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7.89 Topics in Computational and Systems Biology (MIT) 7.89 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 PhD program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology. Acknowledgments In addition to the staff listed on this page, the followi 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 PhD program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology. Acknowledgments In addition to the staff listed on this page, the followi

Subjects

computational | computational | systems | systems | biology | biology | seminar | seminar | literature review | literature review | statistics | statistics | developmental | developmental | biochemistry | biochemistry | genetics | genetics | physics | physics | genomics | genomics | signal transduction | signal transduction | regulation | regulation | medicine | medicine | kinetics | kinetics | protein structure | protein structure | devices | devices | synthesis | synthesis | networks | networks | mapping | mapping

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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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7.345 Survival in Extreme Conditions: The Bacterial Stress Response (MIT) 7.345 Survival in Extreme Conditions: The Bacterial Stress Response (MIT)

Description

Bacteria survive in almost all environments on Earth, including some considered extremely harsh. From the steaming hot springs of Yellowstone to the frozen tundra of the arctic to the barren deserts of Chile, microbes have been found thriving. Their tenacity to survive in such extreme and varied conditions allows them to play fundamental roles in global nutrient cycling. Microbes also cause a wide range of human diseases and can survive inhospitable conditions found in the human body. In this course, we will examine the molecular systems that bacteria use to adapt to changes in their environment. We will consider stresses commonly encountered, such as starvation, oxidative stress and heat shock, and also discuss how the adaptive responses affect the evolution of the bacteria. This course Bacteria survive in almost all environments on Earth, including some considered extremely harsh. From the steaming hot springs of Yellowstone to the frozen tundra of the arctic to the barren deserts of Chile, microbes have been found thriving. Their tenacity to survive in such extreme and varied conditions allows them to play fundamental roles in global nutrient cycling. Microbes also cause a wide range of human diseases and can survive inhospitable conditions found in the human body. In this course, we will examine the molecular systems that bacteria use to adapt to changes in their environment. We will consider stresses commonly encountered, such as starvation, oxidative stress and heat shock, and also discuss how the adaptive responses affect the evolution of the bacteria. This course

Subjects

bacteria | bacteria | microbes | microbes | signal transduction pathways | signal transduction pathways | cellular response | cellular response | model systems | model systems | Escherichia coli | Escherichia coli | Bacillus subtilis | Bacillus subtilis | oxidative stress | oxidative stress | starvation | starvation | heat shock | heat shock | dormant state | dormant state | microbial stress response | microbial stress response | bacterial genetics | bacterial genetics | microbiology | microbiology | sporulation | sporulation | sRNAs | sRNAs | histidine kinases | histidine kinases | response regulators | response regulators | mRNAs | mRNAs | RpoS | RpoS | small molecules | small molecules | efflux pumps | efflux pumps | Pseudomonas aeruginosa | Pseudomonas aeruginosa

License

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7.340 Ubiquitination: The Proteasome and Human Disease (MIT) 7.340 Ubiquitination: The Proteasome and Human Disease (MIT)

Description

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. This seminar provides a deeper understanding of the post-translational mechanisms evolved by eukaryotic cells to target proteins for degradation. Students learn how proteins are recognized and degraded by specific machinery (the proteasome) through their previous tagging with another small protein, ubiquitin. Additional topics include principles of ubiquitin-proteasome function, its control of the most important cellular pathways, and the implication of this system in different human diseases. Finally, spe 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. This seminar provides a deeper understanding of the post-translational mechanisms evolved by eukaryotic cells to target proteins for degradation. Students learn how proteins are recognized and degraded by specific machinery (the proteasome) through their previous tagging with another small protein, ubiquitin. Additional topics include principles of ubiquitin-proteasome function, its control of the most important cellular pathways, and the implication of this system in different human diseases. Finally, spe

Subjects

ubiquitination | ubiquitination | ubiquitin | ubiquitin | proteasome | proteasome | post-translational mechanisms | post-translational mechanisms | ubiquitin-conjugation system | ubiquitin-conjugation system | neurodegenerative diseases | neurodegenerative diseases | immune response | immune response | cell cycle regulation | cell cycle regulation | apoptosis | apoptosis | signal transduction pathways | signal transduction pathways | tumorigenesis | tumorigenesis | protein degradation | protein degradation | Endoplasmic Reticulum Associated Degradation Pathway | Endoplasmic Reticulum Associated Degradation Pathway | ligases | ligases | translocated proteins | translocated proteins | misfolded proteins | misfolded proteins | trafficking membranes | trafficking membranes | cell cycle control | cell cycle control | programmed cell death | programmed cell death | Huntington's Disease | Huntington's Disease | Von Hippel-Lindau Disease | Von Hippel-Lindau Disease

