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7.01SC Fundamentals of Biology (MIT) 7.01SC Fundamentals of Biology (MIT)

Description

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. 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.

Subjects

amino acids | amino acids | carboxyl group | carboxyl group | amino group | amino group | side chains | side chains | polar | polar | hydrophobic | hydrophobic | primary structure | primary structure | secondary structure | secondary structure | tertiary structure | tertiary structure | quaternary structure | quaternary structure | x-ray crystallography | x-ray crystallography | alpha helix | alpha helix | beta sheet | beta sheet | ionic bond | ionic bond | non-polar bond | non-polar bond | van der Waals interactions | van der Waals interactions | proton gradient | proton gradient | cyclic photophosphorylation | cyclic photophosphorylation | sunlight | sunlight | ATP | ATP | chlorophyll | chlorophyll | chlorophyll a | chlorophyll a | electrons | electrons | hydrogen sulfide | hydrogen sulfide | biosynthesis | biosynthesis | non-cyclic photophosphorylation | non-cyclic photophosphorylation | photosystem II | photosystem II | photosystem I | photosystem I | cyanobacteria | cyanobacteria | chloroplast | chloroplast | stroma | stroma | thylakoid membrane | thylakoid membrane | Genetics | Genetics | Mendel | Mendel | Mendel's Laws | Mendel's Laws | cloning | cloning | restriction enzymes | restriction enzymes | vector | vector | insert DNA | insert DNA | ligase | ligase | library | library | E.Coli | E.Coli | phosphatase | phosphatase | yeast | yeast | transformation | transformation | ARG1 gene | ARG1 gene | ARG1 mutant yeast | ARG1 mutant yeast | yeast wild-type | yeast wild-type | cloning by complementation | cloning by complementation | Human Beta Globin gene | Human Beta Globin gene | protein tetramer | protein tetramer | vectors | vectors | antibodies | antibodies | human promoter | human promoter | splicing | splicing | mRNA | mRNA | cDNA | cDNA | reverse transcriptase | reverse transcriptase | plasmid | plasmid | electrophoresis | electrophoresis | DNA sequencing | DNA sequencing | primer | primer | template | template | capillary tube | capillary tube | laser detector | laser detector | human genome project | human genome project | recombinant DNA | recombinant DNA | clone | clone | primer walking | primer walking | subcloning | subcloning | computer assembly | computer assembly | shotgun sequencing | shotgun sequencing | open reading frame | open reading frame | databases | databases | polymerase chain reaction (PCR) | polymerase chain reaction (PCR) | polymerase | polymerase | nucleotides | nucleotides | Thermus aquaticus | Thermus aquaticus | Taq polymerase | Taq polymerase | thermocycler | thermocycler | resequencing | resequencing | in vitro fertilization | in vitro fertilization | pre-implantation diagnostics | pre-implantation diagnostics | forensics | forensics | genetic engineering | genetic engineering | DNA sequences | DNA sequences | therapeutic proteins | therapeutic proteins | E. coli | E. coli | disease-causing mutations | disease-causing mutations | cleavage of DNA | cleavage of DNA | bacterial transformation | bacterial transformation | recombinant DNA revolution | recombinant DNA revolution | biotechnology industry | biotechnology industry | Robert Swanson | Robert Swanson | toxin gene | toxin gene | pathogenic bacterium | pathogenic bacterium | biomedical research | biomedical research | S. Pyogenes | S. Pyogenes | origin of replication | origin of replication

License

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7.347 Epigenetic Regulation of Stem Cells (MIT) 7.347 Epigenetic Regulation of Stem Cells (MIT)

Description

During development a single totipotent cell gives rise to the vast array of cell types present in the adult human body, yet each cell has essentially the same DNA sequence. As cells differentiate, distinct sets of genes must be coordinately activated and repressed, ultimately leading to a cell-type specific pattern of gene expression and a particular cell fate. In eukaryotic organisms, DNA is packaged in a complex protein super structure known as chromatin. Modification and reorganization of chromatin play a critical role in coordinating the cell-type specific gene expression programs that are required as a cell transitions from a pluripotent stem cell to a fully differentiated cell type. Epigenetics refers to such heritable changes that occur in chromatin without altering the primary DNA During development a single totipotent cell gives rise to the vast array of cell types present in the adult human body, yet each cell has essentially the same DNA sequence. As cells differentiate, distinct sets of genes must be coordinately activated and repressed, ultimately leading to a cell-type specific pattern of gene expression and a particular cell fate. In eukaryotic organisms, DNA is packaged in a complex protein super structure known as chromatin. Modification and reorganization of chromatin play a critical role in coordinating the cell-type specific gene expression programs that are required as a cell transitions from a pluripotent stem cell to a fully differentiated cell type. Epigenetics refers to such heritable changes that occur in chromatin without altering the primary DNA

