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  1. Research

    Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome

    Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies.

    Ryan L. Collins, Harrison Brand, Claire E. Redin, Carrie Hanscom, Caroline Antolik, Matthew R. Stone, Joseph T. Glessner, Tamara Mason, Giulia Pregno, Naghmeh Dorrani, Giorgia Mandrile, Daniela Giachino, Danielle Perrin, Cole Walsh, Michelle Cipicchio, Maura Costello…

    Genome Biology 2017 18:36

    Published on: 6 March 2017

  2. Erratum

    Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

    Yasin Şenbabaoğlu, Ron S. Gejman, Andrew G. Winer, Ming Liu, Eliezer M. Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon J. Manley, Danny N. Khalil, Samuel D. Kaffenberger, Yingbei Chen…

    Genome Biology 2017 18:46

    Published on: 1 March 2017

    The original article was published in Genome Biology 2016 17:231

  3. Method

    Single-cell transcriptome conservation in cryopreserved cells and tissues

    A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains t...

    Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, Maria Mendez-Lago, Diego A. Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Marti, Enriqueta Felip, Ana Vivancos, Hadas Keren-Shaul, Simon Heath, Marta Gut, Ido Amit, Ivo Gut and Holger Heyn

    Genome Biology 2017 18:45

    Published on: 1 March 2017

  4. METHOD

    BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most me...

    Ines de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A. J. Ponder, Kerstin B. Meyer and Florian Markowetz

    Genome Biology 2017 18:39

    Published on: 24 February 2017

  5. METHOD

    epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data

    The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We dev...

    Martin Vincent, Kamilla Mundbjerg, Jakob Skou Pedersen, Gangning Liang, Peter A. Jones, Torben Falck Ørntoft, Karina Dalsgaard Sørensen and Carsten Wiuf

    Genome Biology 2017 18:38

    Published on: 21 February 2017

  6. Research

    Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage

    Precise genome editing via homology-directed repair (HDR) after double-stranded DNA (dsDNA) cleavage facilitates functional genomic research and holds promise for gene therapy. However, HDR efficiency remains ...

    Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D. Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng and Xiao-Bing Zhang

    Genome Biology 2017 18:35

    Published on: 20 February 2017

  7. Research

    Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

    Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyplo...

    Lei Fang, Hao Gong, Yan Hu, Chunxiao Liu, Baoliang Zhou, Tao Huang, Yangkun Wang, Shuqi Chen, David D. Fang, Xiongming Du, Hong Chen, Jiedan Chen, Sen Wang, Qiong Wang, Qun Wan, Bingliang Liu…

    Genome Biology 2017 18:33

    Published on: 20 February 2017

  8. Research

    RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells

    Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other’s e...

    Carla Bosia, Francesco Sgrò, Laura Conti, Carlo Baldassi, Davide Brusa, Federica Cavallo, Ferdinando Di Cunto, Emilia Turco, Andrea Pagnani and Riccardo Zecchina

    Genome Biology 2017 18:37

    Published on: 20 February 2017

  9. Research

    The genome landscape of indigenous African cattle

    The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step...

    Jaemin Kim, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Salim Bashir, Boubacar Diallo, Morris Agaba, Kwondo Kim, Woori Kwak, Samsun Sung, Minseok Seo, Hyeonsoo Jeong, Taehyung Kwon, Mengistie Taye, Ki-Duk Song, Dajeong Lim…

    Genome Biology 2017 18:34

    Published on: 20 February 2017

  10. Research Highlight

    Mouse genomic screen reveals novel host regulator of metastasis

    Tumor cells have to overcome challenges in the host tissue microenvironment to metastasize successfully to distant organs. In a recent Nature study, a genome-wide functional screen demonstrated that deficiency of...

    Toni Celià-Terrassa and Yibin Kang

    Genome Biology 2017 18:31

    Published on: 16 February 2017

  11. Research

    RNF40 regulates gene expression in an epigenetic context-dependent manner

    Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an ex...

    Wanhua Xie, Sankari Nagarajan, Simon J. Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri and Steven A. Johnsen

    Genome Biology 2017 18:32

    Published on: 16 February 2017

  12. Research

    Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

    The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contamina...

    Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Özgür Bayram, Tiziano Benocci, Susanna A. Braus-Stromeyer, Camila Caldana, David Cánovas…

    Genome Biology 2017 18:28

    Published on: 14 February 2017

  13. Research

    Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

    The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a sm...

    Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca…

    Genome Biology 2017 18:27

    Published on: 13 February 2017

    The Erratum to this article has been published in Genome Biology 2017 18:63

  14. Review

    Software tools for visualizing Hi-C data

    High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation fr...

    Galip Gürkan Yardımcı and William Stafford Noble

    Genome Biology 2017 18:26

    Published on: 3 February 2017

  15. Research

    Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects

    The CRISPR-Cas9 system is a widely utilized platform for transgenic animal production in various species, although its off-target effects should be addressed. Several applications of this tool have been propos...

    Yuanpeng Gao, Haibo Wu, Yongsheng Wang, Xin Liu, Linlin Chen, Qian Li, Chenchen Cui, Xu Liu, Jingcheng Zhang and Yong Zhang

    Genome Biology 2017 18:13

    Published on: 1 February 2017

  16. Correspondence

    Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies

    Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methyl...

    Mohammad W. Hattab, Andrey A. Shabalin, Shaunna L. Clark, Min Zhao, Gaurav Kumar, Robin F. Chan, Lin Ying Xie, Rick Jansen, Laura K. M. Han, Patrik K. E. Magnusson, Gerard van Grootheest, Christina M. Hultman, Brenda W. J. H. Penninx, Karolina A. Aberg and Edwin J. C. G. van den Oord

    Genome Biology 2017 18:24

    Published on: 30 January 2017

  17. Correspondence

    Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies

    We thank Hattab and colleagues for their correspondence and their investigation of cell-type mixture correction methods in methyl-CG binding domain sequencing. Here, we speculate on why surrogate variable anal...

    Kevin McGregor, Aurélie Labbe and Celia M. T. Greenwood

    Genome Biology 2017 18:25

    Published on: 30 January 2017

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