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 http://ocw.mit.edu/terms/index.htm

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7.342 Cancer Biology: From Basic Research to the Clinic (MIT) 7.342 Cancer Biology: From Basic Research to the Clinic (MIT)

Description

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. In 1971, President Nixon declared the "War on Cancer," but after three decades the war is still raging. How much progress have we made toward winning the war and what are we doing to improve the fight? Understanding the molecular and cellular events involved in tumor formation, progression, and metastasis is crucial to the development of innovative therapy for cancer patients. Insights into these processes have been gleaned through basic research using biochemical, molecular, and genetic ana 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. In 1971, President Nixon declared the "War on Cancer," but after three decades the war is still raging. How much progress have we made toward winning the war and what are we doing to improve the fight? Understanding the molecular and cellular events involved in tumor formation, progression, and metastasis is crucial to the development of innovative therapy for cancer patients. Insights into these processes have been gleaned through basic research using biochemical, molecular, and genetic ana

Subjects

cancer | cancer | tumor | tumor | metastasis | metastasis | genetic analysis | genetic analysis | cancer biology | cancer biology | model organisms | model organisms | genetic pathways | genetic pathways | uncontrolled growth | uncontrolled growth | tumor suppressor genes | tumor suppressor genes | oncogenes | oncogenes | tumor initiation | tumor initiation | cell cycle | cell cycle | chromosomal aberration | chromosomal aberration | apoptosis | apoptosis | cell death | cell death | signal transduction pathways | signal transduction pathways | proto-oncogene | proto-oncogene | mutation | mutation | DNA mismatch repair | DNA mismatch repair | telomeres | telomeres | mouse models | mouse models | tissue specificity | tissue specificity | malignancy | malignancy | stem cells | stem cells | therapeutic resistance | therapeutic resistance | differentiation | differentiation | caner research | caner research | cancer therapeutics | cancer therapeutics | chemotherapy | chemotherapy

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9.530 Cellular and Molecular Computation (MIT) 9.530 Cellular and Molecular Computation (MIT)

Description

Life as an emergent property of networks of chemical reactions involving proteins and nucleic acids. Mathematical theories of metabolism, gene regulation, signal transduction, chemotaxis, excitability, motility, mitosis, development, and immunity. Applications to directed molecular evolution, DNA computing, and metabolic and genetic engineering. Life as an emergent property of networks of chemical reactions involving proteins and nucleic acids. Mathematical theories of metabolism, gene regulation, signal transduction, chemotaxis, excitability, motility, mitosis, development, and immunity. Applications to directed molecular evolution, DNA computing, and metabolic and genetic engineering.

Subjects

emergent | emergent | network | network | chemical reactions | chemical reactions | proteins | proteins | nucleic acids | nucleic acids | metabolism | metabolism | gene regulation | gene regulation | signal transduction | signal transduction | chemotaxis | chemotaxis | excitability | excitability | motility | motility | mitosis | mitosis | development | development | immunity | immunity | molecular evolution | molecular evolution | DNA computing | DNA computing | metabolic | metabolic | genetic engineering | genetic engineering | Neural networks | Neural networks

License

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20.400J Perspectives in Biological Engineering (MIT) 20.400J Perspectives in Biological Engineering (MIT)

Description

This seminar-format course provides an in-depth presentation and discussion of how engineering and biological approaches can be combined to solve problems in science and technology, emphasizing integration of biological information and methodologies with engineering analysis, synthesis, and design. Emphasis is placed on molecular mechanisms underlying cellular processes, including signal transduction, gene expression networks, and functional responses. This seminar-format course provides an in-depth presentation and discussion of how engineering and biological approaches can be combined to solve problems in science and technology, emphasizing integration of biological information and methodologies with engineering analysis, synthesis, and design. Emphasis is placed on molecular mechanisms underlying cellular processes, including signal transduction, gene expression networks, and functional responses.