Subjects

Stem cells | Stem cells | induced pluripotency | induced pluripotency | Epigenetics | Epigenetics | chromatin | chromatin | histone | histone | epigenome | epigenome | genome-wide analyses | genome-wide analyses | high-throughput sequencing technologies | high-throughput sequencing technologies | Chromatin Immunoprecipitation sequencing | Chromatin Immunoprecipitation sequencing | ncRNAs | ncRNAs | epigenetic regulation | epigenetic regulation | DNA methylation | DNA methylation | post-translational modification of histones | post-translational modification of histones | roles of chromatin-assembly modifying complexes | roles of chromatin-assembly modifying complexes | non-coding RNAs | non-coding RNAs | nuclear organization | nuclear organization | developmental fate | developmental fate | stem cell therapy | stem cell therapy

License

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7.342 Personal Genomics and Medicine: What's in Your Genome? (MIT) 7.342 Personal Genomics and Medicine: What's in Your Genome? (MIT)

Description

Human genome sequencing has revolutionized our understanding of disease susceptibility, drug metabolism and human ancestry. This course will explore how these advances have been made possible by revolutionary new sequencing methodologies that have decreased costs and increased throughput of genome analysis, making it possible to examine genetic correlates for a variety of biological processes and disorders. The course will combine discussions of primary scientific research papers with hands-on data analysis and small group presentations. 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 Human genome sequencing has revolutionized our understanding of disease susceptibility, drug metabolism and human ancestry. This course will explore how these advances have been made possible by revolutionary new sequencing methodologies that have decreased costs and increased throughput of genome analysis, making it possible to examine genetic correlates for a variety of biological processes and disorders. The course will combine discussions of primary scientific research papers with hands-on data analysis and small group presentations. 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

Subjects

genome sequencing | genome sequencing | genome analysis | genome analysis | disease susceptibility | disease susceptibility | drug metabolism | drug metabolism | human ancestry | human ancestry | mitochondrial DNA | mitochondrial DNA | tyrosine kinase inhibitors | tyrosine kinase inhibitors | BCR-ABL gene fusion | BCR-ABL gene fusion | PCSK9 inhibitors | PCSK9 inhibitors | hypercholesterolemia | hypercholesterolemia | genetic testing | genetic testing | next generation sequencing | next generation sequencing | Single-nucleotide polymorphisms (SNPs) | Single-nucleotide polymorphisms (SNPs) | copy number variations (CNVs) | copy number variations (CNVs) | genome-wide association studies (GWAS) | genome-wide association studies (GWAS) | Chronic myelogenous leukemia (CML) | Chronic myelogenous leukemia (CML) | mosaics | mosaics | chimeras | chimeras | bioinformatics | bioinformatics

License

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7.01SC Fundamentals of Biology (MIT)

Description

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.

Subjects

amino acids | carboxyl group | amino group | side chains | polar | hydrophobic | primary structure | secondary structure | tertiary structure | quaternary structure | x-ray crystallography | alpha helix | beta sheet | ionic bond | non-polar bond | van der Waals interactions | proton gradient | cyclic photophosphorylation | sunlight | ATP | chlorophyll | chlorophyll a | electrons | hydrogen sulfide | biosynthesis | non-cyclic photophosphorylation | photosystem II | photosystem I | cyanobacteria | chloroplast | stroma | thylakoid membrane | Genetics | Mendel | Mendel's Laws | cloning | restriction enzymes | vector | insert DNA | ligase | library | E.Coli | phosphatase | yeast | transformation | ARG1 gene | ARG1 mutant yeast | yeast wild-type | cloning by complementation | Human Beta Globin gene | protein tetramer | vectors | antibodies | human promoter | splicing | mRNA | cDNA | reverse transcriptase | plasmid | electrophoresis | DNA sequencing | primer | template | capillary tube | laser detector | human genome project | recombinant DNA | clone | primer walking | subcloning | computer assembly | shotgun sequencing | open reading frame | databases | polymerase chain reaction (PCR) | polymerase | nucleotides | Thermus aquaticus | Taq polymerase | thermocycler | resequencing | in vitro fertilization | pre-implantation diagnostics | forensics | genetic engineering | DNA sequences | therapeutic proteins | E. coli | disease-causing mutations | cleavage of DNA | bacterial transformation | recombinant DNA revolution | biotechnology industry | Robert Swanson | toxin gene | pathogenic bacterium | biomedical research | S. Pyogenes | origin of replication

License

Content within individual OCW courses is (c) by the individual authors unless otherwise noted. MIT OpenCourseWare materials are licensed by the Massachusetts Institute of Technology under a Creative Commons License (Attribution-NonCommercial-ShareAlike). For further information see https://ocw.mit.edu/terms/index.htm

