

Graduate (Fall)
(Subject meets with 20.102)
Prereq: Calculus II (GIR) and 1.00
Units: 3-0-15
______
Studies the logic and technology needed to discover genetic and environmental risks for common human cancers and vascular diseases. Includes an introduction to metakaryotic stem cell biology. Analyzes large, organized historical public health databases using quantitative cascade computer models that include population stratification of stem cell mutation rates in fetal/juvenile tissues and growth rates in preneoplastic colonies and atherosclerotic plaques. Means to test hypotheses (CAST) that certain genes carry mutations conferring risk for common cancers via genetic analyses in large human cohorts. Involves de novo computer modeling of a lifetime disease experience or test of a student-developed hypothesis.
W. G. Thilly

20.219 Selected Topics in Biological Engineering
______

Graduate (Fall, Spring) Can be repeated for credit
Not offered regularly; consult department
Prereq: Permission of instructor
Units arranged
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Staff

20.230[J] Immunology
______

Undergrad (Spring)
(Same subject as 7.23[J])
(Subject meets with 7.63[J], 20.630[J])
Prereq: 7.06
Units: 5-0-7
Lecture: MW9.30-11 (4-370) Recitation: W12 (56-167) or W EVE (7 PM) (66-168) or R4 (66-160)
______
Comprehensive survey of molecular, genetic, and cellular aspects of the immune system. Topics include innate and adaptive immunity; cells and organs of the immune system; hematopoiesis; immunoglobulin, T cell receptor, and major histocompatibility complex (MHC) proteins and genes; development and functions of B and T lymphocytes; immune responses to infections and tumors; hypersensitivity, autoimmunity, and immunodeficiencies. Particular attention to the development and function of the immune system as a whole, as studied by modern methods and techniques. Students taking graduate version explore the subject in greater depth, including study of recent primary literature.
S.Spranger, M. Birnbaum
Textbooks (Spring 2024)

20.260 Computational Analysis of Biological Data
______

Undergrad (Spring)
(Subject meets with 20.460)
Prereq: 6.100A or permission of instructor
Units: 3-0-6
Lecture: TR1-3 (16-220)
______
Presents foundational methods for analysis of complex biological datasets. Covers fundamental concepts in probability, statistics, and linear algebra underlying computational tools that enable generation of biological insights. Assignments focus on practical examples spanning basic science and medical applications. Assumes basic knowledge of calculus and programming (experience with MATLAB, Python, or R is recommended). Students taking graduate version complete additional assignments.
D. Lauffenburger, F. White
No required or recommended textbooks

20.265 Genetics for Biological Engineering
______

Undergrad (Spring); second half of term
Not offered regularly; consult department
Prereq: 6.100A or permission of instructor
Units: 3-0-3
Subject Cancelled Subject Cancelled
______
Covers topics in genetics from an engineering perspective. Designed to be taken before, concurrently with, or after a traditional genetics class. Focuses primarily on the quantitative methods and algorithms used in genetics and genomics. Provides a strong foundation in genomics and bioinformatics and prepares students, through real-world problem-solving, for upper-level classes in those topics. Basics of modern genomics tools and approaches -- including RNAseq, high-throughout genome sequencing, genome-wide association studies, metagenomics, and others -- presented. Requires some experience with Python programming.
Staff

20.305[J] Principles of Synthetic Biology
______

Undergrad (Fall)
(Same subject as 6.8721[J])
(Subject meets with 6.8720[J], 20.405[J])
Prereq: None
Units: 3-0-9
______
Introduces the basics of synthetic biology, including quantitative cellular network characterization and modeling. Considers the discovery and genetic factoring of useful cellular activities into reusable functions for design. Emphasizes the principles of biomolecular system design and diagnosis of designed systems. Illustrates cutting-edge applications in synthetic biology and enhances skills in analysis and design of synthetic biological applications. Students taking graduate version complete additional assignments.
R. Weiss

20.309[J] Instrumentation and Measurement for Biological Systems
______

Undergrad (Fall, Spring)
(Same subject as 2.673[J])
(Subject meets with 20.409)
Prereq: (Biology (GIR), Physics II (GIR), 6.100B, and 18.03) or permission of instructor
Units: 3-6-3
Lecture: TRF12 (4-237) Lab: TBA
______
Sensing and measurement aimed at quantitative molecular/cell/tissue analysis in terms of genetic, biochemical, and biophysical properties. Methods include light and fluorescence microscopies, and electro-mechanical probes (atomic force microscopy, optical traps, MEMS devices). Application of statistics, probability, signal and noise analysis, and Fourier techniques to experimental data. Enrollment limited; preference to Course 20 undergraduates.
Fall: S. Manalis, P. Blainey, M. Jonas, S. Wasserman
Spring: A. Hansen, E. Boyden, M. Jonas, S. Wasserman
No required or recommended textbooks

20.310[J] Molecular, Cellular, and Tissue Biomechanics
______

Undergrad (Spring)
(Same subject as 2.797[J], 3.053[J], 6.4840[J])
(Subject meets with 2.798[J], 3.971[J], 6.4842[J], 10.537[J], 20.410[J])
Prereq: Biology (GIR) and 18.03
Units: 4-0-8
Lecture: TR1-2.30 (4-237) Recitation: TBA
______
Develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena over a range of length scales. Topics include structure of tissues and the molecular basis for macroscopic properties; chemical and electrical effects on mechanical behavior; cell mechanics, motility and adhesion; biomembranes; biomolecular mechanics and molecular motors. Experimental methods for probing structures at the tissue, cellular, and molecular levels. Students taking graduate version complete additional assignments.
P. So, R. Raman
No textbook information available

20.315 Physical Biology
______

Undergrad (Fall, Spring)
Not offered regularly; consult department
(Subject meets with 20.415)
Prereq: 5.60, 20.110, or permission of instructor
Units: 3-0-9
Credit cannot also be received for 8.241
______
Focuses on current major research topics in quantitative, physical biology. Covers synthetic structural biology, synthetic cell biology, microbial systems biology and evolution, cellular decision making, neuronal circuits, and development and morphogenesis. Emphasizes current motivation and historical background, state-of-the-art measurement methodologies and techniques, and quantitative physical modeling frameworks. Experimental techniques include structural biology, next-generation sequencing, fluorescence imaging and spectroscopy, and quantitative biochemistry. Modeling approaches include stochastic rate equations, statistical thermodynamics, and statistical inference. Students taking graduate version complete additional assignments. 20.315 and 20.415 meet with 8.241 when offered concurrently.
M. Bathe

