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The Build-a-Genome Course

Build-a-Genome is an intensive laboratory course at Johns Hopkins University that introduces undergraduates to the burgeoning field of synthetic biology. In addition to lectures that provide a comprehensive overview of the field, the course contains a unique laboratory component ...

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DNA Synthesis Security

It is generally assumed that genetic engineering advances will, inevitably, facilitate the misapplication of biotechnology toward the production of biological weapons. Unexpectedly, however, some of these very advances in the areas of DNA synthesis and sequencing may enable the i ...

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Scalable Computing for Evolutionary Genomics

Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of cal ...

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Sharing Programming Resources Between Biundefined Projects Through Remote Procedure Call and Native Call Stack Strategies

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality mul ...

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Genomics Data Resources: Frameworks and Standards

The emergence of genomics tools for the evolutionary and comparative biology community led to a rapid explosion in the number of online resources targeted at this specialized community, including Web-based comparative genomics software, such as the Artemis Comparison Tool (WebACT ...

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Genetical Genomics for Evolutionary Studies

Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitati ...

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Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases

This chapter describes bioinformatic tools for analyzing epigenome differences between species and in diseased versus normal cells. We illustrate the interplay of several Web-based tools in a case study of CpG island evolution between human and mouse. Starting from a list of orthologo ...

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Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN

Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Similarly, in metatranscriptomics and metaproteomics, the RNA and protein sequences of such samples are studied. The analysis of these kinds of data often starts by asking t ...

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Statistical Methods in Metabolomics

Metabolomics is the relatively new field in bioinformatics that uses measurements on metabolite abundance as a tool for disease diagnosis and other medical purposes. Although closely related to proteomics, the statistical analysis is potentially simpler since biochemists have ...

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Characterization and Evolutionary Analysis of ProteinProtein Interaction Networks

While researchers have known the importance of the protein–protein interaction for decades, recent innovations in large-scale screening techniques have caused a shift in the paradigm of protein function analysis. Where the focus was once on the individual protein, attention is now di ...

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Using Genomic Tools to Study Regulatory Evolution

Differences in gene regulation are thought to play an important role in speciation and adaptation. Comparative genomic studies of gene expression levels have identified a large number of differentially expressed genes among species, and, in a number of cases, also pointed to connections ...

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Nonredundant Representation of Ancestral Recombinations Graphs

The network structure that captures the common evolutionary history of a diploid population has been termed an ancestral recombinations graph. When the structure is a tree the number of internal nodes is usually where K is the number of samples. However, when the structure is not a tree, this number h ...

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Ancestral Population Genomics

The full genomes of several closely related species are now available, opening an emerging field of investigation borrowing both from population genetics and phylogenetics. Providing we can properly model sequence evolution within populations undergoing speciation events, ...

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Association Mapping and Disease: Evolutionary Perspectives

In this chapter, we give a short introduction to the genetics of complex disease with special emphasis on evolutionary models for disease genes and the effect of different models on the genetic architecture, and finally give a survey of the state-of-the-art of genome-wide association studie ...

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Estimating Recombination Rates from Genetic Variation in Humans

Recombination acts to shuffle the existing genetic variation within a population, leading to various approaches for detecting its action and estimating the rate at which it occurs. Here, we discuss the principal methodological and analytical approaches taken to understanding the d ...

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Evolution of Protein Domain Architectures

This chapter reviews the current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this directly impacts which domain architectures can be formed in different species. Studies relating domain family s ...

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The Origin and Evolution of New Genes

New genes are a major source of genetic innovation in genomes. However, until recently, understanding how new genes originate and how they evolve was hampered by the lack of appropriate genetic datasets. The advent of the genomic era brought about a revolution in the amount of data available to study ...

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Methods to Detect Selection on Noncoding DNA

Vast tracts of noncoding DNA contain elements that regulate gene expression in higher eukaryotes. Describing these regulatory elements and understanding how they evolve represent major challenges for biologists. Advances in the ability to survey genome-scale DNA sequence data ...

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Selection on the Protein-Coding Genome

Populations evolve as mutations arise in individual organisms and, through hereditary transmission, may become “fixed” (shared by all individuals) in the population. Most mutations are lethal or have negative fitness consequences for the organism. Others have essentially no effe ...

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Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

RNA viruses evolve very rapidly, often recombine, and are subject to strong host (immune response) and anthropogenic (antiretroviral drugs) selective forces. Given their compact and extensively sequenced genomes, comparative analysis of RNA viral data can provide important ins ...

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