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Oxford at Said: A human genome in minutes and what it will mean to you

Description

Oxford Nanopore is a British company, spun out of the University of Oxford in 2005 and founded on the science of Prof Hagan Bayley. It is developing new technology that has the potential to improve greatly the speed and cost of DNA sequencing. Wales; http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

Subjects

genome | genomics | hagan bailey | DNA sequencing | Oxford Nanopore | genome | genomics | hagan bailey | DNA sequencing | Oxford Nanopore

License

http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

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8.592 Statistical Physics in Biology (MIT) 8.592 Statistical Physics in Biology (MIT)

Description

Statistical Physics in Biology is a survey of problems at the interface of statistical physics and modern biology. Topics include: bioinformatic methods for extracting information content of DNA; gene finding, sequence comparison, and phylogenetic trees; physical interactions responsible for structure of biopolymers; DNA double helix, secondary structure of RNA, and elements of protein folding; Considerations of force, motion, and packaging; protein motors, membranes. We also look at collective behavior of biological elements, cellular networks, neural networks, and evolution.Technical RequirementsAny number of biological sequence comparison software tools can be used to import the .fna files found on this course site. Statistical Physics in Biology is a survey of problems at the interface of statistical physics and modern biology. Topics include: bioinformatic methods for extracting information content of DNA; gene finding, sequence comparison, and phylogenetic trees; physical interactions responsible for structure of biopolymers; DNA double helix, secondary structure of RNA, and elements of protein folding; Considerations of force, motion, and packaging; protein motors, membranes. We also look at collective behavior of biological elements, cellular networks, neural networks, and evolution.Technical RequirementsAny number of biological sequence comparison software tools can be used to import the .fna files found on this course site.

Subjects

Bioinformatics | Bioinformatics | DNA | DNA | gene finding | gene finding | sequence comparison | sequence comparison | phylogenetic trees | phylogenetic trees | biopolymers | biopolymers | DNA double helix | DNA double helix | secondary structure of RNA | secondary structure of RNA | protein folding | protein folding | protein motors | membranes | protein motors | membranes | cellular networks | cellular networks | neural networks | neural networks | evolution | evolution | statistical physics | statistical physics | molecular biology | molecular biology | deoxyribonucleic acid | deoxyribonucleic acid | genes | genes | genetics | genetics | gene sequencing | gene sequencing | phylogenetics | phylogenetics | double helix | double helix | RNA | RNA | ribonucleic acid | ribonucleic acid | force | force | motion | motion | packaging | packaging | protein motors | protein motors | membranes | membranes | biochemistry | biochemistry | genome | genome | optimization | optimization | partitioning | partitioning | pattern recognition | pattern recognition | collective behavior | collective behavior

License

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20.020 Introduction to Biological Engineering Design (MIT) 20.020 Introduction to Biological Engineering Design (MIT)

Description

Includes audio/video content: AV special element video. This class is a 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 will introduce (1) components and control of prokaryotic and eukaryotic behavior, (2) DNA synthesis, standards, and abstraction in biological engineering, and (3) issues of human practice, including biological safety; security; ownership, sharing, and innovation; and ethics. Enrollment preference is given to freshmen. This subject was originally developed and first taught in Spring 2008 by Drew Endy and Natalie Kuldell. Many of Drew's Includes audio/video content: AV special element video. This class is a 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 will introduce (1) components and control of prokaryotic and eukaryotic behavior, (2) DNA synthesis, standards, and abstraction in biological engineering, and (3) issues of human practice, including biological safety; security; ownership, sharing, and innovation; and ethics. Enrollment preference is given to freshmen. This subject was originally developed and first taught in Spring 2008 by Drew Endy and Natalie Kuldell. Many of Drew's

Subjects

biology | biology | chemistry | chemistry | synthetic biology | synthetic biology | project | project | biotech | biotech | genetic engineering | genetic engineering | GMO | GMO | ethics | ethics | biomedical ethics | biomedical ethics | genetics | genetics | recombinant DNA | recombinant DNA | DNA | DNA | gene sequencing | gene sequencing | gene synthesis | gene synthesis | biohacking | biohacking | computational biology | computational biology | iGEM | iGEM | BioBrick | BioBrick | systems biology | systems biology

License

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2.72 Elements of Mechanical Design (MIT) 2.72 Elements of Mechanical Design (MIT)

Description

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 deliv 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 deliv