20.320 Analysis of Biomolecular and Cellular Systems
______

Undergrad (Fall)
Prereq: 6.100B, 18.03, and 20.110; Coreq: 5.07 or 7.05
Units: 4-0-8
______
Analysis of molecular and cellular processes across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis on experimental methods, quantitative analysis, and computational modeling.
F. White, K. D. Wittrup

20.330[J] Fields, Forces and Flows in Biological Systems
______

Undergrad (Spring)
(Same subject as 2.793[J], 6.4830[J])
Prereq: Biology (GIR), Physics II (GIR), and 18.03
Units: 4-0-8
Lecture: MWF11 (4-163) Recitation: M3 (16-220) or T10 (56-167) or W10 (56-180) or W12 (56-154) +final
______
Introduction to electric fields, fluid flows, transport phenomena and their application to biological systems. Flux and continuity laws, Maxwell's equations, electro-quasistatics, electro-chemical-mechanical driving forces, conservation of mass and momentum, Navier-Stokes flows, and electrokinetics. Applications include biomolecular transport in tissues, electrophoresis, and microfluidics.
J. Han, S. Manalis
No textbook information available

20.334 Biological Systems Modeling
______

Undergrad (Fall); first half of term
Prereq: 20.330 or permission of instructor
Units: 1-0-5
______
Practices the use of modern numerical analysis tools (e.g., COMSOL) for biological systems with multi-physics behavior. Covers modeling of diffusion, reaction, convection and other transport mechanisms. Analysis of microfluidic devices as examples. Discusses practical issues and challenges in numerical modeling. No prior knowledge of modeling software required. Includes weekly modeling homework and one final modeling project.
J. Han

20.345 Bioinstrumentation Project Lab
______

Undergrad (Spring)
Not offered regularly; consult department
Prereq: 20.309, (Biology (GIR) and (2.004 or 6.3000)), or permission of instructor
Units: 2-7-3
______
In-depth examination of instrumentation design, principles and techniques for studying biological systems, from single molecules to entire organisms. Lectures cover optics, advanced microscopy techniques, electronics for biological measurement, magnetic resonance imaging, computed tomography, MEMs, microfluidic devices, and limits of detection. Students select two lab exercises during the first half of the semester and complete a final design project in the second half. Lab emphasizes design process and skillful realization of a robust system. Enrollment limited; preference to Course 20 majors and minors.
E. Boyden, A. Jasanoff, P. So, M. Jonas, J. Sutton, S. Wasserman

20.352 Principles of Neuroengineering
______

Undergrad (Fall)
Not offered regularly; consult department
(Subject meets with 9.422[J], 20.452[J], MAS.881[J])
Prereq: Permission of instructor
Units: 3-0-9
______
Covers how to innovate technologies for brain analysis and engineering, for accelerating the basic understanding of the brain, and leading to new therapeutic insight and inventions. Focuses on using physical, chemical and biological principles to understand technology design criteria governing ability to observe and alter brain structure and function. Topics include optogenetics, noninvasive brain imaging and stimulation, nanotechnologies, stem cells and tissue engineering, and advanced molecular and structural imaging technologies. Includes design projects. Students taking graduate version complete additional assignments. Designed for students with engineering maturity who are ready for design.
Staff

20.361[J] Molecular and Engineering Aspects of Biotechnology
______

Not offered academic year 2023-2024Undergrad (Spring)
(Same subject as 7.37[J], 10.441[J])
Prereq: (7.06 and (2.005, 3.012, 5.60, or 20.110)) or permission of instructor
Units: 4-0-8
Credit cannot also be received for 7.371
______
Covers biological and bioengineering principles underlying the development and therapeutic use of recombinant proteins and stem cells; glycoengineering of recombinant proteins; normal and pathological signaling by growth factors and their receptors; receptor trafficking; monoclonal antibodies as therapeutics; protein pharmacology and delivery; stem cell-derived tissues as therapeutics; RNA therapeutics; combinatorial protein engineering; and new antitumor drugs.
Staff

20.363[J] Biomaterials Science and Engineering
______

Undergrad (Fall)
(Same subject as 3.055[J])
(Subject meets with 3.963[J], 20.463[J])
Prereq: 20.110 or permission of instructor
Units: 3-0-9
______
Covers, at a molecular scale, the analysis and design of materials used in contact with biological systems, and biomimetic strategies aimed at creating new materials based on principles found in biology. Topics include molecular interaction between bio- and synthetic molecules and surfaces; design, synthesis, and processing approaches for materials that control cell functions; and application of materials science to problems in tissue engineering, drug delivery, vaccines, and cell-guiding surfaces. Students taking graduate version complete additional assignments.
D. Irvine, K. Ribbeck

20.365 Engineering the Immune System in Cancer and Beyond
______

Undergrad (Spring)
(Subject meets with 20.465)
Prereq: (5.60 or 20.110) and permission of instructor
Units: 3-0-6
Lecture: TR1-2.30 (56-614)
______
Examines strategies in clinical and preclinical development for manipulating the immune system to treat and protect against disease. Begins with brief review of immune system. Discusses interaction of tumors with the immune system, followed by approaches by which the immune system can be modulated to attack cancer. Also covers strategies based in biotechnology, chemistry, materials science, and molecular biology to induce immune responses to treat infection, transplantation, and autoimmunity. Students taking graduate version complete additional assignments.
D. Irvine
No required or recommended textbooks

20.370[J] Cellular Neurophysiology and Computing
______

Not offered academic year 2023-2024Undergrad (Spring)
(Same subject as 2.791[J], 6.4810[J], 9.21[J])
(Subject meets with 2.794[J], 6.4812[J], 9.021[J], 20.470[J], HST.541[J])
Prereq: (Physics II (GIR), 18.03, and (2.005, 6.2000, 6.3000, 10.301, or 20.110)) or permission of instructor
Units: 5-2-5
______
Integrated overview of the biophysics of cells from prokaryotes to neurons, with a focus on mass transport and electrical signal generation across cell membrane. First third of course focuses on mass transport through membranes: diffusion, osmosis, chemically mediated, and active transport. Second third focuses on electrical properties of cells: ion transport to action potential generation and propagation in electrically excitable cells. Synaptic transmission. Electrical properties interpreted via kinetic and molecular properties of single voltage-gated ion channels. Final third focuses on biophysics of synaptic transmission and introduction to neural computing. Laboratory and computer exercises illustrate the concepts. Students taking graduate version complete different assignments. Preference to juniors and seniors.
Staff

