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  • The Human Genome
Genomics, Computing, Economics, and Society, Fall 2005
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This course will focus on understanding aspects of modern technology displaying exponential ...

This course will focus on understanding aspects of modern technology displaying exponential growth curves and the impact on global quality of life through a weekly updated class project integrating knowledge and providing practical tools for political and business decision-making concerning new aspects of bioengineering, personalized medicine, genetically modified organisms, and stem cells. Interplays of economic, ethical, ecological, and biophysical modeling will be explored through multi-disciplinary teams of students, and individual brief reports.

Subject:
Economics
Material Type:
Activity/Lab
Full Course
Lecture Notes
Syllabus
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Church, George McDonald
Fundamentals of Biology, Fall 2011
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Fundamentals of Biology focuses on the basic principles of biochemistry, molecular biology, ...

Fundamentals of Biology focuses on the basic principles of biochemistry, molecular biology, genetics, and recombinant DNA. These principles are necessary to understanding the basic mechanisms of life and anchor the biological knowledge that is required to understand many of the challenges in everyday life, from human health and disease to loss of biodiversity and environmental quality.

Subject:
Biology
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Eric Lander
Graham Walker
Hazel Sive
Robert Weinberg
Sallie Chisholm Mischke Michelle
Tyler Jacks
Computational Functional Genomics, Spring 2005
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Study and discussion of computational approaches and algorithms for contemporary problems in ...

Study and discussion of computational approaches and algorithms for contemporary problems in functional genomics. Topics include DNA chip design, experimental data normalization, expression data representation standards, proteomics, gene clustering, self-organizing maps, Boolean networks, statistical graph models, Bayesian network models, continuous dynamic models, statistical metrics for model validation, model elaboration, experiment planning, and the computational complexity of functional genomics problems.

Subject:
Computer Science
Biology
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Gifford, David
Jaakkola, Tommi Sakari
Molecular Biology and Genetics in Modern Medicine, Fall 2007
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" This course provides a foundation for understanding the relationship between molecular ...

" This course provides a foundation for understanding the relationship between molecular biology, developmental biology, genetics, genomics, bioinformatics, and medicine. It develops explicit connections between basic research, medical understanding, and the perspective of patients. Principles of human genetics are reviewed. We translate clinical understanding into analysis at the level of the gene, chromosome and molecule; we cover the concepts and techniques of molecular biology and genomics, and the strategies and methods of genetic analysis, including an introduction to bioinformatics. Material in the course extends beyond basic principles to current research activity in human genetics."

Subject:
Biology
Genetics
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Giersch, Anne
Housman, David
HIV Problem Space
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This problem space enables investigators to explore data from a published study ...

This problem space enables investigators to explore data from a published study by Markham et al on HIV evolution within individual patients. The study involved 15 injection drug users in Baltimore, Maryland (USA) who became infected with HIV between 1989 and 1992. Patients came in at approximately six-month intervals ("visits") to have blood samples taken. From these samples, the researchers extracted and sequenced multiple copies of proviral DNA. Patients' CD4 counts were also measured at each visit to assess their level of immune function. In this problem space, you will have access to the following materials: * background information on HIV/AIDS, * the original Markham et al. reference and other primary literature, * viral sequences from each visit of each patient, * patients' CD4 counts at each visit, * phylogenetic trees of the virus sequences from each patient, * a phylogenetic tree of each patient's starting consensus viral sequence, * a published activity using this data from the book Microbes Count!, * and additional materials prepared by other users of the problem space. You can use this data to explore a number of different questions. Here are a few general questions to get you started: * Does the virus evolve the same way in different patients? * Are there any specific mutations that cause rapid immune decline? * What types of natural selection might be influencing HIV evolution? * Is HIV being transmitted between patients after initial infection?

Subject:
Biology
Material Type:
Activity/Lab
Data Set
Diagram/Illustration
Lesson Plan
Teaching/Learning Strategy
Provider:
BioQUEST Curriculum Consortium
Provider Set:
Bedrock
Author:
Anton Weisstein
Biomedical Information Technology, Fall 2008
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" This course teaches the design of contemporary information systems for biological ...