Subjects

integration of biological information and methodologies | integration of biological information and methodologies | engineering analysis | engineering analysis | synthesis | synthesis | design | design | molecular mechanisms underlying cellular processes | molecular mechanisms underlying cellular processes | signal transduction | signal transduction | gene expression networks | gene expression networks | functional responses | functional responses | 20.400 | 20.400 | 7.548 | 7.548

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HST.176 Cellular and Molecular Immunology (MIT) HST.176 Cellular and Molecular Immunology (MIT)

Description

This course covers cells and tissues of the immune system, lymphocyte development, the structure and function of antigen receptors, the cell biology of antigen processing and presentation, including molecular structure and assembly of MHC molecules, the biology of cytokines, leukocyte-endothelial interactions, and the pathogenesis of immunologically mediated diseases. The course is structured as a series of lectures and tutorials in which clinical cases are discussed with faculty tutors. Lecturers Frederick W. Alt Marcus Altfeld Paul Anderson Jon C. Aster Hugh Auchincloss Steven P. Balk Samuel M. Behar Richard S. Blumberg Francisco Bonilla Bobby Cherayil Benjamin Davis David Hafler Nir Harcohen Bruce Horwitz David M. Lee Andrew Lichtman Diane Mathis Richard Mitchell Hidde Ploegh Emmett This course covers cells and tissues of the immune system, lymphocyte development, the structure and function of antigen receptors, the cell biology of antigen processing and presentation, including molecular structure and assembly of MHC molecules, the biology of cytokines, leukocyte-endothelial interactions, and the pathogenesis of immunologically mediated diseases. The course is structured as a series of lectures and tutorials in which clinical cases are discussed with faculty tutors. Lecturers Frederick W. Alt Marcus Altfeld Paul Anderson Jon C. Aster Hugh Auchincloss Steven P. Balk Samuel M. Behar Richard S. Blumberg Francisco Bonilla Bobby Cherayil Benjamin Davis David Hafler Nir Harcohen Bruce Horwitz David M. Lee Andrew Lichtman Diane Mathis Richard Mitchell Hidde Ploegh Emmett

Subjects

immunology | immunology | immune system | immune system | lymphocyte | lymphocyte | antigen | antigen | receptors | receptors | antibody | antibody | T cells | T cells | signal transduction | signal transduction | immunity | immunity | transplantation | transplantation | autoimmunity | autoimmunity

License

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20.320 Analysis of Biomolecular and Cellular Systems (MIT) 20.320 Analysis of Biomolecular and Cellular Systems (MIT)

Description

This course focuses on computational and experimental analysis of biological systems across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. The two central themes of the course are modeling of complex dynamic systems and protein design and engineering. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling. This course focuses on computational and experimental analysis of biological systems across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. The two central themes of the course are modeling of complex dynamic systems and protein design and engineering. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.

Subjects

biological engineering | biological engineering | kinase | kinase | PyMOL | PyMOL | PyRosetta | PyRosetta | MATLAB | MATLAB | Michaelis-Menten | Michaelis-Menten | bioreactor | bioreactor | bromodomain | bromodomain | protein-ligand interactions | protein-ligand interactions | titration analysis | titration analysis | fractional separation | fractional separation | isothermal titration calorimetry | isothermal titration calorimetry | ITC | ITC | mass spectrometry | mass spectrometry | MS | MS | co-immunoprecipitation | co-immunoprecipitation | Co-IP | Co-IP | Forster resonance energy transfer | Forster resonance energy transfer | FRET | FRET | primary ligation assay | primary ligation assay | PLA | PLA | surface plasmon resonance | surface plasmon resonance | SPR | SPR | enzyme kinetics | enzyme kinetics | kinase engineering | kinase engineering | competitive inhibition | competitive inhibition | epidermal growth factor receptor | epidermal growth factor receptor | mitogen-activated protein kinase | mitogen-activated protein kinase | MAPK | MAPK | genome editing | genome editing | Imatinib | Imatinib | Gleevec | Gleevec | Glivec | Glivec | drug delivery | drug delivery | kinetics of molecular processes | kinetics of molecular processes | dynamics of molecular processes | dynamics of molecular processes | kinetics of cellular processes | kinetics of cellular processes | dynamics of cellular processes | dynamics of cellular processes | intracellular scale | intracellular scale | extracellular scale | extracellular scale | and cell population scale | and cell population scale | biotechnology applications | biotechnology applications | gene regulation networks | gene regulation networks | nucleic acid hybridization | nucleic acid hybridization | signal transduction pathways | signal transduction pathways | cell populations in tissues | cell populations in tissues | cell populations in bioreactors | cell populations in bioreactors | experimental methods | experimental methods | quantitative analysis | quantitative analysis | computational modeling | computational modeling