20.373 Foundations of Cell Therapy Manufacturing
______

Undergrad (Spring)
Not offered regularly; consult department
(Subject meets with 20.473)
Prereq: None
Units: 3-0-6
______
Seminar examines cell therapy manufacturing, the ex vivo production of human cells to be delivered to humans as a product for medical benefit. Includes a review of cell biology and immunology. Addresses topics such as governmental regulations applying to cell therapy production; the manufacture of cell-based therapeutics, including cell culture unit operations, genetic engineering or editing of cells; process engineering of cell therapy products; and the analytics of cell therapy manufacturing processes. Students taking graduate version complete additional assignments.
K. Van Vliet

20.375 Applied Developmental Biology and Tissue Engineering
______

Undergrad (Spring)
Not offered regularly; consult department
(Subject meets with 20.475)
Prereq: (7.06, 20.320, and (7.003 or 20.109)) or permission of instructor
Units: 3-0-9
______
Addresses the integration of engineering and biology design principles to create human tissues and organs for regenerative medicine to drug development. Provides an overview of embryogenesis, how morphogenic phenomena are governed by biochemical and biophysical cues. Analyzes <em>in vitro</em> generation of human brain, gut, and other organoids from stem cells. Studies the roles of biomaterials and microreactors in improving organoid formation and function; organoid use in modeling disease and physiology <em>in vitro</em>; and engineering and biological principles of reconstructing tissues and organs from postnatal donor cells using biomaterials scaffolds and bioreactors. Includes select applications, such as liver disease, brain disorders, and others. Students taking graduate version complete additional assignments.
L. Griffith, D. Lauffenburger

20.380 Biological Engineering Design
______

Undergrad (Fall, Spring)
Prereq: 7.06, 20.320, and 20.330
Units: 5-0-7
Lecture: TR9-12 (56-614)
______
Illustrates how knowledge and principles of biology, biochemistry, and engineering are integrated to create new products for societal benefit. Uses case study format to examine recently developed products of pharmaceutical and biotechnology industries: how a product evolves from initial idea, through patents, testing, evaluation, production, and marketing. Emphasizes scientific and engineering principles, as well as the responsibility scientists, engineers, and business executives have for the consequences of their technology. Instruction and practice in written and oral communication provided. Enrollment limited; preference to Course 20 undergraduates.
Fall: J. Collins, A. Koehler, S. Clarke, P. Bhargava, J. Buck
Spring: K. Ribbeck, K. Pate, P. Bhargava, C. Ricci-Tam
No required or recommended textbooks

20.381 Biological Engineering Design II
______

Undergrad (Spring)
Prereq: 20.380 or permission of instructor
Units: 0-12-0
TBA.
______
Continuation of 20.380 that focuses on practical implementation of design proposals. Student teams choose a feasible scope of work related to their 20.380 design proposals and execute it in the lab.
J. Buck
No textbook information available

20.385 Design in Synthetic Biology
______

Undergrad (Spring)
Prereq: (20.020, 20.109, and 20.320) or permission of instructor
Units: 3-3-3
Lecture: TR2-5 (36-144)
______
Provides an understanding of the state of research in synthetic biology and development of project management skills. Critical evaluation of primary research literature covering a range of approaches to the design, modeling and programming of cellular behaviors. Focuses on developing the skills needed to read, present and discuss primary research literature, and to manage and lead small teams. Students mentor a small undergraduate team of 20.020 students. Open to advanced students with appropriate background in biology. Students may have the option to continue projects for participation in the iGEM competition.
J. Buck
No textbook information available

20.390[J] Computational Systems Biology: Deep Learning in the Life Sciences
______

Not offered academic year 2024-2025Undergrad (Spring)
(Same subject as 6.8711[J])
(Subject meets with 6.8710[J], 20.490, HST.506[J])
Prereq: (7.05 and (6.100B or 6.9080)) or permission of instructor
Units: 3-0-9
Lecture: TR12.30-2 (10-250)
______
Presents innovative approaches to computational problems in the life sciences, focusing on deep learning-based approaches with comparisons to conventional methods. Topics include protein-DNA interaction, chromatin accessibility, regulatory variant interpretation, medical image understanding, medical record understanding, therapeutic design, and experiment design (the choice and interpretation of interventions). Focuses on machine learning model selection, robustness, and interpretation. Teams complete a multidisciplinary final research project using TensorFlow or other framework. Provides a comprehensive introduction to each life sciences problem, but relies upon students understanding probabilistic problem formulations. Students taking graduate version complete additional assignments.
B. Berger
No textbook information available

20.405[J] Principles of Synthetic Biology
______

Graduate (Fall)
(Same subject as 6.8720[J])
(Subject meets with 6.8721[J], 20.305[J])
Prereq: None
Units: 3-0-9
______
Introduces the basics of synthetic biology, including quantitative cellular network characterization and modeling. Considers the discovery and genetic factoring of useful cellular activities into reusable functions for design. Emphasizes the principles of biomolecular system design and diagnosis of designed systems. Illustrates cutting-edge applications in synthetic biology and enhances skills in analysis and design of synthetic biological applications. Students taking graduate version complete additional assignments.
R. Weiss

20.409 Biological Engineering II: Instrumentation and Measurement
______

Graduate (Fall, Spring)
(Subject meets with 2.673[J], 20.309[J])
Prereq: Permission of instructor
Units: 2-7-3
Lecture: TRF12 (4-237) Lab: TBA
______
Sensing and measurement aimed at quantitative molecular/cell/tissue analysis in terms of genetic, biochemical, and biophysical properties. Methods include light and fluorescence microscopies, electronic circuits, and electro-mechanical probes (atomic force microscopy, optical traps, MEMS devices). Application of statistics, probability, signal and noise analysis, and Fourier techniques to experimental data. Limited to 5 graduate students.
E. Boyden, A. Jasanoff, P. So, M. Jonas, J. Sutton, S. Wasserman
No required or recommended textbooks

