Nature Reviews Genetics Contents March 2015 Volume 16 Number 3 pp 127-192

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TABLE OF CONTENTS
March 2015 Volume 16 Number 3
Impact Factor 39.794 *	In this issue Research Highlights Reviews Analysis Perspectives Also this month Article series: Single-cell omics Modelling Modes of transcriptional regulation  Featured article: A copy number variation map of the human genome Mehdi Zarrei, Jeffrey R. MacDonald, Daniele Merico & Stephen W. Scherer
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RESEARCH HIGHLIGHTS Top Synthetic biology: GMOs in lockdown p127 | doi:10.1038/nrg3909 PDF Human evolution: Phoneme–genome data set evolves p128 | doi:10.1038/nrg3911 PDF Gene expression: Layers of gene regulation p128 | doi:10.1038/nrg3918 PDF Gene expression: Spatial characterization of proteomes p129 | doi:10.1038/nrg3910 PDF Gene therapy: Insulating from genotoxicity p130 | doi:10.1038/nrg3904 PDF Cancer genetics: Omics analyses of tumour immunity p130 | doi:10.1038/nrg3906 PDF Disease genomics: Autism sibling differences p130 | doi:10.1038/nrg3907 PDF IN BRIEF Pathogen genetics: Evolution of host-adapted pathogens | Plant genomics: Maize evolution and spread | Human evolution: mtDNA and genetic ancestry | Genetic testing: Classifying pathogenic variation | Functional genomics: Multiallelic copy number variation | Model organisms: Updated Drosophila reference sequence PDF Genetics JOBS of the week PhD positions in Population Genetics Vienna Graduate School of Population Genetics Deputy Director- Division of Cancer Epidemiology and Genetics National Cancer Institute (NCI), National Institutes of Health (NIH) Postdoctoral Position in Molecular Biology and Genetics South Dakota State University Professor of Animal Genetics ETH Zurich Endowed Chair in Molecular Genetics University of Arizona in Tucson More Science jobs from Genetics EVENT Yeast Genetics & Genomics 21.07.15 Cold Spring Harbour, USA More science events from
REVIEWS		Top
Article series: Single-cell omics Computational and analytical challenges in single-cell transcriptomics Oliver Stegle, Sarah A. Teichmann & John C. Marioni p133 | doi:10.1038/nrg3833 High-throughput RNA sequencing (RNA-seq) is a powerful method for transcriptome-wide analysis that has recently been applied to single cells. This Review discusses the analytical and computational challenges of processing and analysing single-cell RNA-seq data, paying special consideration to differences relative to the analysis of RNA-seq data generated from bulk cell populations and discussing how single-cell-specific biological insights can be obtained. Abstract | Full Text | PDF
Article series: Modelling Quantitative and logic modelling of molecular and gene networks Nicolas Le Novère p146 | doi:10.1038/nrg3885 The use of mathematical modelling to elucidate genetic, molecular and cellular processes is an integral part of systems biology. This Review presents the main methods to model and simulate molecular and gene networks (kinetic and logic modelling), describes their inherent advantages and limitations, and highlights recent developments that reveal the potential of hybrid approaches. Abstract | Full Text | PDF
Article series: Modes of transcriptional regulation Chromatin regulation at the frontier of synthetic biology Albert J. Keung, J. Keith Joung, Ahmad S. Khalil & James J. Collins p159 | doi:10.1038/nrg3900 Synthetic biology approaches to characterize gene regulation have largely used transcription factor circuits in bacteria. However, the multilayered regulation of genes by chromatin in eukaryotes provides opportunities for more sophisticated control of gene expression. This Review describes diverse approaches for engineering eukaryotic chromatin states, the insights gained into physiological gene regulation principles, and the broad potential applications throughout biomedical research and industry. Abstract | Full Text | PDF
ANALYSIS		Top
A copy number variation map of the human genome Mehdi Zarrei, Jeffrey R. MacDonald, Daniele Merico & Stephen W. Scherer p172 | doi:10.1038/nrg3871 Copy number variation (CNV) accounts for much of the variability across genomes and can influence phenotypes. In this Analysis, the authors construct a CNV map using high-quality data from published studies to provide more detailed insights into CNV, which will be useful for both clinical and research applications in the future. Abstract | Full Text | PDF | Supplementary information
PERSPECTIVES		Top
OPINION Evolution of adaptive immunity from transposable elements combined with innate immune systems Eugene V. Koonin & Mart Krupovic p184 | doi:10.1038/nrg3859 Transposable elements are key drivers of evolutionary innovation across many species. This Opinion article proposes evolutionary scenarios in which transposable elements have acted on innate immunity loci to generate adaptive immune systems and discusses striking parallels between the evolution of different adaptive immune systems: CRISPR-Cas in bacteria and archaea, and V(D)J recombination in vertebrates. Abstract | Full Text | PDF
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Nature Insight Frontiers in biology This year's Frontiers in Biology Insight covers the amygdala and how technology is helping us to understand its complex connectivity, innate lymphoid cells, nutrient-sensing mechanisms in mammals, a form of cell death called necroptosis, and the regulation and function of DNA methylation and its use as a cellular marker.  Access the Insight online.
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