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 http://ocw.mit.edu/terms/index.htm

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20.320 Biomolecular Kinetics and Cell Dynamics (MIT) 20.320 Biomolecular Kinetics and Cell Dynamics (MIT)

Description

This class covers analysis of kinetics and dynamics of molecular and cellular processes across a hierarchy of scales, including intracellular, extracellular, and cell population levels; a spectrum of biotechnology applications are also taken into consideration. Topics include gene regulation networks; nucleic acid hybridization; signal transduction pathways; and cell populations in tissues and bioreactors. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling. This class covers analysis of kinetics and dynamics of molecular and cellular processes across a hierarchy of scales, including intracellular, extracellular, and cell population levels; a spectrum of biotechnology applications are also taken into consideration. Topics include gene regulation networks; nucleic acid hybridization; signal transduction pathways; and cell populations in tissues and bioreactors. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.

Subjects

kinetics of molecular processes | kinetics of molecular processes | dynamics of molecular processes | dynamics of molecular processes | kinetics of cellular processes | kinetics of cellular processes | dynamics of cellular processes | dynamics of cellular processes | intracellular scale | intracellular scale | extracellular scale | extracellular scale | and cell population scale | and cell population scale | biotechnology applications | biotechnology applications | gene regulation networks | gene regulation networks | nucleic acid hybridization | nucleic acid hybridization | signal transduction pathways | signal transduction pathways | cell populations in tissues | cell populations in tissues | cell populations in bioreactors | cell populations in bioreactors | experimental methods | experimental methods | quantitative analysis | quantitative analysis | computational modeling | computational modeling | cell population scale | cell population scale

License

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20.320 Biomolecular Kinetics and Cell Dynamics (MIT)

Description

This class covers analysis of kinetics and dynamics of molecular and cellular processes across a hierarchy of scales, including intracellular, extracellular, and cell population levels; a spectrum of biotechnology applications are also taken into consideration. Topics include gene regulation networks; nucleic acid hybridization; signal transduction pathways; and cell populations in tissues and bioreactors. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.

Subjects

kinetics of molecular processes | dynamics of molecular processes | kinetics of cellular processes | dynamics of cellular processes | intracellular scale | extracellular scale | and cell population scale | biotechnology applications | gene regulation networks | nucleic acid hybridization | signal transduction pathways | cell populations in tissues | cell populations in bioreactors | experimental methods | quantitative analysis | computational modeling | cell population scale

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 http://ocw.mit.edu/terms/index.htm

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HST.176 Cellular and Molecular Immunology (MIT)

Description

This course covers cells and tissues of the immune system, lymphocyte development, the structure and function of antigen receptors, the cell biology of antigen processing and presentation, including molecular structure and assembly of MHC molecules, the biology of cytokines, leukocyte-endothelial interactions, and the pathogenesis of immunologically mediated diseases. The course is structured as a series of lectures and tutorials in which clinical cases are discussed with faculty tutors. Lecturers Frederick W. Alt Marcus Altfeld Paul Anderson Jon C. Aster Hugh Auchincloss Steven P. Balk Samuel M. Behar Richard S. Blumberg Francisco Bonilla Bobby Cherayil Benjamin Davis David Hafler Nir Harcohen Bruce Horwitz David M. Lee Andrew Lichtman Diane Mathis Richard Mitchell Hidde Ploegh Emmett

Subjects

immunology | immune system | lymphocyte | antigen | receptors | antibody | T cells | signal transduction | immunity | transplantation | autoimmunity

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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7.340 Ubiquitination: The Proteasome and Human Disease (MIT)

Description

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. This seminar provides a deeper understanding of the post-translational mechanisms evolved by eukaryotic cells to target proteins for degradation. Students learn how proteins are recognized and degraded by specific machinery (the proteasome) through their previous tagging with another small protein, ubiquitin. Additional topics include principles of ubiquitin-proteasome function, its control of the most important cellular pathways, and the implication of this system in different human diseases. Finally, spe

Subjects

ubiquitination | ubiquitin | proteasome | post-translational mechanisms | ubiquitin-conjugation system | neurodegenerative diseases | immune response | cell cycle regulation | apoptosis | signal transduction pathways | tumorigenesis | protein degradation | Endoplasmic Reticulum Associated Degradation Pathway | ligases | translocated proteins | misfolded proteins | trafficking membranes | cell cycle control | programmed cell death | Huntington's Disease | Von Hippel-Lindau Disease

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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Cell Signalling

Description

A chapter which describes the mechanisms of signal transduction in a eukaryotic cell, including the activation of G-proteins and kinase cascades (49 figures). The unit is intended as ~10hrs study at level 2/3. It also provides background reading for the experimental investigation 'Investigating intracellular signalling pathways' (http://open.jorum.ac.uk/xmlui/handle/123456789/1581).