20.410[J] Molecular, Cellular, and Tissue Biomechanics
______

Graduate (Spring)
(Same subject as 2.798[J], 3.971[J], 6.4842[J], 10.537[J])
(Subject meets with 2.797[J], 3.053[J], 6.4840[J], 20.310[J])
Prereq: Biology (GIR) and 18.03
Units: 3-0-9
Lecture: TR1-2.30 (4-237)
______
Develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena over a range of length scales. Topics include structure of tissues and the molecular basis for macroscopic properties; chemical and electrical effects on mechanical behavior; cell mechanics, motility and adhesion; biomembranes; biomolecular mechanics and molecular motors. Experimental methods for probing structures at the tissue, cellular, and molecular levels. Students taking graduate version complete additional assignments.
P. So, R. Raman
No textbook information available

20.415 Physical Biology
______

Graduate (Spring)
Not offered regularly; consult department
(Subject meets with 20.315)
Prereq: Permission of instructor
Units: 3-0-9
Credit cannot also be received for 8.241
______
Focuses on current major research topics in quantitative, physical biology. Topics include synthetic structural biology, synthetic cell biology, microbial systems biology and evolution, cellular decision making, neuronal circuits, and development and morphogenesis. Emphasizes current motivation and historical background, state-of-the-art measurement methodologies and techniques, and quantitative physical modeling frameworks. Experimental techniques include structural biology, next-generation sequencing, fluorescence imaging and spectroscopy, and quantitative biochemistry. Modeling approaches include stochastic rate equations, statistical thermodynamics, and statistical inference. Students taking graduate version complete additional assignments. 20.315 and 20.415 meet with 8.241 when offered concurrently.
Staff

20.416[J] Topics in Biophysics and Physical Biology
______

Not offered academic year 2023-2024Graduate (Fall)
(Same subject as 7.74[J], 8.590[J])
Prereq: None
Units: 2-0-4 [P/D/F]
______
Provides broad exposure to research in biophysics and physical biology, with emphasis on the critical evaluation of scientific literature. Weekly meetings include in-depth discussion of scientific literature led by distinct faculty on active research topics. Each session also includes brief discussion of non-research topics including effective presentation skills, writing papers and fellowship proposals, choosing scientific and technical research topics, time management, and scientific ethics.
J. Gore, N. Fakhri

20.420[J] Principles of Molecular Bioengineering
______

Graduate (Fall)
(Same subject as 10.538[J])
Prereq: 7.06 and 18.03
Units: 3-0-9
______
Provides an introduction to the mechanistic analysis and engineering of biomolecules and biomolecular systems. Covers methods for measuring, modeling, and manipulating systems, including biophysical experimental tools, computational modeling approaches, and molecular design. Equips students to take systematic and quantitative approaches to the investigation of a wide variety of biological phenomena.
A. Jasanoff, E. Fraenkel

20.430[J] Fields, Forces, and Flows in Biological Systems
______

Graduate (Fall)
(Same subject as 2.795[J], 6.4832[J], 10.539[J])
Prereq: Permission of instructor
Units: 3-0-9
______
Molecular diffusion, diffusion-reaction, conduction, convection in biological systems; fields in heterogeneous media; electrical double layers; Maxwell stress tensor, electrical forces in physiological systems. Fluid and solid continua: equations of motion useful for porous, hydrated biological tissues. Case studies of membrane transport, electrode interfaces, electrical, mechanical, and chemical transduction in tissues, convective-diffusion/reaction, electrophoretic, electroosmotic flows in tissues/MEMs, and ECG. Electromechanical and physicochemical interactions in cells and biomaterials; musculoskeletal, cardiovascular, and other biological and clinical examples. Prior undergraduate coursework in transport recommended.
M. Bathe, A. Hansen

20.440 Analysis of Biological Networks
______

Graduate (Spring)
Prereq: 20.420 and permission of instructor
Units: 6-0-9
Lecture: MW2-3.30,F2.30 (32-124)
______
Explores computational and experimental approaches to analyzing complex biological networks and systems. Includes genomics, transcriptomics, proteomics, metabolomics and microscopy. Stresses the practical considerations required when designing and performing experiments. Also focuses on selection and implementation of appropriate computational tools for processing, visualizing, and integrating different types of experimental data, including supervised and unsupervised machine learning methods, and multi-omics modelling. Students use statistical methods to test hypotheses and assess the validity of conclusions. In problem sets, students read current literature, develop their skills in Python and R, and interpret quantitative results in a biological manner. In the second half of term, students work in groups to complete a project in which they apply the computational approaches covered.
B. Bryson, P. Blainey
No required or recommended textbooks

20.445[J] Methods and Problems in Microbiology
______

Graduate (Fall)
(Same subject as 1.86[J], 7.492[J])
Prereq: None
Units: 3-0-9
______
Students will read and discuss primary literature covering key areas of microbial research with emphasis on methods and approaches used to understand and manipulate microbes. Preference to first-year Microbiology and Biology students.
M. Laub, Staff

20.446[J] Microbial Genetics and Evolution
______

Graduate (Fall)
(Same subject as 1.87[J], 7.493[J], 12.493[J])
Prereq: 7.03, 7.05, or permission of instructor
Units: 4-0-8
______
Covers aspects of microbial genetic and genomic analyses, central dogma, horizontal gene transfer, and evolution.
A. D. Grossman, Staff

20.450 Applied Microbiology
______

Graduate (Fall)
Not offered regularly; consult department
Prereq: (20.420 and 20.440) or permission of instructor
Units: 4-0-8
______
Compares the complex molecular and cellular interactions in health and disease between commensal microbial communities, pathogens and the human or animal host. Special focus is given to current research on microbe/host interactions, infection of significant importance to public health, and chronic infectious disease. Classwork will include lecture, but emphasize critical evaluation and class discussion of recent scientific papers, and the development of new research agendas in the fields presented.
J. Niles, K. Ribbeck

