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Cell Types and Their Origins

Günter P. Wagner

in Homology, Genes, and Evolutionary Innovation

Published in print:
2014
Published Online:
October 2017
ISBN:
9780691156460
eISBN:
9781400851461
Item type:
chapter
Publisher:
Princeton University Press
DOI:
10.23943/princeton/9780691156460.003.0009
Subject:
Biology, Evolutionary Biology / Genetics

This chapter examines the developmental evolution of cell types, the lowest level of biological organization for which questions of identity (that is, cell identity) play a major role. Higher ... More


 Evolution of the DNA World and the Chance Events That Accompanied It: More about Complexity

Paul F. Lurquin and Linda Stone

in Evolution and Religious Creation Myths: How Scientists Respond

Published in print:
2007
Published Online:
September 2007
ISBN:
9780195315387
eISBN:
9780199785674
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195315387.003.0006
Subject:
Religion, Religion and Society

First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas ... More


The Genetics of Evolutionary Novelties

Günter P. Wagner

in Homology, Genes, and Evolutionary Innovation

Published in print:
2014
Published Online:
October 2017
ISBN:
9780691156460
eISBN:
9781400851461
Item type:
chapter
Publisher:
Princeton University Press
DOI:
10.23943/princeton/9780691156460.003.0007
Subject:
Biology, Evolutionary Biology / Genetics

This chapter examines the molecular genetics of evolutionary novelties. In particular, it investigates which molecular mechanisms might be involved in the origination of novel gene regulatory ... More


The unity of type: ancient homologies in the genome

Antonio Fontdevila

in The Dynamic Genome: A Darwinian Approach

Published in print:
2011
Published Online:
September 2011
ISBN:
9780199541379
eISBN:
9780191728532
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199541379.003.0002
Subject:
Biology, Evolutionary Biology / Genetics, Developmental Biology

The controversy on the ‘unity of type’, exploited as an antievolutionist argument and based on the difficulty of revealing ancient homologies, is introduced using a historical approach. First the ... More


Models of Cellular Regulation

Baltazar Aguda, Avner Friedman, and Visiting Associate Professor, The Ohio State University

Published in print:
2008
Published Online:
September 2008
ISBN:
9780198570912
eISBN:
9780191718717
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198570912.001.0001
Subject:
Physics, Soft Matter / Biological Physics

The human genome of three billion letters has been sequenced. So have the genomes of thousands of other organisms. With unprecedented resolution, modern technologies are allowing us to peek into the ... More


Lessons and Challenges

Günter P. Wagner

in Homology, Genes, and Evolutionary Innovation

Published in print:
2014
Published Online:
October 2017
ISBN:
9780691156460
eISBN:
9781400851461
Item type:
chapter
Publisher:
Princeton University Press
DOI:
10.23943/princeton/9780691156460.003.0014
Subject:
Biology, Evolutionary Biology / Genetics

This book has argued for the reality of a class of biological entities that have a hard time finding their place in a theory of evolution based on genetics and population biology. These entities, or ... More


Homology, Genes, and Evolutionary Innovation

Günter P. Wagner

Published in print:
2014
Published Online:
October 2017
ISBN:
9780691156460
eISBN:
9781400851461
Item type:
book
Publisher:
Princeton University Press
DOI:
10.23943/princeton/9780691156460.001.0001
Subject:
Biology, Evolutionary Biology / Genetics

Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing—is one of the most fundamental yet challenging concepts in evolutionary ... More


Genetic networks

Ernesto Estrada

in The Structure of Complex Networks: Theory and Applications

Published in print:
2011
Published Online:
December 2013
ISBN:
9780199591756
eISBN:
9780191774959
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199591756.003.0013
Subject:
Physics, Theoretical, Computational, and Statistical Physics

This chapter discusses the structural analysis of genetic networks. It starts by introducing general concepts of molecular biology and by accounting for the different kinds of genetic networks that ... More


The Connectionist Framework for Gene Regulation

Roger Sansom

in Ingenious Genes: How Gene Regulation Networks Evolve to Control Development

Published in print:
2011
Published Online:
August 2013
ISBN:
9780262195812
eISBN:
9780262298209
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262195812.003.0004
Subject:
Philosophy, Philosophy of Science

This chapter discusses the adaptivity of a gene regulation network to be determined by the proportion of times that it reacts adaptively to its microenvironment. A gene regulation network is accurate ... More


Gene-regulatory networks: from DNA to metabolites and back

Baltazar D. Aguda and Avner Friedman

in Models of Cellular Regulation

Published in print:
2008
Published Online:
September 2008
ISBN:
9780198570912
eISBN:
9780191718717
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198570912.003.0004
Subject:
Physics, Soft Matter / Biological Physics

DNA has at least three functions essential to life: (i) its chemistry provides a mechanism for replicating genes (via the Watson–Crick base pairing); (ii) in its long strands are nucleotide sequences ... More