" This course teaches the design of contemporary information systems for biological and medical data. Examples are chosen from biology and medicine to illustrate complete life cycle information systems, beginning with data acquisition, following to data storage and finally to retrieval and analysis. Design of appropriate databases, client-server strategies, data interchange protocols, and computational modeling architectures. Students are expected to have some familiarity with scientific application software and a basic understanding of at least one contemporary programming language (e.g. C, C++, Java, Lisp, Perl, Python). A major term project is required of all students. This subject is open to motivated seniors having a strong interest in biomedical engineering and information system design with the ability to carry out a significant independent project. This course was offered as part of the Singapore-MIT Alliance (SMA) program as course number SMA 5304."

Subject:
Biology
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Bhowmick, Sourav Saha
Dewey Jr, C. Forbes
Yu, Hanry
Elements of Mechanical Design, Spring 2009
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" This is an advanced course on modeling, design, integration and best ...

" This is an advanced course on modeling, design, integration and best practices for use of machine elements such as bearings, springs, gears, cams and mechanisms. Modeling and analysis of these elements is based upon extensive application of physics, mathematics and core mechanical engineering principles (solid mechanics, fluid mechanics, manufacturing, estimation, computer simulation, etc.). These principles are reinforced via (1) hands-on laboratory experiences wherein students conduct experiments and disassemble machines and (2) a substantial design project wherein students model, design, fabricate and characterize a mechanical system that is relevant to a real world application. Students master the materials via problems sets that are directly related to, and coordinated with, the deliverables of their project. Student assessment is based upon mastery of the course materials and the student's ability to synthesize, model and fabricate a mechanical device subject to engineering constraints (e.g. cost and time/schedule)."

Subject:
Engineering
Manufacturing
Genetics
Chemistry
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Culpepper, Martin
Quantitative Genomics, Fall 2005
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Subject assesses the relationships between sequence, structure, and function in complex biological ...

Subject assesses the relationships between sequence, structure, and function in complex biological networks as well as progress in realistic modeling of quantitative, comprehensive functional-genomics analyses. Topics include: algorithmic, statistical, database, and simulation approaches; and practical applications to biotechnology, drug discovery, and genetic engineering. Future opportunities and current limitations critically assessed. Problem sets and project emphasize creative, hands-on analyses using these concepts.

Subject:
Biology
Genetics
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Berwick, Robert
Kho, Alvin
Kohane, Isaac
Mirny, Leonid
The Fountain of Life: From Dolly to Customized Embryonic Stem Cells, Fall 2007
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" During development, the genetic content of each cell remains, with a ...

" During development, the genetic content of each cell remains, with a few exceptions, identical to that of the zygote. Most differentiated cells therefore retain all of the genetic information necessary to generate an entire organism. It was through pioneering technology of somatic cell nuclear transfer (SCNT) that this concept was experimentally proven. Only 10 years ago the sheep Dolly was the first mammal to be cloned from an adult organism, demonstrating that the differentiated state of a mammalian cell can be fully reversible to a pluripotent embryonic state. A key conclusion from these experiments was that the difference between pluripotent cells such as embryonic stem (ES) cells and unipotent differentiated cells is solely a consequence of reversible changes. These changes, which have proved to involve reversible alterations to both DNA and to proteins that bind DNA, are known as epigenetic, to distinguish them from genetic alterations to DNA sequence. In this course we will explore such epigenetic changes and study different approaches that can return a differentiated cell to an embryonic state in a process referred to as epigenetic reprogramming, which will ultimately allow generation of patient-specific stem cells and application to regenerative therapy. This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching."

Subject:
Biology
Genetics
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Meissner, Alexander
Foundations of Computational and Systems Biology, Spring 2014
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This course is an introduction to computational biology emphasizing the fundamentals of ...

This course is 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 systems. Topics covered in the course include principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction and network modeling, as well as currently emerging research areas.

Subject:
Biology
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Burge, Christopher
Fraenkel, Ernest
Gifford, David
Genetics
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Genetics is the branch of biology that studies the means by which ...