Subjects

bioukoer | ukoer | signal transduction | g-proteins | receptors | protein kinases | kinase cascades | transcription factors | protein phosphatases | glucose metabolism | Biological sciences | C000

License

Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales http://creativecommons.org/licenses/by-nc-sa/2.0/uk/ http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

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Curated collection of Cell Biology resources

Description

This is an evaluated collection of links to resources for learning and understanding Cell Biology within a bioscience context. This forms part of the UK Centre for Bioscience OeRBITAL project.

Subjects

ukoer | oerbital | cell | cell signalling | signal transduction | molecular biology | cell biology | Biological sciences | C000

License

Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales http://creativecommons.org/licenses/by-nc-sa/2.0/uk/ http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

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Curated collection of Molecular Biology resources

Description

This is an evaluated collection of links to resources for learning and teaching subjects relating to Molecular Biology. This forms part of the UK Centre for Bioscience OeRBITAL project.

Subjects

ukoer | oerbital | molecular biology | molecular structure and function | cell biology | signal transduction | biotechnology | bioinformatics | bioenergetics and metabolism | Biological sciences | C000

License

Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales http://creativecommons.org/licenses/by-nc-sa/2.0/uk/ http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

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20.320 Biomolecular Kinetics and Cell Dynamics (MIT)

Description

This class covers analysis of kinetics and dynamics of molecular and cellular processes across a hierarchy of scales, including intracellular, extracellular, and cell population levels; a spectrum of biotechnology applications are also taken into consideration. Topics include gene regulation networks; nucleic acid hybridization; signal transduction pathways; and cell populations in tissues and bioreactors. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.

Subjects

kinetics of molecular processes | dynamics of molecular processes | kinetics of cellular processes | dynamics of cellular processes | intracellular scale | extracellular scale | and cell population scale | biotechnology applications | gene regulation networks | nucleic acid hybridization | signal transduction pathways | cell populations in tissues | cell populations in bioreactors | experimental methods | quantitative analysis | computational modeling | cell population scale

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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7.89 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 PhD program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology. Acknowledgments In addition to the staff listed on this page, the followi

Subjects

computational | systems | biology | seminar | literature review | statistics | developmental | biochemistry | genetics | physics | genomics | signal transduction | regulation | medicine | kinetics | protein structure | devices | synthesis | networks | mapping

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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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.

Subjects

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

License

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7.345 Survival in Extreme Conditions: The Bacterial Stress Response (MIT)

Description

Bacteria survive in almost all environments on Earth, including some considered extremely harsh. From the steaming hot springs of Yellowstone to the frozen tundra of the arctic to the barren deserts of Chile, microbes have been found thriving. Their tenacity to survive in such extreme and varied conditions allows them to play fundamental roles in global nutrient cycling. Microbes also cause a wide range of human diseases and can survive inhospitable conditions found in the human body. In this course, we will examine the molecular systems that bacteria use to adapt to changes in their environment. We will consider stresses commonly encountered, such as starvation, oxidative stress and heat shock, and also discuss how the adaptive responses affect the evolution of the bacteria. This course

Subjects

bacteria | microbes | signal transduction pathways | cellular response | model systems | Escherichia coli | Bacillus subtilis | oxidative stress | starvation | heat shock | dormant state | microbial stress response | bacterial genetics | microbiology | sporulation | sRNAs | histidine kinases | response regulators | mRNAs | RpoS | small molecules | efflux pumps | Pseudomonas aeruginosa

License

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7.340 Ubiquitination: The Proteasome and Human Disease (MIT)

Description

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. This seminar provides a deeper understanding of the post-translational mechanisms evolved by eukaryotic cells to target proteins for degradation. Students learn how proteins are recognized and degraded by specific machinery (the proteasome) through their previous tagging with another small protein, ubiquitin. Additional topics include principles of ubiquitin-proteasome function, its control of the most important cellular pathways, and the implication of this system in different human diseases. Finally, spe