Introduction: What This Book Aims to Do and What It Is Not

Günter P. Wagner

in Homology, Genes, and Evolutionary Innovation

Published in print:
2014
Published Online:
October 2017
ISBN:
9780691156460
eISBN:
9781400851461
Item type:
chapter
Publisher:
Princeton University Press
DOI:
10.23943/princeton/9780691156460.003.0001
Subject:
Biology, Evolutionary Biology / Genetics

This book examines homology, the correspondence of characters from different species or even within the same organism, from a mechanistic perspective. Homology is explained by derivation from a ... More


Mammalian homeo box genes: evolutionary and regulatory aspects of a network gene system

Frank H. Riddle and Claudia Kappen

in Origins of the Human Brain

Published in print:
1996
Published Online:
March 2012
ISBN:
9780198523901
eISBN:
9780191689048
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198523901.003.0009
Subject:
Psychology, Cognitive Psychology

The homeo box was first discovered as a common DNA sequence element in homeotic genes of the fruit fly Drosophila melanogaster. Homeotic genes are organized in two gene clusters in the Drosophila ... More


Comparison of Mixture Bayesian and Mixture Regression Approaches to Infer Gene Networks

Sandra L. Rodriguez–Zas and Bruce R. Southey

in Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics

Published in print:
2014
Published Online:
December 2014
ISBN:
9780198709022
eISBN:
9780191779619
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198709022.003.0004
Subject:
Mathematics, Probability / Statistics, Biostatistics

Most Bayesian network applications to gene network reconstruction assume a single distributional model across all the samples and treatments analyzed. This assumption is likely to be unrealistic ... More


Bayesian Models for Variable Selection that Incorporate Biological Information *

Marina Vannucci and Francesco C. Stingo

in Bayesian Statistics 9

Published in print:
2011
Published Online:
January 2012
ISBN:
9780199694587
eISBN:
9780191731921
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199694587.003.0022
Subject:
Mathematics, Probability / Statistics

Variable selection has been the focus of much research in recent years. Bayesian methods have found many successful applications, particularly in situations where the amount of measured variables can ... More


Qualitative Approaches to the Analysis of Genetic Regulatory Networks

Hidde de Jong and Delphine Ropers

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/9780262195485.003.0007
Subject:
Mathematics, Mathematical Biology

This chapter discusses three approaches for analyzing qualitative properties of the dynamics of genetic regulatory networks, based on increasingly-abstract modeling formalisms: discrete abstractions ... More


Synthetic Gene Regulatory Systems

Mads Kærn and Ron Weiss

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/9780262195485.003.0013
Subject:
Mathematics, Mathematical Biology

This chapter focuses on the mathematical design and experimental implementation of selected synthetic gene regulatory networks that embody important architectural properties. The chapter is organized ... More


Network Inference in Breast Cancer with Gaussian Graphical Models and Extensions

Marine Jeanmougin, Camille Charbonnier, Mickaël Guedj, and Julien Chiquet

in Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics

Published in print:
2014
Published Online:
December 2014
ISBN:
9780198709022
eISBN:
9780191779619
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198709022.003.0005
Subject:
Mathematics, Probability / Statistics, Biostatistics

Clustering genes with high correlations will group genes with close expression profiles, defining clusters of co-expressed genes. However, such correlations do not provide any clue on the chain of ... More


Development on the wing: how to make a wing pattern different

Chris D. Jiggins

in The Ecology and Evolution of Heliconius Butterflies

Published in print:
2016
Published Online:
April 2017
ISBN:
9780199566570
eISBN:
9780191833922
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199566570.003.0009
Subject:
Biology, Evolutionary Biology / Genetics, Biodiversity / Conservation Biology

Butterfly wings form as imaginal disks in the caterpillar, and are patterned by a gene regulatory network that increases in complexity through development, providing an exemplary system for the study ... More


Why Gene Regulation Networks Are the Controllers of Development

Roger Sansom

in Ingenious Genes: How Gene Regulation Networks Evolve to Control Development

Published in print:
2011
Published Online:
August 2013
ISBN:
9780262195812
eISBN:
9780262298209
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262195812.003.0005
Subject:
Philosophy, Philosophy of Science

This chapter discusses the different types of systems that fall under different types of control, with the aim of understanding the control which is exhibited in development. It identifies a new ... More


From genes to gene regulatory networks: the progressive historical construction of a genetic theory of development and evolution

Michel Morange

in Towards a Theory of Development

Published in print:
2014
Published Online:
August 2014
ISBN:
9780199671427
eISBN:
9780191781117
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199671427.003.0011
Subject:
Biology, Developmental Biology

Within the field of evo-devo, different models coexist that give genes more or less important roles in the control of development and evolution. The gene regulatory network (GRN) model proposed by ... More


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