Genetics is the branch of biology that studies the means by which traits are passed on from one generation to the next and the causes of similarities and differences between related individuals. In this course, the student will take a close look at chromosomes, DNA, and genes. The student will learn how hereditary information is transferred, how it can change, how it can lead to human disease and be tested to indicate disease, and much more. Upon successful completion of this course, students will be able to: give a brief synopsis of the history of genetics by explaining the fundamental genetic concepts covered in this course as they were discovered through time; identify the links between Mendel's discoveries (often represented by Punnett squares) with mitosis and meiosis, dominance, penetrance, and linkage; recognize the role of simple probability in genetic inheritance; apply advanced genetic concepts, including genetic mapping and transposons, to practical applications, including pedigree analysis and corn kernel color; identify the cause behind several genetic diseases currently prevalent in society (such as color blindness and hemophilia) and recognize the importance of genetic illness throughout history; compare and contrast advanced concepts of chromosomal, bacterial, human, and population genetics; recognize the similarities and differences between nuclear, chloroplast, and mitochondrial DNA; describe the fundamentals of population genetics, calculate gene frequencies in a give scenario, predict future gene frequencies over future generations, and define the role of evolution in gene frequency shift over time; recall, analyze, synthesize, and build on the foundational material to then learn the cutting-edge technological advances in genetics, including genomics, population and evolutionary genetics, and QTL mapping. (Biology 305)

Subject:
Biology
Genetics
Material Type:
Full Course
Provider:
The Saylor Foundation
Introduction to Biology, Fall 2004
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The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover ...

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.

Subject:
Biology
Material Type:
Full Course
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
DNA Build
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Students reinforce their knowledge that DNA is the genetic material for all ...

Students reinforce their knowledge that DNA is the genetic material for all living things by modeling it using toothpicks and gumdrops that represent the four biochemicals (adenine, thiamine, guanine, and cytosine) that pair with each other in a specific pattern, making a double helix. They investigate specific DNA sequences that code for certain physical characteristics such as eye and hair color. Student teams trade DNA "strands" and de-code the genetic sequences to determine the physical characteristics (phenotype) displayed by the strands (genotype) from other groups. Students extend their knowledge to learn about DNA fingerprinting and recognizing DNA alterations that may result in genetic disorders.

Subject:
Engineering
Genetics
Material Type:
Activity/Lab
Provider:
TeachEngineering
Provider Set:
TeachEngineering NGSS Aligned Resources
Author:
Denise W. Carlson
Integrated Teaching and Learning Program,
Janet Yowell
Malinda Schaefer Zarske
Megan Schroeder
West Nile Virus Problem Space
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As an emerging disease in the public eye, WNV continues to generate ...

As an emerging disease in the public eye, WNV continues to generate scientific interest as well. Researchers are exploring questions about its origin, evolution, transmission by multiple vectors and host tissues, replication in multiple hosts, viremic period, viral loads, seroconversion and antibody production, detection, vaccine potential, etc. Central to these investigations are the use of molecular data including nucleic acid sequences and the use of bioinformatics. There are multiple ways this data can be used in courses. Other instructors have used West Nile Virus to: * Help students become familiar with Biology Workbench, including the use of Nucleic Acid Tools such as ClustalW and SixFrame as well as Alignment Tools such as DrawGram, BoxShade, and MView, etc. * Locate and download sequence data on line using Biology WorkBench, NCBI, and more. Edit the sequences for comparing sequence data obtained from multiple sources and/or for making shorter labels. * Learn more about the West Nile Virus, including structure of the virus, transmission cycle, replication cycle, viremia, blood titers and the disease in reservoir and incidental hosts, vectors for virus, natural history in the US and around the world, and testing for WNV.

Subject:
Biology
Material Type:
Activity/Lab
Diagram/Illustration
Lecture Notes
Lesson Plan
Teaching/Learning Strategy
Provider:
BioQUEST Curriculum Consortium
Provider Set:
Bedrock
Author:
Ethel D. Stanley
Who Robbed the Bank?
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Students use DNA profiling to determine who robbed a bank. After they ...

