Recent technological advances have enabled comprehensive determination of the molecular composition of living cells. The chemical interactions between many of these molecules are known, giving rise to genome-scale reconstructed biochemical reaction networks underlying cellular functions. Mathematical descriptions of the totality of these chemical interactions lead to genome-scale models that allow the computation of physiological functions. Reflecting these recent developments, this textbook explains how such quantitative and computable genotype-phenotype relationships are built using a genome-wide basis of information about the gene portfolio of a target organism. It describes how biological knowledge is assembled to reconstruct biochemical reaction networks, the formulation of computational models of biological functions, and how these models can be used to address key biological questions and enable predictive biology. Developed through extensive classroom use, the book is designed to provide students with a solid conceptual framework and an invaluable set of modeling tools and computational approaches.

Biophysical models have been used in biology for decades, but they have been limited in scope and size. In this book, Bernhard O. Palsson shows how network reconstructions that are based on genomic and bibliomic data, and take the form of established stoichiometric matrices, can be converted into dynamic models using metabolomic and fluxomic data. The Mass Action Stoichiometric Simulation (MASS) procedure can be used for any cellular process for which data is available and allows a scalable step-by-step approach to the practical construction of network models. Specifically, it can treat integrated processes that need explicit accounting of small molecules and protein, which allows simulation at the molecular level. The material has been class-tested by the author at both the undergraduate and graduate level. All computations in the text are available online in MATLAB (R) and Mathematica (R) workbooks, allowing hands-on practice with the material.

Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This textbook, devoted to systems biology, describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The prerequisites are some knowledge of linear algebra and biochemistry. Though the links between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, in an associated website Palsson provides problem sets, projects and Powerpoint slides, and keeps the presentation in the book concrete with illustrative material and experimental results.

Continuous cell lines derived from human cancers are the mostwidely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions offundamental importance to the relevanceof human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative oftumors at that site is naive and misleading."

This book describes all human leukemia-lymphoma cell lines that have been established and that grow continuously under standardised in vitro conditions. These lines are derived from cells belonging to all the major hematopoietic cell lineages, i.e. B- and T-lymphocytes, natural killer cells, granulocytic cells and megakaryocytic cells. The clinical data, the culture conditions and the major phenotypic features of the cell lines are described with citations. This book is the first book describing human leukemia-lymphoma cell lines and will be of interest to scientists involved in the areas of hematology, oncology, immunology, molecular biology and cytogenetics. Cancer Cell Lines, Volumes 1-3: These 3 volumes provide a comprehensive text on the culture of established cell lines from every type of human cancer. The volumes provide a basic manual and reference resource for every cancer research scientist using human cancer cells.

If you wish to grow or characterize embryonic stem cells or persuade them to differentiate into a particular cell type, then this book contains information that is vital to your success. The aim is to provide clear simple instructions and protocols for growing, maintaining and characterizing embryonic stem cells and details of the various methods used to make stem cells differentiate into specific cell types. The contents will be of interest to stem cell biologists, tissue engineers and scientists wishing to use embryonic stem cells for therapeutic purposes. Each chapter has been written and edited by internationally respected scientists working at the cutting edge of technological developments in human embryonic stem cells.

The aim of volume 7 of Human Cell Culture is to provide clear and precise methods for growing primary cultures of adult stem cells from various human tissues and describe culture conditions in which these adult stem cells differentiate along their respective lineages. The book will be of value to biomedical scientists and of special interest to stem cell biologists and tissue engineers. Each chapter is written by experts actively involved in growing human adult stem cells.

The aim of volume 7 of Human Cell Culture is to provide clear and precise methods for growing primary cultures of adult stem cells from various human tissues and describe culture conditions in which these adult stem cells differentiate along their respective lineages. The book will be of value to biomedical scientists and of special interest to stem cell biologists and tissue engineers. Each chapter is written by experts actively involved in growing human adult stem cells.

If you wish to grow or characterize embryonic stem cells or persuade them to differentiate into a particular cell type, then this book contains information that is vital to your success. The aim is to provide clear simple instructions and protocols for growing, maintaining and characterizing embryonic stem cells and details of the various methods used to make stem cells differentiate into specific cell types.The contents will be of interest to stem cell biologists, tissue engineers and scientists wishing to use embryonic stem cells for therapeutic purposes. Each chapter has been written and edited by internationally respected scientists working at the cutting edge of technological developments in human embryonic stem cells.

The human body contains many specialized tissues that are capable of fulfilling an incredible variety of functions necessary for our survival. This volume in the Human Cell Culture Series focuses on mesenchymal tissues and cells. The in vitro study of mesenchymal cells is perhaps the oldest form of human cell culture, beginning with the culturing of fibroblasts. Fibroblasts have long been generically described in the literature, arising from many tissue types upon in vitro cell culture. However, recent studies, many enabled by new molecular biology techniques, have shown considerable diversity in fibroblast type and function, as described within this volume. Mesenchymal tissue types that are described within include bone, cartilage, tendons and ligaments, muscle, adipose tissue, and skin (dermis). The proper function of these tissues is predominantly dependent upon the proper proliferation, differentiation, and function of the mesenchymal cells which make up the tissue. Recent advancements in primary human mesenchymal cell culture have led to remarkable progress in the study of these tissues. Landmark experiments have now demonstrated a stem cell basis for many of these tissues, and, furthermore, significant plasticity and inter-conversion of stem cells between these tissues, resulting in a great deal of contemporary excitement and controversy. Newly-developed mesenchymal cell culture techniques have even lead to novel clinical practices for the treatment of disease.

This book describes all human leukemia-lymphoma cell lines that have been established and that grow continuously under standardised in vitro conditions. These lines are derived from cells belonging to all the major hematopoietic cell lineages, i.e. B- and T-lymphocytes, natural killer cells, granulocytic cells and megakaryocytic cells. The clinical data, the culture conditions and the major phenotypic features of the cell lines are described with citations. This book is the first book describing human leukemia-lymphoma cell lines and will be of interest to scientists involved in the areas of hematology, oncology, immunology, molecular biology and cytogenetics. Cancer Cell Lines, Volumes 1-3: These 3 volumes provide a comprehensive text on the culture of established cell lines from every type of human cancer. The volumes provide a basic manual and reference resource for every cancer research scientist using human cancer cells.

Continuous cell lines derived from human cancers are the mostwidely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions offundamental importance to the relevanceof human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative oftumors at that site is naive and misleading."

Continuous cell lines derived from human cancers are the most widely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions of fundamental importance to the relevance of human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative of tumors at that site is naive and misleading."

Continuous cell lines derived from human cancers are the most widely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions of fundamental importance to the relevance of human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative of tumors at that site is naive and misleading."