20.452[J] Principles of Neuroengineering
______

Not offered academic year 2023-2024Graduate (Fall)
(Same subject as 9.422[J], MAS.881[J])
(Subject meets with 20.352)
Prereq: Permission of instructor
Units: 3-0-9
______
Covers how to innovate technologies for brain analysis and engineering, for accelerating the basic understanding of the brain, and leading to new therapeutic insight and inventions. Focuses on using physical, chemical and biological principles to understand technology design criteria governing ability to observe and alter brain structure and function. Topics include optogenetics, noninvasive brain imaging and stimulation, nanotechnologies, stem cells and tissue engineering, and advanced molecular and structural imaging technologies. Includes design projects. Designed for students with engineering maturity who are ready for design. Students taking graduate version complete additional assignments.
E. S. Boyden, III

20.454[J] Revolutionary Ventures: How to Invent and Deploy Transformative Technologies
______

Graduate (Fall)
(Same subject as 9.455[J], 15.128[J], MAS.883[J])
Prereq: Permission of instructor
Units: 2-0-7
______
Seminar on envisioning and building ideas and organizations to accelerate engineering revolutions. Focuses on emerging technology domains, such as neurotechnology, imaging, cryotechnology, gerontechnology, and bio-and-nano fabrication. Draws on historical examples as well as live case studies of existing or emerging organizations, including labs, institutes, startups, and companies. Goals range from accelerating basic science to developing transformative products or therapeutics. Each class is devoted to a specific area, often with invited speakers, exploring issues from the deeply technical through the strategic. Individually or in small groups, students prototype new ventures aimed at inventing and deploying revolutionary technologies.
E. Boyden, J. Bonsen, J. Jacobson

20.460 Computational Analysis of Biological Data
______

Graduate (Spring)
(Subject meets with 20.260)
Prereq: None
Units: 3-0-6
Lecture: TR1-3 (16-220)
______
Presents foundational methods for analysis of complex biological datasets. Covers fundamental concepts in probability, statistics, and linear algebra underlying computational tools that enable generation of biological insights. Assignments focus on practical examples spanning basic science and medical applications. Assumes basic knowledge of calculus and programming (experience with MATLAB, Python, or R is recommended). Students taking graduate version complete additional assignments.
D. Lauffenburger, F. White
No required or recommended textbooks

20.463[J] Biomaterials Science and Engineering
______

Graduate (Fall)
(Same subject as 3.963[J])
(Subject meets with 3.055[J], 20.363[J])
Prereq: 20.110 or permission of instructor
Units: 3-0-9
______
Covers, at a molecular scale, the analysis and design of materials used in contact with biological systems, and biomimetic strategies aimed at creating new materials based on principles found in biology. Topics include molecular interaction between bio- and synthetic molecules and surfaces; design, synthesis, and processing approaches for materials that control cell functions; and application of materials science to problems in tissue engineering, drug delivery, vaccines, and cell-guiding surfaces. Students taking graduate version complete additional assignments.
D. Irvine, K. Ribbeck

20.465 Engineering the Immune System in Cancer and Beyond
______

Graduate (Spring)
(Subject meets with 20.365)
Prereq: Permission of instructor
Units: 3-0-6
Lecture: TR1-2.30 (56-614)
______
Examines strategies in clinical and preclinical development for manipulating the immune system to treat and protect against disease. Begins with brief review of immune system. Discusses interaction of tumors with the immune system, followed by approaches by which the immune system can be modulated to attack cancer. Also covers strategies based in biotechnology, chemistry, materials science, and molecular biology to induce immune responses to treat infection, transplantation, and autoimmunity. Students taking graduate version complete additional assignments.
D. Irvine
No required or recommended textbooks

20.470[J] Cellular Neurophysiology and Computing
______

Not offered academic year 2023-2024Graduate (Spring)
(Same subject as 2.794[J], 6.4812[J], 9.021[J], HST.541[J])
(Subject meets with 2.791[J], 6.4810[J], 9.21[J], 20.370[J])
Prereq: (Physics II (GIR), 18.03, and (2.005, 6.2000, 6.3000, 10.301, or 20.110)) or permission of instructor
Units: 5-2-5
______
Integrated overview of the biophysics of cells from prokaryotes to neurons, with a focus on mass transport and electrical signal generation across cell membrane. First third of course focuses on mass transport through membranes: diffusion, osmosis, chemically mediated, and active transport. Second third focuses on electrical properties of cells: ion transport to action potential generation and propagation in electrically excitable cells. Synaptic transmission. Electrical properties interpreted via kinetic and molecular properties of single voltage-gated ion channels. Final third focuses on biophysics of synaptic transmission and introduction to neural computing. Laboratory and computer exercises illustrate the concepts. Students taking graduate version complete different assignments.
Staff

20.473 Foundations of Cell Therapy Manufacturing
______

Graduate (Spring)
Not offered regularly; consult department
(Subject meets with 20.373)
Prereq: None
Units: 3-0-6
______
Seminar examines cell therapy manufacturing, the ex vivo production of human cells to be delivered to humans as a product for medical benefit. Includes a review of cell biology and immunology. Addresses topics such as governmental regulations applying to cell therapy production; the manufacture of cell-based therapeutics, including cell culture unit operations, genetic engineering or editing of cells; process engineering of cell therapy products; and the analytics of cell therapy manufacturing processes. Students taking graduate version complete additional assignments.
Staff

20.475 Applied Developmental Biology and Tissue Engineering
______

Graduate (Spring)
Not offered regularly; consult department
(Subject meets with 20.375)
Prereq: Permission of instructor
Units: 3-0-9
______
This subject addresses the integration of engineering and biology design principles to create human tissues and organs for regenerative medicine to drug development. Overview of embryogenesis; how morphogenic phenomena are governed by biochemical and biophysical cues. Analysis of in vitro generation of human brain, gut, and other organoids from stem cells. Roles of biomaterials and microreactors in improving organoid formation and function. Organoid use in modeling disease and physiology in vitro. Engineering and biological principles of reconstructing tissues and organs from postnatal donor cells using biomaterials scaffolds and bioreactors. Select applications such as liver disease, brain disorders, and others. Graduate students will have additional assignments.
L. Griffith, D. Lauffenburger

20.486[J] Case Studies and Strategies in Drug Discovery and Development
______

Graduate (Spring)
Not offered regularly; consult department
(Same subject as 7.549[J], 15.137[J], HST.916[J])
Prereq: None
Units: 2-0-4
______
Aims to develop appreciation for the stages of drug discovery and development, from target identification, to the submission of preclinical and clinical data to regulatory authorities for marketing approval. Following introductory lectures on the process of drug development, students working in small teams analyze how one of four new drugs or drug candidates traversed the discovery/development landscape. For each case, an outside expert from the sponsoring drug company or pivotal clinical trial principal investigator provides guidance and critiques the teams' presentations to the class.
A. W. Wood