Students use DNA profiling to determine who robbed a bank. After they learn how the FBI's Combined DNA Index System (CODIS) is used to match crime scene DNA with tissue sample DNA, students use CODIS principles and sample DNA fragments to determine which of three suspects matches evidence obtain at a crime location. They communicate their results as if they were biomedical engineers reporting to a police crime scene investigation.

Subject:
Engineering
Genetics
Material Type:
Activity/Lab
Provider:
TeachEngineering
Provider Set:
TeachEngineering NGSS Aligned Resources
Author:
Denise W. Carlson
Frank Burkholder
Integrated Teaching and Learning Program,
Malinda Schaefer Zarske
Freshman Seminar: Structural Basis of Genetic Material: Nucleic Acids, Fall 2005
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Since the discovery of the structure of the DNA double helix in ...

Since the discovery of the structure of the DNA double helix in 1953 by Watson and Crick, the information on detailed molecular structures of DNA and RNA, namely, the foundation of genetic material, has expanded rapidly. This discovery is the beginning of the "Big Bang" of molecular biology and biotechnology. In this seminar, students discuss, from a historical perspective and current developments, the importance of pursuing the detailed structural basis of genetic materials.

Subject:
Biology
Genetics
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Zhang, Shuguang
Systems Biology, Fall 2004
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Introduction to quantitative methods and modeling techniques to address key questions in ...

Introduction to quantitative methods and modeling techniques to address key questions in modern biology. Overview of quantitative modeling techniques in evolutionary biology, molecular biology and genetics, cell biology and developmental biology. Description of key experiments that validate models. Specific topics include: Evolutionary biology: theoretical models for evolution, evolution in test tube, evolution experiments with viruses and bacteria, complexity and evolution; Molecular biology and genetics: protein design, bioinformatics and genomics, constructing and modeling of genetic networks, control theory and genetic networks; Cell biology: forces and motion, cell motility, signal transduction pathways, chemotaxis and pheromone response; Development biology: pattern formation, self-organization, and models of Drosophila development.

Subject:
Biology
Physics
Psychology
Material Type:
Full Course
Textbook
Provider:
M.I.T.
Provider Set:
M.I.T. OpenCourseWare
Author:
Oudenaarden, Alexander van
DNA: The Human Body Recipe
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As a class, students work through an example showing how DNA provides ...

As a class, students work through an example showing how DNA provides the "recipe" for making our body proteins. They see how the pattern of nucleotide bases (adenine, thymine, guanine, cytosine) forms the double helix ladder shape of DNA, and serves as the code for the steps required to make genes. They also learn some ways that engineers and scientists are applying their understanding of DNA in our world.

Subject:
Engineering
Genetics
Material Type:
Activity/Lab
Lesson Plan
Teaching/Learning Strategy
Provider:
TeachEngineering
Provider Set:
TeachEngineering NGSS Aligned Resources
Author:
Denise W. Carlson
Frank Burkholder
Integrated Teaching and Learning Program,
Jessica Todd
Malinda Schaefer Zarske
Understanding Evolution
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Your one-stop source for learning and teaching about evolution. This website includes ...

Your one-stop source for learning and teaching about evolution. This website includes information about how evolution works, how evolution impacts our lives, evidence for evolution, and the history of evolutionary thought. There's also an entire Understanding Evolution for Teachers sub-site, which includes lesson plans, a conceptual framework, and discussion of classroom situations that may arise when teaching evolution.

Subject:
Biology
Geology
Material Type:
Activity/Lab
Lesson Plan
Teaching/Learning Strategy
Provider:
University of California Museum of Paleontology and National Center for Science Education
Macro-Microarray
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In this activity, learners explore the "nuts and bolts" of gene chips. ...

In this activity, learners explore the "nuts and bolts" of gene chips. Learners construct a simple model of a DNA microarray (also known as gene chips) and learn how microarrays can be used to identify and treat disease--including cancer. This resource includes references and an explanation of microarrays.

Subject:
Genetics
Material Type:
Activity/Lab
Provider:
Exploratorium
Author:
Julie Yu
National Science Foundation
The Exploratorium