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  1. Method

    BRIE: transcriptome-wide splicing quantification in single cells

    Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity in transcription, but the limitations of the technology have prevented its application to dissect variability in RNA proces...

    Yuanhua Huang and Guido Sanguinetti

    Genome Biology 2017 18:123

    Published on: 27 June 2017

  2. Research Highlight

    Epigenomics: dissecting hybridization and polyploidization

    Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication a...

    Scott A. Jackson

    Genome Biology 2017 18:117

    Published on: 19 June 2017

  3. Review

    Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era

    Studies on genetic–epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in ...

    Catherine Do, Alyssa Shearer, Masako Suzuki, Mary Beth Terry, Joel Gelernter, John M. Greally and Benjamin Tycko

    Genome Biology 2017 18:120

    Published on: 19 June 2017

  4. Research

    Differentiated demographic histories and local adaptations between Sherpas and Tibetans

    The genetic relationships reported by recent studies between Sherpas and Tibetans are controversial. To gain insights into the population history and the genetic basis of high-altitude adaptation of the two gr...

    Chao Zhang, Yan Lu, Qidi Feng, Xiaoji Wang, Haiyi Lou, Jiaojiao Liu, Zhilin Ning, Kai Yuan, Yuchen Wang, Ying Zhou, Lian Deng, Lijun Liu, Yajun Yang, Shilin Li, Lifeng Ma, Zhiying Zhang…

    Genome Biology 2017 18:115

    Published on: 15 June 2017

  5. Research

    The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility

    Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and tem...

    Teddy Jégu, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M. Mahfouz…

    Genome Biology 2017 18:114

    Published on: 15 June 2017

  6. Correspondence

    Correspondence on Lovell et al.: response to Bornelöv et al.

    While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that ...

    Peter V. Lovell and Claudio V. Mello

    Genome Biology 2017 18:113

    Published on: 14 June 2017

  7. Research Highlight

    Epigenetic aging clocks in mice and men

    Epigenetic clocks provide powerful tools to evaluate nutritional, hormonal, and genetic effects on aging. What can we learn from differences between species in how these clocks tick?

    Wolfgang Wagner

    Genome Biology 2017 18:107

    Published on: 14 June 2017

  8. Correspondence

    Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

    Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that hav...

    Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Ken Pendavis, Shane C. Burgess, Manfred Grabherr, Miriam Friedman-Einat and Leif Andersson

    Genome Biology 2017 18:112

    Published on: 14 June 2017

  9. Method

    CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion

    CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exo...

    Haiwei Mou, Jordan L. Smith, Lingtao Peng, Hao Yin, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M. Ozata, Yingxiang Li, Daniel G. Anderson, Charles P. Emerson, Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng…

    Genome Biology 2017 18:108

    Published on: 14 June 2017

  10. Research

    “Like sugar in milk”: reconstructing the genetic history of the Parsi population

    The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations...

    Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G. Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi…

    Genome Biology 2017 18:110

    Published on: 14 June 2017

  11. Research

    Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

    The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversificat...

    Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A. M. Martin, Peter W. H. Holland, Simen R. Sandve and Daniel J. Macqueen

    Genome Biology 2017 18:111

    Published on: 14 June 2017

  12. Research

    Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements

    The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation ...

    Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter W. J. Rigby, Damien P. Devos, Jose L. Gómez-Skarmeta and Jaime J. Carvajal

    Genome Biology 2017 18:106

    Published on: 14 June 2017

  13. Research

    Multiple gene movements into and out of haploid sex chromosomes

    Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out f...

    Agnieszka P. Lipinska, Nicholas R. T. Toda, Svenja Heesch, Akira F. Peters, J. Mark Cock and Susana M. Coelho

    Genome Biology 2017 18:104

    Published on: 8 June 2017

  14. Research

    Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons

    Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produc...

    Qingxin Song, Tianzhen Zhang, David M. Stelly and Z. Jeffrey Chen

    Genome Biology 2017 18:99

    Published on: 31 May 2017

  15. Research

    The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

    The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and...

    Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He and Heng Zhang

    Genome Biology 2017 18:103

    Published on: 31 May 2017

  16. 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

  17. 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

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