20.487[J] Optical Microscopy and Spectroscopy for Biology and Medicine
______

Graduate (Spring)
Not offered regularly; consult department
(Same subject as 2.715[J])
Prereq: Permission of instructor
Units: 3-0-9
______
Introduces the theory and the design of optical microscopy and its applications in biology and medicine. The course starts from an overview of basic optical principles allowing an understanding of microscopic image formation and common contrast modalities such as dark field, phase, and DIC. Advanced microscopy imaging techniques such as total internal reflection, confocal, and multiphoton will also be discussed. Quantitative analysis of biochemical microenvironment using spectroscopic techniques based on fluorescence, second harmonic, Raman signals will be covered. We will also provide an overview of key image processing techniques for microscopic data.
Staff

20.490 Computational Systems Biology: Deep Learning in the Life Sciences
______

Graduate (Spring)
(Subject meets with 6.8710[J], 6.8711[J], 20.390[J], HST.506[J])
Prereq: Biology (GIR) and (6.041 or 18.600)
Units: 3-0-9
Lecture: TR12.30-2 (10-250)
______
Presents innovative approaches to computational problems in the life sciences, focusing on deep learning-based approaches with comparisons to conventional methods. Topics include protein-DNA interaction, chromatin accessibility, regulatory variant interpretation, medical image understanding, medical record understanding, therapeutic design, and experiment design (the choice and interpretation of interventions). Focuses on machine learning model selection, robustness, and interpretation. Teams complete a multidisciplinary final research project using TensorFlow or other framework. Provides a comprehensive introduction to each life sciences problem, but relies upon students understanding probabilistic problem formulations. Students taking graduate version complete additional assignments.
E. Alm, B. Berger
No textbook information available

20.507[J] Introduction to Biological Chemistry
______

Undergrad (Fall) Rest Elec in Sci & Tech
(Same subject as 5.07[J])
Prereq: 5.12
Units: 5-0-7
Credit cannot also be received for 7.05
______
Chemical and physical properties of the cell and its building blocks. Structures of proteins and principles of catalysis. The chemistry of organic/inorganic cofactors required for chemical transformations within the cell. Basic principles of metabolism and regulation in pathways, including glycolysis, gluconeogenesis, fatty acid synthesis/degradation, pentose phosphate pathway, Krebs cycle and oxidative phosphorylation, DNA replication, and transcription and translation.
B. Pentelute, E. Nolan

20.535[J] Protein Engineering
______

Graduate (Spring)
(Same subject as 10.535[J])
Prereq: 18.03 and (5.07 or 7.05)
Units: 3-0-9
Lecture: TR9.30-11 (66-154)
______
Introduces the field of protein engineering. Develops understanding of key biophysical chemistry concepts in protein structure/function and their applications. Explores formulation of simple kinetic, statistical, and transport models for directed evolution and drug biodistribution. Students read and critically discuss seminal papers from the literature.
K. D. Wittrup
No required or recommended textbooks

20.554[J] Advances in Chemical Biology
______

Graduate (Fall)
(Same subject as 5.54[J], 7.540[J])
Prereq: 5.07, 5.13, 7.06, and permission of instructor
Units: 3-0-9
______
Introduction to current research at the interface of chemistry, biology, and bioengineering. Topics include imaging of biological processes, metabolic pathway engineering, protein engineering, mechanisms of DNA damage, RNA structure and function, macromolecular machines, protein misfolding and disease, metabolomics, and methods for analyzing signaling network dynamics. Lectures are interspersed with class discussions and student presentations based on current literature.
L. Kiessling, M. Shoulders, O. Johnson

20.560 Statistics for Biological Engineering
______

Graduate (Spring); second half of term
Not offered regularly; consult department
Prereq: Permission of instructor
Units: 2-0-2 [P/D/F]
______
Provides basic tools for analyzing experimental data, interpreting statistical reports in the literature, and reasoning under uncertain situations. Topics include probability theory, statistical tests, data exploration, Bayesian statistics, and machine learning. Emphasizes discussion and hands-on learning. Experience with MATLAB, Python, or R recommended.
E. Alm, D. Lauffenburger

20.561[J] Eukaryotic Cell Biology: Principles and Practice
______

Graduate (Fall)
(Same subject as 7.61[J])
Prereq: Permission of instructor
Units: 4-0-8
______
Emphasizes methods and logic used to analyze structure and function of eukaryotic cells in diverse systems (e.g., yeast, fly, worm, mouse, human; development, stem cells, neurons). Combines lectures and in-depth roundtable discussions of literature readings with the active participation of faculty experts. Focuses on membranes (structure, function, traffic), organelles, the cell surface, signal transduction, cytoskeleton, cell motility and extracellular matrix. Ranges from basic studies to applications to human disease, while stressing critical analysis of experimental approaches. Enrollment limited.
M. Krieger, M. Yaffe

20.586[J] Science and Business of Biotechnology
______

Graduate (Spring)
(Same subject as 7.546[J], 15.480[J])
Prereq: None. Coreq: 15.401; permission of instructor
Units: 3-0-6
Lecture: R EVE (3-6 PM) (Whitehead-AUDITORIUM) Recitation: T4 (68-180) or T EVE (5 PM) (68-180)
______
Covers the new types of drugs and other therapeutics in current practice and under development, the financing and business structures of early-stage biotechnology companies, and the evaluation of their risk/reward profiles. Includes a series of live case studies with industry leaders of both established and emerging biotechnology companies as guest speakers, focusing on the underlying science and engineering as well as core financing and business issues. Students must possess a basic background in cellular and molecular biology.
J. Chen, A. Koehler, A. Lo, H. Lodish
No required or recommended textbooks