Subjects

biology | biology | chemistry | chemistry | synthetic biology | synthetic biology | project | project | biotech | biotech | genetic engineering | genetic engineering | GMO | GMO | ethics | ethics | biomedical ethics | biomedical ethics | genetics | genetics | recombinant DNA | recombinant DNA | DNA | DNA | gene sequencing | gene sequencing | gene synthesis | gene synthesis | biohacking | biohacking | computational biology | computational biology | iGEM | iGEM | BioBrick | BioBrick | systems biology | systems biology | machine design | machine design | hardware | hardware | machine element | machine element | design process | design process | design layout | design layout | prototype | prototype | mechanism | mechanism | engineering | engineering | fabrication | fabrication | lathe | lathe | precision engineering | precision engineering | group project | group project | project management | project management | CAD | CAD | fatigue | fatigue | Gantt chart | Gantt chart

License

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7.349 Stem Cells: A Cure or Disease? (MIT) 7.349 Stem Cells: A Cure or Disease? (MIT)

Description

Have you ever considered going to a pharmacy to order some new cardiomyocytes (heart muscle cells) for your ailing heart? It might sound crazy, but recent developments in stem cell science have made this concept not so futuristic. In this course, we will explore the underlying biology behind the idea of using stem cells to treat disease, specifically analyzing the mechanisms that enable a single genome to encode multiple cell states ranging from neurons to fibroblasts to T cells. Overall, we hope to provide a comprehensive overview of this exciting new field of research and its clinical relevance. 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 literat Have you ever considered going to a pharmacy to order some new cardiomyocytes (heart muscle cells) for your ailing heart? It might sound crazy, but recent developments in stem cell science have made this concept not so futuristic. In this course, we will explore the underlying biology behind the idea of using stem cells to treat disease, specifically analyzing the mechanisms that enable a single genome to encode multiple cell states ranging from neurons to fibroblasts to T cells. Overall, we hope to provide a comprehensive overview of this exciting new field of research and its clinical relevance. 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 literat

Subjects

stem cells | stem cells | stem cell therapy | stem cell therapy | cellular reprogramming | cellular reprogramming | transdifferentiation | transdifferentiation | pluripotency | pluripotency | epigenetics | epigenetics | genome-wide sequencing | genome-wide sequencing | transcription-mediated reprogramming | transcription-mediated reprogramming | embryonic stem cell technology | embryonic stem cell technology | transcription factors | transcription factors | chromatin structure | chromatin structure | H3K4me3 | H3K4me3 | H3K27me3 | H3K27me3 | histone deacetylase 1 | histone deacetylase 1 | RNAi screens | RNAi screens | Oct4 | Oct4 | cloning | cloning | Dolly | Dolly | in vitro differentiation | in vitro differentiation | regenerative medicine | regenerative medicine

License

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7.89J Topics in Computational and Systems Biology (MIT) 7.89J Topics in Computational and Systems Biology (MIT)

Description

This is a seminar based on research literature. Papers covered are selected to illustrate important problems and approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments. The MIT Initiative in Computational and Systems Biology (CSBi) is a campus-wide research and education program that links biology, engineering, and computer science in a multidisciplinary approach to the systematic analysis and modeling of complex biological phenomena. This course is one of a series of core subjects offered through the CSB Ph.D. program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology. This is a seminar based on research literature. Papers covered are selected to illustrate important problems and approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments. The MIT Initiative in Computational and Systems Biology (CSBi) is a campus-wide research and education program that links biology, engineering, and computer science in a multidisciplinary approach to the systematic analysis and modeling of complex biological phenomena. This course is one of a series of core subjects offered through the CSB Ph.D. program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology.

Subjects

Computational Biology | Computational Biology | Systems Biology | Systems Biology | Genomics | Genomics | Protein Function | Protein Function | Nucleic Acid Binding Factors | Nucleic Acid Binding Factors | microarray analysis | microarray analysis | genome-wide mapping | genome-wide mapping | gene expression | gene expression | evolutionary dynamics | evolutionary dynamics | sequencing | sequencing | translation | translation | network motifs | network motifs | pathway modeling | pathway modeling | synthetic biology | synthetic biology | metagenomics | metagenomics | signal transduction | signal transduction

License

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7.13 Experimental Microbial Genetics (MIT) 7.13 Experimental Microbial Genetics (MIT)