Subjects

ubiquitination | ubiquitin | proteasome | post-translational mechanisms | ubiquitin-conjugation system | neurodegenerative diseases | immune response | cell cycle regulation | apoptosis | signal transduction pathways | tumorigenesis | protein degradation | Endoplasmic Reticulum Associated Degradation Pathway | ligases | translocated proteins | misfolded proteins | trafficking membranes | cell cycle control | programmed cell death | Huntington's Disease | Von Hippel-Lindau Disease

License

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7.342 Cancer Biology: From Basic Research to the Clinic (MIT)

Description

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. In 1971, President Nixon declared the "War on Cancer," but after three decades the war is still raging. How much progress have we made toward winning the war and what are we doing to improve the fight? Understanding the molecular and cellular events involved in tumor formation, progression, and metastasis is crucial to the development of innovative therapy for cancer patients. Insights into these processes have been gleaned through basic research using biochemical, molecular, and genetic ana

Subjects

cancer | tumor | metastasis | genetic analysis | cancer biology | model organisms | genetic pathways | uncontrolled growth | tumor suppressor genes | oncogenes | tumor initiation | cell cycle | chromosomal aberration | apoptosis | cell death | signal transduction pathways | proto-oncogene | mutation | DNA mismatch repair | telomeres | mouse models | tissue specificity | malignancy | stem cells | therapeutic resistance | differentiation | caner research | cancer therapeutics | chemotherapy

License

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20.320 Analysis of Biomolecular and Cellular Systems (MIT)

Description

This course focuses on computational and experimental analysis of biological systems across a hierarchy of scales, including genetic, molecular, cellular, and cell population levels. The two central themes of the course are modeling of complex dynamic systems and protein design and engineering. Topics include gene sequence analysis, molecular modeling, metabolic and gene regulation networks, signal transduction pathways and cell populations in tissues. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.

Subjects

biological engineering | kinase | PyMOL | PyRosetta | MATLAB | Michaelis-Menten | bioreactor | bromodomain | protein-ligand interactions | titration analysis | fractional separation | isothermal titration calorimetry | ITC | mass spectrometry | MS | co-immunoprecipitation | Co-IP | Forster resonance energy transfer | FRET | primary ligation assay | PLA | surface plasmon resonance | SPR | enzyme kinetics | kinase engineering | competitive inhibition | epidermal growth factor receptor | mitogen-activated protein kinase | MAPK | genome editing | Imatinib | Gleevec | Glivec | drug delivery | kinetics of molecular processes | dynamics of molecular processes | kinetics of cellular processes | dynamics of cellular processes | intracellular scale | extracellular scale | and cell population scale | biotechnology applications | gene regulation networks | nucleic acid hybridization | signal transduction pathways | cell populations in tissues | cell populations in bioreactors | experimental methods | quantitative analysis | computational modeling

License

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20.400J Perspectives in Biological Engineering (MIT)

Description

This seminar-format course provides an in-depth presentation and discussion of how engineering and biological approaches can be combined to solve problems in science and technology, emphasizing integration of biological information and methodologies with engineering analysis, synthesis, and design. Emphasis is placed on molecular mechanisms underlying cellular processes, including signal transduction, gene expression networks, and functional responses.

Subjects

integration of biological information and methodologies | engineering analysis | synthesis | design | molecular mechanisms underlying cellular processes | signal transduction | gene expression networks | functional responses | 20.400 | 7.548

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HST.176 Cellular and Molecular Immunology (MIT)

Description

This course covers cells and tissues of the immune system, lymphocyte development, the structure and function of antigen receptors, the cell biology of antigen processing and presentation, including molecular structure and assembly of MHC molecules, the biology of cytokines, leukocyte-endothelial interactions, and the pathogenesis of immunologically mediated diseases. The course is structured as a series of lectures and tutorials in which clinical cases are discussed with faculty tutors. Lecturers Frederick W. Alt Marcus Altfeld Paul Anderson Jon C. Aster Hugh Auchincloss Steven P. Balk Samuel M. Behar Richard S. Blumberg Francisco Bonilla Bobby Cherayil Benjamin Davis David Hafler Nir Harcohen Bruce Horwitz David M. Lee Andrew Lichtman Diane Mathis Richard Mitchell Hidde Ploegh Emmett

Subjects

immunology | immune system | lymphocyte | antigen | receptors | antibody | T cells | signal transduction | immunity | transplantation | autoimmunity

License

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