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  1. Software

    Millstone: software for multiplex microbial genome analysis and engineering

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a...

    Daniel B. Goodman, Gleb Kuznetsov, Marc J. Lajoie, Brian W. Ahern, Michael G. Napolitano, Kevin Y. Chen, Changping Chen and George M. Church

    Genome Biology 2017 18:101

    Published on: 25 May 2017

  2. Method

    Optimizing complex phenotypes through model-guided multiplex genome engineering

    We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide m...

    Gleb Kuznetsov, Daniel B. Goodman, Gabriel T. Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J. Lajoie and George M. Church

    Genome Biology 2017 18:100

    Published on: 25 May 2017

  3. Research

    N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration

    Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that ...

    Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu…

    Genome Biology 2017 18:98

    Published on: 24 May 2017

  4. Research Highlight

    Going beyond genetics to discover cancer targets

    Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.

    Gabriel J. Sandoval and William C. Hahn

    Genome Biology 2017 18:95

    Published on: 22 May 2017

  5. Research

    A comparative evaluation of genome assembly reconciliation tools

    The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or par...

    Hind Alhakami, Hamid Mirebrahim and Stefano Lonardi

    Genome Biology 2017 18:93

    Published on: 18 May 2017

  6. Research

    The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana

    Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enri...

    Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen and Frédéric Berger

    Genome Biology 2017 18:94

    Published on: 18 May 2017

  7. Research

    Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins

    Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Condit...

    Rolen M. Quadros, Hiromi Miura, Donald W. Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P. Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M. Buckley, Parthasarathy Seshacharyulu, Surinder K. Batra, Mark A. Behlke, Sarah A. Zeiner, Ashley M. Jacobi…

    Genome Biology 2017 18:92

    Published on: 17 May 2017

  8. Meeting Report

    Missing heritability and where to find it

    A report on the 11th Genomics of Rare Disease meeting held at the Wellcome Genome Campus, Hinxton, Cambridge, UK, 5–7 April, 2017.

    Santhosh Girirajan

    Genome Biology 2017 18:89

    Published on: 11 May 2017

  9. Correspondence

    Horizontal gene transfer is not a hallmark of the human genome

    Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been...

    Steven L. Salzberg

    Genome Biology 2017 18:85

    Published on: 8 May 2017

  10. Open Letter

    Challenges and emerging directions in single-cell analysis

    Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enable...

    Guo-Cheng Yuan, Long Cai, Michael Elowitz, Tariq Enver, Guoping Fan, Guoji Guo, Rafael Irizarry, Peter Kharchenko, Junhyong Kim, Stuart Orkin, John Quackenbush, Assieh Saadatpour, Timm Schroeder, Ramesh Shivdasani and Itay Tirosh

    Genome Biology 2017 18:84

    Published on: 8 May 2017

  11. Review

    Multi-omics approaches to disease

    High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which ...

    Yehudit Hasin, Marcus Seldin and Aldons Lusis

    Genome Biology 2017 18:83

    Published on: 5 May 2017

  12. Research

    Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana

    Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arab...

    Fernando A. Rabanal, Terezie Mandáková, Luz M. Soto-Jiménez, Robert Greenhalgh, David L. Parrott, Stefan Lutzmayer, Joshua G. Steffen, Viktoria Nizhynska, Richard Mott, Martin A. Lysak, Richard M. Clark and Magnus Nordborg

    Genome Biology 2017 18:75

    Published on: 3 May 2017

  13. Research

    PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice

    Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression b...

    Emily Maclary, Michael Hinten, Clair Harris, Shriya Sethuraman, Srimonta Gayen and Sundeep Kalantry

    Genome Biology 2017 18:82

    Published on: 3 May 2017

  14. Research

    The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants

    The evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridipl...

    Adam J. Bewick, Chad E. Niederhuth, Lexiang Ji, Nicholas A. Rohr, Patrick T. Griffin, Jim Leebens-Mack and Robert J. Schmitz

    Genome Biology 2017 18:65

    Published on: 1 May 2017

  15. Research

    Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance

    Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutatio...

    Gustavo C. Cerqueira, Ian H. Cheeseman, Steve F. Schaffner, Shalini Nair, Marina McDew-White, Aung Pyae Phyo, Elizabeth A. Ashley, Alexandre Melnikov, Peter Rogov, Bruce W. Birren, François Nosten, Timothy J. C. Anderson and Daniel E. Neafsey

    Genome Biology 2017 18:78

    Published on: 28 April 2017

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