Description

In this class, students engage in independent research projects to probe various aspects of the physiology of the bacterium Pseudomonas aeruginosa PA14, an opportunistic pathogen isolated from the lungs of cystic fibrosis patients. Students use molecular genetics to examine survival in stationary phase, antibiotic resistance, phase variation, toxin production, and secondary metabolite production. Projects aim to discover the molecular basis for these processes using both classical and cutting-edge techniques. These include plasmid manipulation, genetic complementation, mutagenesis, PCR, DNA sequencing, enzyme assays, and gene expression studies. Instruction and practice in written and oral communication are also emphasized. WARNING NOTICE The experiments described in these materials In this class, students engage in independent research projects to probe various aspects of the physiology of the bacterium Pseudomonas aeruginosa PA14, an opportunistic pathogen isolated from the lungs of cystic fibrosis patients. Students use molecular genetics to examine survival in stationary phase, antibiotic resistance, phase variation, toxin production, and secondary metabolite production. Projects aim to discover the molecular basis for these processes using both classical and cutting-edge techniques. These include plasmid manipulation, genetic complementation, mutagenesis, PCR, DNA sequencing, enzyme assays, and gene expression studies. Instruction and practice in written and oral communication are also emphasized. WARNING NOTICE The experiments described in these materials

Subjects

microbiology | microbiology | genetics | genetics | pseudomonas | pseudomonas | bacteria | bacteria | genes | genes | pathogen | pathogen | mutagenesis | mutagenesis | PCR | PCR | DNA sequencing | DNA sequencing | enzyme assays | enzyme assays | gene expression | gene expression | molecular genetics | molecular genetics | plasmid manipulation | plasmid manipulation | genetic complementation | genetic complementation | laboratory | laboratory | protocol | protocol | vector | vector | mutant | mutant | cystic fibrosis | cystic fibrosis

License

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7.13 Experimental Microbial Genetics (MIT) 7.13 Experimental Microbial Genetics (MIT)

Description

Also referred to as the Microbial Genetics Project Lab, this is a hands-on research course designed to introduce the student to the strategies and challenges associated with microbiology research. Students take on independent and original research projects that are designed to be instructive with the goal of advancing a specific field of research in microbiology. Also referred to as the Microbial Genetics Project Lab, this is a hands-on research course designed to introduce the student to the strategies and challenges associated with microbiology research. Students take on independent and original research projects that are designed to be instructive with the goal of advancing a specific field of research in microbiology.

Subjects

microbiology | microbiology | genetics | genetics | rhodococcus | rhodococcus | bacteria | bacteria | genes | genes | plasmid manipulation | plasmid manipulation | mutagenesis | mutagenesis | PCR | PCR | DNA sequencing | DNA sequencing | enzyme assays | enzyme assays | gene expression | gene expression | molecular genetics | molecular genetics | Gram-positive | Gram-positive | gram-negative | gram-negative | bioconversion processes | bioconversion processes | synthesis | synthesis | precursors | precursors | metabolites | metabolites | genetic complementation | genetic complementation | laboratory | laboratory | lab | lab

License

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9.12 Experimental Molecular Neurobiology (MIT) 9.12 Experimental Molecular Neurobiology (MIT)

Description

Designed for students without previous experience in techniques of cellular and molecular biology, this class teaches basic experimental techniques in cellular and molecular neurobiology. Experimental approaches covered include tissue culture of neuronal cell lines, dissection and culture of brain cells, DNA manipulation, synaptic protein analysis, immunocytochemistry, and fluorescent microscopy. Designed for students without previous experience in techniques of cellular and molecular biology, this class teaches basic experimental techniques in cellular and molecular neurobiology. Experimental approaches covered include tissue culture of neuronal cell lines, dissection and culture of brain cells, DNA manipulation, synaptic protein analysis, immunocytochemistry, and fluorescent microscopy.

Subjects

molecular biology | molecular biology | GFP | GFP | RFP | RFP | neurons | neurons | experimental techniques | experimental techniques | genetic sequencing | genetic sequencing | vector design | vector design | plasmid | plasmid | polymerase chain reaction | polymerase chain reaction | transfection | transfection | cell culture | cell culture | gel electrophoresis | gel electrophoresis | Western blotting | Western blotting | Northern blotting | Northern blotting | Southern blotting | Southern blotting | perfusion | perfusion | lab animals | lab animals | brain dissection | brain dissection

License

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16.72 Air Traffic Control (MIT) 16.72 Air Traffic Control (MIT)

Description

This course introduces the various aspects of present and future Air Traffic Control systems. Among the topics in the present system that we will discuss are the systems-analysis approach to problems of capacity and safety, surveillance, including the National Airspace System and Automated Terminal Radar Systems, navigation subsystem technology, aircraft guidance and control, communications, collision avoidance systems and sequencing and spacing in terminal areas. The class will then talk about future directions and development and have a critical discussion of past proposals and of probable future problem areas. This course introduces the various aspects of present and future Air Traffic Control systems. Among the topics in the present system that we will discuss are the systems-analysis approach to problems of capacity and safety, surveillance, including the National Airspace System and Automated Terminal Radar Systems, navigation subsystem technology, aircraft guidance and control, communications, collision avoidance systems and sequencing and spacing in terminal areas. The class will then talk about future directions and development and have a critical discussion of past proposals and of probable future problem areas.