20.630[J] Immunology
______

Graduate (Spring)
(Same subject as 7.63[J])
(Subject meets with 7.23[J], 20.230[J])
Prereq: 7.06 and permission of instructor
Units: 5-0-7
Lecture: MW9.30-11 (4-370) Recitation: W12 (56-167) or W EVE (7 PM) (66-168) or R4 (66-160)
______
Comprehensive survey of molecular, genetic, and cellular aspects of the immune system. Topics include innate and adaptive immunity; cells and organs of the immune system; hematopoiesis; immunoglobulin, T cell receptor, and major histocompatibility complex (MHC) proteins and genes; development and functions of B and T lymphocytes; immune responses to infections and tumors; hypersensitivity, autoimmunity, and immunodeficiencies. Particular attention to the development and function of the immune system as a whole, as studied by modern methods and techniques. Students taking graduate version explore the subject in greater depth, including study of recent primary literature.
S. Spranger, M. Birnbaum
Textbooks (Spring 2024)

20.902 Independent Study in Biological Engineering
______

Undergrad (Fall, Spring) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
Opportunity for independent study under regular supervision by a faculty member. Projects require prior approval, as well as a substantive paper. Minimum 12 units required.
Fall: D. Fares
Spring: D. Fares
No required or recommended textbooks

20.903 Independent Study in Biological Engineering
______

Undergrad (Fall, Spring, Summer) Can be repeated for credit
Prereq: Permission of instructor
Units arranged [P/D/F]
TBA.
______
Opportunity for independent study under regular supervision by a faculty member. Projects require prior approval, as well as a substantive paper. Minimum 6-12 units required.
Fall: D. Fares
Spring: D. Fares
Summer: D. Fares
No required or recommended textbooks

20.920 Practical Work Experience
______

Undergrad (Fall, IAP, Spring, Summer)
Prereq: None
Units: 0-1-0 [P/D/F]
TBA.
______
For Course 20 students participating in off-campus professional experiences in biological engineering. Before registering for this subject, students must have an offer from a company or organization and must identify a BE supervisor. Upon completion, student must submit a letter from the company or organization describing the experience, along with a substantive final report from the student approved by the MIT supervisor. Subject to departmental approval. Consult departmental undergraduate office.
Fall: D. Fares
IAP: D. Fares
Spring: D. Fares
Summer: D. Fares
No required or recommended textbooks

20.930[J] Research Experience in Biopharma
______

Graduate (Fall)
(Same subject as 7.930[J])
Prereq: None
Units: 2-10-0
______
Provides exposure to industrial science and develops skills necessary for success in such an environment. Under the guidance of an industrial mentor, students participate in on-site research at a local biopharmaceutical company where they observe and participate in industrial science. Serves as a real-time case study to internalize the factors that shape R&D in industry, including the purpose and scope of a project, key decision points in the past and future, and strategies for execution. Students utilize company resources and work with a scientific team to contribute to the goals of their assigned project; they then present project results to the company and class, emphasizing the logic that dictated their work and their ideas for future directions. Lecture component focuses on professional development.
Burge, Clarke

20.945 Practical Experience in Biological Engineering
______

Graduate (IAP, Spring, Summer)
Prereq: None
Units: 0-1-0 [P/D/F]
TBA.
______
For Course 20 doctoral students participating in off-campus research, academic experiences, or internships in biological engineering. For internship experiences, an offer of employment from a company or organization is required prior to enrollment; employers must document work accomplished. A written report is required upon completion of a minimum of four weeks of off-campus experience. Proposals must be approved by department.
IAP: F. White
Spring: Staff
Summer: D. Fares
No textbook information available (IAP 2024); No required or recommended textbooks (Spring 2024)

20.950 Research Problems in Biological Engineering
______

Graduate (Fall, IAP, Spring, Summer) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
Directed research in the fields of bioengineering and environmental health. Limited to BE students.
Fall: D. Fares
IAP: D. Fares
Spring: D. Fares
Summer: D. Fares
No textbook information available (IAP 2024); No required or recommended textbooks (Spring 2024)

20.951 Thesis Proposal
______

Graduate (Fall, Spring, Summer)
Prereq: Permission of instructor
Units: 0-24-0 [P/D/F]
TBA.
______
Thesis proposal research and presentation to the thesis committee.
Fall: D. Fares
Spring: D. Fares
Summer: D. Fares
No required or recommended textbooks

20.960 Teaching Experience in Biological Engineering
______

Graduate (Fall, Spring) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
For qualified graduate students interested in teaching. Tutorial, laboratory, or classroom teaching under the supervision of a faculty member. Enrollment limited by availability of suitable teaching assignments.
Fall: D. Fares
Spring: D. Fares
No required or recommended textbooks

20.BME Undergraduate Research in Biomedical Engineering
______

Undergrad (Fall, Spring) Can be repeated for credit
Prereq: None
Units arranged [P/D/F]
TBA.
______
Individual research project with biomedical or clinical focus, arranged with appropriate faculty member or approved supervisor. Forms and instructions for the proposal and final report are available in the BE Undergraduate Office.
Fall: J. Han
Spring: J. Han
No required or recommended textbooks

20.C01[J] Machine Learning for Molecular Engineering
______

Undergrad (Spring)
(Same subject as 3.C01[J], 10.C01[J])
(Subject meets with 3.C51[J], 7.C01, 7.C51, 10.C51[J], 20.C51[J])
Prereq: Calculus II (GIR) and 6.100A; Coreq: 6.C01
Units: 2-0-4
Credit cannot also be received for 1.C01, 1.C51, 2.C01, 2.C51, 3.C51, 7.C01, 7.C51, 10.C51, 20.C51, 22.C01, 22.C51, SCM.C51
Lecture: F11 (6-120)
______
Building on core material in 6.C01, provides an introduction to the use of machine learning to solve problems arising in the science and engineering of biology, chemistry, and materials. Equips students to design and implement machine learning approaches to challenges such as analysis of omics (genomics, transcriptomics, proteomics, etc.), microscopy, spectroscopy, or crystallography data and design of new molecules and materials such as drugs, catalysts, polymer, alloys, ceramics, and proteins. Students taking graduate version complete additional assignments. Students cannot receive credit without simultaneous completion of 6.C01.
R. Gomez-Bombarelli, C. Coley, E. Fraenkel, J. Davis
No required or recommended textbooks

