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Pathway analysis: Pathway signatures and classification

Ming Yi and Robert M. Stephens

in Statistics and Informatics in Molecular Cancer Research

Published in print:
2009
Published Online:
September 2009
ISBN:
9780199532872
eISBN:
9780191714467
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199532872.003.0006
Subject:
Mathematics, Probability / Statistics, Biostatistics

Although the use of DNA microarrays and other high throughput (HTP) technologies is increasingly widespread and affordable, retrieval and interpretation of underlying biological themes from HTP data ... More


Networks: An Introduction

Mark Newman

Published in print:
2010
Published Online:
September 2010
ISBN:
9780199206650
eISBN:
9780191594175
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199206650.001.0001
Subject:
Physics, Theoretical, Computational, and Statistical Physics

The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet ... More


INFORMATION PROCESSING BY BIOLOGICAL AND ARTIFICIAL SMART STRUCTURES

Vinod K. Wadhawan

in Smart Structures: Blurring the Distinction Between the Living and the Nonliving

Published in print:
2007
Published Online:
January 2008
ISBN:
9780199229178
eISBN:
9780191711282
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199229178.003.0002
Subject:
Physics, Condensed Matter Physics / Materials

This chapter begins with a brief survey of the history of logical thought, and of the basics of the interplay of natural processes that have led to the evolution of computational intelligence, both ... More


Biological networks: A discussion of various networks of interest in biology, including biochemical networks, neural networks, and ecological networks

M. E. J. Newman

in Networks: An Introduction

Published in print:
2010
Published Online:
September 2010
ISBN:
9780199206650
eISBN:
9780191594175
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199206650.003.0005
Subject:
Physics, Theoretical, Computational, and Statistical Physics

Networks are widely used in many branches of biology as a convenient representation of patterns of interaction between appropriate biological elements. Molecular biologists, for example, use networks ... More


Introduction: A short introduction to networks and why we study them

M. E. J. Newman

in Networks: An Introduction

Published in print:
2010
Published Online:
September 2010
ISBN:
9780199206650
eISBN:
9780191594175
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199206650.003.0001
Subject:
Physics, Theoretical, Computational, and Statistical Physics

A network is, in its simplest form, a collection of points joined together in pairs by lines. In the jargon of the field the points are referred to as vertices or nodes and the lines are referred to ... More


MODERN ARCHITECTURE OF RANDOM GRAPHS

S. N. Dorogovtsev and J. F. F. Mendes

in Evolution of Networks: From Biological Nets to the Internet and WWW

Published in print:
2003
Published Online:
January 2010
ISBN:
9780198515906
eISBN:
9780191705670
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198515906.003.0001
Subject:
Physics, Soft Matter / Biological Physics

This introductory chapter outlines the set of issues and problems that are considered in the text. Namely, what is common to all networks? What are the general principles of the organization and ... More


Networks

Mark Newman

Published in print:
2018
Published Online:
October 2018
ISBN:
9780198805090
eISBN:
9780191843235
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198805090.001.0001
Subject:
Physics, Theoretical, Computational, and Statistical Physics

The study of networks, including computer networks, social networks, and biological networks, has attracted enormous interest in recent years. The rise of the Internet and the wide availability of ... More


Stoichiometric and Constraint-based Modeling

Steffen Klamt and Jörg Stelling

in System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Published in print:
2006
Published Online:
August 2013
ISBN:
9780262195485
eISBN:
9780262257060
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262195485.003.0005
Subject:
Mathematics, Mathematical Biology

This chapter explains the main concepts of stoichiometric network analysis (SNA). Stoichiometric modeling has become an important approach for understanding the function of metabolic networks. Hence, ... More


Modeling and Analysis of Stochastic Biochemical Networks

Mustafa Khammash

in Control Theory and Systems Biology

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262013345
eISBN:
9780262258906
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262013345.003.0002
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies

This chapter introduces types of stochastic modeling used to address the probabilistic nature of processes. It reviews some of the key approaches for this modeling and considers the analysis of ... More


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