Subjects

air traffic control | air traffic control | air traffic control systems | air traffic control systems | systems-analysis | systems-analysis | capacity | capacity | safety | safety | surveillance | surveillance | NAS | NAS | ARTS | ARTS | navigation subsystem technology | navigation subsystem technology | aircraft guidance and control | aircraft guidance and control | communications | communications | collision avoidance systems | collision avoidance systems | sequencing and spacing | sequencing and spacing | terminal areas | terminal areas | NGATS | NGATS

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18.417 Introduction to Computational Molecular Biology (MIT) 18.417 Introduction to Computational Molecular Biology (MIT)

Description

This course introduces the basic computational methods used to understand the cell on a molecular level. It covers subjects such as the sequence alignment algorithms: dynamic programming, hashing, suffix trees, and Gibbs sampling. Furthermore, it focuses on computational approaches to: genetic and physical mapping; genome sequencing, assembly, and annotation; RNA expression and secondary structure; protein structure and folding; and molecular interactions and dynamics. This course introduces the basic computational methods used to understand the cell on a molecular level. It covers subjects such as the sequence alignment algorithms: dynamic programming, hashing, suffix trees, and Gibbs sampling. Furthermore, it focuses on computational approaches to: genetic and physical mapping; genome sequencing, assembly, and annotation; RNA expression and secondary structure; protein structure and folding; and molecular interactions and dynamics.

Subjects

basic computational methods cell on a molecular level | basic computational methods cell on a molecular level | sequence alignment algorithms | sequence alignment algorithms | dynamic programming | dynamic programming | hashing | hashing | suffix trees | suffix trees | Gibbs sampling | Gibbs sampling | genetic and physical mapping | genetic and physical mapping | genome sequencing | genome sequencing | assembly | assembly | and annotation | and annotation | RNA expression and secondary structure | RNA expression and secondary structure | protein structure and folding | protein structure and folding | and molecular interactions and dynamics | and molecular interactions and dynamics | annotation | annotation | molecular interactions and dynamics | molecular interactions and dynamics

License

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20.453J Biomedical Information Technology (MIT) 20.453J Biomedical Information Technology (MIT)

Description

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 desig 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 desig

Subjects

20.453 | 20.453 | 2.771 | 2.771 | HST.958 | HST.958 | imaging | imaging | medical imaging | medical imaging | metadata | metadata | molecular biology | molecular biology | medical records | medical records | DICOM | DICOM | RDF | RDF | OWL | OWL | SPARQL | SPARQL | SBML | SBML | CellML | CellML | semantic web | semantic web | BioHaystack | BioHaystack | database | database | schema | schema | ExperiBase | ExperiBase | genomics | genomics | proteomics | proteomics | bioinformatics | bioinformatics | computational biology | computational biology | clinical decision support | clinical decision support | clinical trial | clinical trial | microarray | microarray | gel electrophoresis | gel electrophoresis | diagnosis | diagnosis | pathway modeling | pathway modeling | XML | XML | SQL | SQL | relational database | relational database | biological data | biological data | ontologies | ontologies | drug development | drug development | drug discovery | drug discovery | drug target | drug target | pharmaceutical | pharmaceutical | gene sequencing | gene sequencing

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20.181 Computation for Biological Engineers (MIT) 20.181 Computation for Biological Engineers (MIT)

Description

This course covers the analytical, graphical, and numerical methods supporting the analysis and design of integrated biological systems. Topics include modularity and abstraction in biological systems, mathematical encoding of detailed physical problems, numerical methods for solving the dynamics of continuous and discrete chemical systems, statistics and probability in dynamic systems, applied local and global optimization, simple feedback and control analysis, statistics and probability in pattern recognition. An official course Web site and Wiki is maintained on OpenWetWare: 20.181 Computation for Biological Engineers. This course covers the analytical, graphical, and numerical methods supporting the analysis and design of integrated biological systems. Topics include modularity and abstraction in biological systems, mathematical encoding of detailed physical problems, numerical methods for solving the dynamics of continuous and discrete chemical systems, statistics and probability in dynamic systems, applied local and global optimization, simple feedback and control analysis, statistics and probability in pattern recognition. An official course Web site and Wiki is maintained on OpenWetWare: 20.181 Computation for Biological Engineers.