20.C51[J] Machine Learning for Molecular Engineering
______

Graduate (Spring)
(Same subject as 3.C51[J], 10.C51[J])
(Subject meets with 3.C01[J], 7.C01, 7.C51, 10.C01[J], 20.C01[J])
Prereq: Calculus II (GIR) and 6.100A; Coreq: 6.C51
Units: 2-0-4
Credit cannot also be received for 1.C01, 1.C51, 2.C01, 2.C51, 3.C01, 7.C01, 7.C51, 10.C01, 20.C01, 22.C01, 22.C51, SCM.C51
Lecture: F11 (6-120)
______
Building on core material in 6.C51, provides an introduction to the use of machine learning to solve problems arising in the science and engineering of biology, chemistry, and materials. Equips students to design and implement machine learning approaches to challenges such as analysis of omics (genomics, transcriptomics, proteomics, etc.), microscopy, spectroscopy, or crystallography data and design of new molecules and materials such as drugs, catalysts, polymer, alloys, ceramics, and proteins. Students taking graduate version complete additional assignments. Students cannot receive credit without simultaneous completion of 6.C51.
R. Gomez-Bombarelli, C. Coley, E. Fraenkel, J. Davis
No required or recommended textbooks

20.EPE UPOP Engineering Practice Experience
______

Undergrad (Fall, Spring) Can be repeated for credit
Engineering School-Wide Elective Subject.
(Offered under: 1.EPE, 2.EPE, 3.EPE, 6.EPE, 8.EPE, 10.EPE, 15.EPE, 16.EPE, 20.EPE, 22.EPE)
Prereq: None
Units: 0-0-1 [P/D/F]
Lecture: TBA
______
Provides students with skills to prepare for and excel in the world of industry. Emphasizes practical application of career theory and professional development concepts. Introduces students to relevant and timely resources for career development, provides students with tools to embark on a successful internship search, and offers networking opportunities with employers and MIT alumni. Students work in groups, led by industry mentors, to improve their resumes and cover letters, interviewing skills, networking abilities, project management, and ability to give and receive feedback. Objective is for students to be able to adapt and contribute effectively to their future employment organizations. A total of two units of credit is awarded for completion of the fall and subsequent spring term offerings. Application required; consult UPOP website for more information.
Fall: D. Fordell, C. Greaney
Spring: D. Fordell, C. Greaney
No required or recommended textbooks

20.EPW UPOP Engineering Practice Workshop
______

Undergrad (Fall, IAP, Spring)
Engineering School-Wide Elective Subject.
(Offered under: 1.EPW, 2.EPW, 3.EPW, 6.EPW, 10.EPW, 16.EPW, 20.EPW, 22.EPW)
Prereq: 2.EPE
Units: 1-0-0 [P/D/F]
TBA.
______
Provides sophomores across all majors with opportunities to develop and practice communication, teamwork, and problem-solving skills to become successful professionals in the workplace, particularly in preparation for their summer industry internship. This immersive, multi-day Team Training Workshop (TTW) is comprised of experiential learning modules focused on expanding skills in areas that employers report being most valuable in the workplace. Modules are led by MIT faculty with the help of MIT alumni and other senior industry professionals. Skills applied through creative simulations, team problem-solving challenges, oral presentations, and networking sessions with prospective employers. Enrollment limited to those in the UPOP program.
IAP: C. Greaney
Spring: C. Greaney
No textbook information available (IAP 2024); No required or recommended textbooks (Spring 2024)

20.S900 Special Subject in Biological Engineering
______

Undergrad (Fall, Spring, Summer) Can be repeated for credit
Prereq: Permission of instructor
Units arranged [P/D/F]
TBA.
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Fall: D. Fares
Spring: D. Fares
Summer: D. Fares
No required or recommended textbooks

20.S901 Special Subject in Biological Engineering
______

Undergrad (Fall, Spring) Can be repeated for credit
Prereq: None
Units arranged [P/D/F]
TBA.
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Fall: D. Fares
Spring: D. Fares
No required or recommended textbooks

20.S940 Special Subject in Biological Engineering
______

Undergrad (Fall, Spring) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Fall: B. Bryson
Spring: Staff
No required or recommended textbooks

20.S947 Special Subject in Biological Engineering
______

Graduate (Fall, IAP, Spring, Summer) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Fall: Staff
IAP: Kastner, D.
Spring: Staff
Summer: Fare, D
No required or recommended textbooks

20.S948 Special Subject in Biological Engineering
______

Graduate (Fall, Spring) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Fall: E. Alm
Spring: Staff
No required or recommended textbooks

20.S949 Special Subject in Biological Engineering
______

Graduate (Fall, Spring) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Fall: Staff
Spring: Staff
No required or recommended textbooks

20.S952 Special Subject in Biological Engineering
______

Graduate (Fall, Spring) Can be repeated for credit
Prereq: Permission of instructor
Units arranged [P/D/F]
Lecture: R EVE (4-6 PM) (32-155)
______
Detailed discussion of selected topics of current interest. Classwork in various areas not covered by regular subjects.
Fall: D. Fares
Spring: D. Fares
No required or recommended textbooks

20.THG Graduate Thesis
______

Graduate (Fall, IAP, Spring, Summer) Can be repeated for credit
Prereq: Permission of instructor
Units arranged
TBA.
______
Program of research leading to the writing of an SM or PhD thesis; to be arranged by the student and the MIT faculty advisor.
Fall: D. Fares
IAP: D. Fares
Spring: D. Fares
Summer: D. Fares
No required or recommended textbooks

20.THU Undergraduate BE Thesis
______

Undergrad (Fall, IAP, Spring) Can be repeated for credit
Prereq: None
Units arranged
TBA.
______
Program of research leading to the writing of an SB thesis; to be arranged by the student under approved supervision.
Fall: C. Ricci-Tam
IAP: C. Ricci-Tam
Spring: C. Ricci-Tam
No required or recommended textbooks

20.UR Undergraduate Research Opportunities
______

Undergrad (Fall, IAP, Spring, Summer) Can be repeated for credit
Prereq: None
Units arranged [P/D/F]
TBA.
______
Laboratory research in the fields of bioengineering or environmental health. May be extended over multiple terms.
Fall: D. Fares
IAP: D. Fares
Spring: D. Fares
Summer: D. Fares
No required or recommended textbooks

20.URG Undergraduate Research Opportunities
______

Undergrad (Fall, IAP, Spring, Summer) Can be repeated for credit
Prereq: None
Units arranged
TBA.
______
Emphasizes direct and active involvement in laboratory research in bioengineering or environmental health. May be extended over multiple terms.
Fall: D. Fares
IAP: D. Fares
Spring: D. Fares
Summer: D. Fares
No required or recommended textbooks


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