Subjects

Phylogenetic Inference | Phylogenetic Inference | Molecular Modeling | Molecular Modeling | Protein Design | Protein Design | Discrete Reaction Event Network Modeling | Discrete Reaction Event Network Modeling | Python | Python | genetics | genetics | DNA sequence | DNA sequence | genomics | genomics | gene sequencing | gene sequencing | UPGMA | UPGMA | Newick notation | Newick notation | parsimony | parsimony | downpass | downpass | uppass | uppass | jukes-cantor | jukes-cantor | invertase | invertase | genetic memory | genetic memory

License

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7.13 Experimental Microbial Genetics (MIT) 7.13 Experimental Microbial Genetics (MIT)

Description

Also referred to as the Microbial Genetics Project Lab, this is a hands-on research course designed to introduce the student to the strategies and challenges associated with microbiology research. Students take on independent and original research projects that are designed to be instructive with the goal of advancing a specific field of research in microbiology. Also referred to as the Microbial Genetics Project Lab, this is a hands-on research course designed to introduce the student to the strategies and challenges associated with microbiology research. Students take on independent and original research projects that are designed to be instructive with the goal of advancing a specific field of research in microbiology.

Subjects

microbiology | microbiology | genetics | genetics | rhodococcus | rhodococcus | bacteria | bacteria | genes | genes | plasmid manipulation | plasmid manipulation | mutagenesis | mutagenesis | PCR | PCR | DNA sequencing | DNA sequencing | enzyme assays | enzyme assays | gene expression | gene expression | molecular genetics | molecular genetics | Gram-positive | Gram-positive | gram-negative | gram-negative | bioconversion processes | bioconversion processes | synthesis | synthesis | precursors | precursors | metabolites | metabolites | genetic complementation | genetic complementation | laboratory | laboratory | lab | lab

License

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7.91J Foundations of Computational and Systems Biology (MIT) 7.91J Foundations of Computational and Systems Biology (MIT)

Description

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. 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.

Subjects

7.91 | 7.91 | 20.490 | 20.490 | 20.390 | 20.390 | 7.36 | 7.36 | 6.802 | 6.802 | 6.874 | 6.874 | HST.506 | HST.506 | computational biology | computational biology | systems biology | systems biology | bioinformatics | bioinformatics | artificial intelligence | artificial intelligence | sequence analysis | sequence analysis | proteomics | proteomics | sequence alignment | sequence alignment | protein folding | protein folding | structure prediction | structure prediction | network modeling | network modeling | phylogenetics | phylogenetics | pairwise sequence comparisons | pairwise sequence comparisons | ncbi | ncbi | blast | blast | protein structure | protein structure | dynamic programming | dynamic programming | genome sequencing | genome sequencing | DNA | DNA | RNA | RNA | x-ray crystallography | x-ray crystallography | NMR | NMR | homologs | homologs | ab initio structure prediction | ab initio structure prediction | DNA microarrays | DNA microarrays | clustering | clustering | proteome | proteome | computational annotation | computational annotation

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7.91J Foundations of Computational and Systems Biology (MIT) 7.91J Foundations of Computational and Systems Biology (MIT)

Description

Serving as an introduction to computational biology, this course emphasizes the fundamentals of nucleic acid and protein sequence analysis, structural analysis, and the analysis of complex biological systems. The principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling are covered. Students are also exposed to currently emerging research areas in the fields of computational and systems biology. Serving as an introduction to computational biology, this course emphasizes the fundamentals of nucleic acid and protein sequence analysis, structural analysis, and the analysis of complex biological systems. The principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling are covered. Students are also exposed to currently emerging research areas in the fields of computational and systems biology.

Subjects

computational biology | computational biology | systems biology | systems biology | bioinformatics | bioinformatics | sequence analysis | sequence analysis | proteomics | proteomics | sequence alignment | sequence alignment | protein folding | protein folding | structure prediction | structure prediction | network modeling | network modeling | phylogenetics | phylogenetics | pairwise sequence comparisons | pairwise sequence comparisons | ncbi | ncbi | blast | blast | protein structure | protein structure | dynamic programming | dynamic programming | genome sequencing | genome sequencing | DNA | DNA | RNA | RNA | x-ray crystallography | x-ray crystallography | NMR | NMR | homologs | homologs | ab initio structure prediction | ab initio structure prediction | DNA microarrays | DNA microarrays | clustering | clustering | proteome | proteome | computational annotation | computational annotation | BE.490J | BE.490J | 7.91 | 7.91 | 7.36 | 7.36 | BE.490 | BE.490 | 20.490 | 20.490

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7.343 An RNA Safari: Exploring the Surprising Diversity of Mammalian Transcriptomes (MIT) 7.343 An RNA Safari: Exploring the Surprising Diversity of Mammalian Transcriptomes (MIT)

Description

The aim of this class is to introduce the exciting and often under appreciated discoveries in RNA biology by exploring the diversity of RNAs—encompassing classical molecules such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and messenger RNAs (mRNAs) as well as newer species, such as microRNAs (miRNAs), long-noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). For each new class of RNA, we will evaluate the evidence for its existence as well as for its proposed function. Students will develop both a deep understanding of the field of RNA biology and the ability to critically assess new papers in this fast-paced field.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 The aim of this class is to introduce the exciting and often under appreciated discoveries in RNA biology by exploring the diversity of RNAs—encompassing classical molecules such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and messenger RNAs (mRNAs) as well as newer species, such as microRNAs (miRNAs), long-noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). For each new class of RNA, we will evaluate the evidence for its existence as well as for its proposed function. Students will develop both a deep understanding of the field of RNA biology and the ability to critically assess new papers in this fast-paced field.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

Subjects

RNA | RNA | ribosomal RNAs (rRNAs) | ribosomal RNAs (rRNAs) | transfer RNAs (tRNAs) | transfer RNAs (tRNAs) | messenger RNAs (mRNAs) | messenger RNAs (mRNAs) | microRNAs (miRNAs) | microRNAs (miRNAs) | long-noncoding RNAs (lncRNAs) | long-noncoding RNAs (lncRNAs) | circular RNAs (circRNAs) | circular RNAs (circRNAs) | high-throughput sequencing | high-throughput sequencing | snRNAs | snRNAs | pre-mRNA splicing | pre-mRNA splicing | snoRNAs | snoRNAs | regulatory molecules | regulatory molecules | siRNA | siRNA | piRNAs | piRNAs | CRISPR-associated RNAs | CRISPR-associated RNAs

License

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7.342 Personal Genomics and Medicine: What's in Your Genome? (MIT)

Description

Human genome sequencing has revolutionized our understanding of disease susceptibility, drug metabolism and human ancestry. This course will explore how these advances have been made possible by revolutionary new sequencing methodologies that have decreased costs and increased throughput of genome analysis, making it possible to examine genetic correlates for a variety of biological processes and disorders. The course will combine discussions of primary scientific research papers with hands-on data analysis and small group presentations. 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

Subjects

genome sequencing | genome analysis | disease susceptibility | drug metabolism | human ancestry | mitochondrial DNA | tyrosine kinase inhibitors | BCR-ABL gene fusion | PCSK9 inhibitors | hypercholesterolemia | genetic testing | next generation sequencing | Single-nucleotide polymorphisms (SNPs) | copy number variations (CNVs) | genome-wide association studies (GWAS) | Chronic myelogenous leukemia (CML) | mosaics | chimeras | bioinformatics

License

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7.347 Epigenetic Regulation of Stem Cells (MIT)

Description

During development a single totipotent cell gives rise to the vast array of cell types present in the adult human body, yet each cell has essentially the same DNA sequence. As cells differentiate, distinct sets of genes must be coordinately activated and repressed, ultimately leading to a cell-type specific pattern of gene expression and a particular cell fate. In eukaryotic organisms, DNA is packaged in a complex protein super structure known as chromatin. Modification and reorganization of chromatin play a critical role in coordinating the cell-type specific gene expression programs that are required as a cell transitions from a pluripotent stem cell to a fully differentiated cell type. Epigenetics refers to such heritable changes that occur in chromatin without altering the primary DNA

Subjects

Stem cells | induced pluripotency | Epigenetics | chromatin | histone | epigenome | genome-wide analyses | high-throughput sequencing technologies | Chromatin Immunoprecipitation sequencing | ncRNAs | epigenetic regulation | DNA methylation | post-translational modification of histones | roles of chromatin-assembly modifying complexes | non-coding RNAs | nuclear organization | developmental fate | stem cell therapy

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The Evolution of the Genome

Description

Computational and stastistical methods help us understand evolution as well as genetic disease. Professor Gerton Lunter is interested in investigating the processes of evolution and biology using computational methods. His focus is on sequencing data; Professor Lunter develops methods to investigate evolutionary questions in population genetics. Wales; http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

Subjects

genetics | computational | statistical | disease | evolution | sequencing | genetics | computational | statistical | disease | evolution | sequencing

License

http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

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7.91J Foundations of Computational and Systems Biology (MIT)

Description

Serving as an introduction to computational biology, this course emphasizes the fundamentals of nucleic acid and protein sequence analysis, structural analysis, and the analysis of complex biological systems. The principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling are covered. Students are also exposed to currently emerging research areas in the fields of computational and systems biology.

Subjects

computational biology | systems biology | bioinformatics | sequence analysis | proteomics | sequence alignment | protein folding | structure prediction | network modeling | phylogenetics | pairwise sequence comparisons | ncbi | blast | protein structure | dynamic programming | genome sequencing | DNA | RNA | x-ray crystallography | NMR | homologs | ab initio structure prediction | DNA microarrays | clustering | proteome | computational annotation | BE.490J | 7.91 | 7.36 | BE.490 | 20.490

License

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