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  1. Method

    Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

    We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation ch...

    Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin and Ekta Khurana

    Genome Biology 2017 18:141

    Published on: 27 July 2017

  2. Research

    Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

    The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence show...

    Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai…

    Genome Biology 2017 18:142

    Published on: 27 July 2017

  3. Method

    ReMixT: clone-specific genomic structure estimation in cancer

    Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequen...

    Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp and Sohrab P. Shah

    Genome Biology 2017 18:140

    Published on: 27 July 2017

  4. Research

    Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

    While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...

    Rurika Oka, Johan Zicola, Blaise Weber, Sarah N. Anderson, Charlie Hodgman, Jonathan I. Gent, Jan-Jaap Wesselink, Nathan M. Springer, Huub C. J. Hoefsloot, Franziska Turck and Maike Stam

    Genome Biology 2017 18:137

    Published on: 21 July 2017

  5. Research

    Characterization of background noise in capture-based targeted sequencing data

    Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are charact...

    Gahee Park, Joo Kyung Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung K. D. Kim, Yeon Jeong Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Hyuck Lee, Dae-Soon Son, Woong-Yang Park and Donghyun Park

    Genome Biology 2017 18:136

    Published on: 21 July 2017

  6. Research

    Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

    The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the eme...

    Catriona P. Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D. Bentley, Angela M. Kearns and Matthew T. G. Holden

    Genome Biology 2017 18:130

    Published on: 20 July 2017

  7. Research

    MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity

    Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we ...

    David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling…

    Genome Biology 2017 18:131

    Published on: 6 July 2017

  8. Correspondence

    Data normalization considerations for digital tumor dissection

    In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...

    Aaron M. Newman, Andrew J. Gentles, Chih Long Liu, Maximilian Diehn and Ash A. Alizadeh

    Genome Biology 2017 18:128

    Published on: 5 July 2017

  9. Correspondence

    Benchmarking: contexts and details matter

    Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Bio...

    Siyuan Zheng

    Genome Biology 2017 18:129

    Published on: 5 July 2017

  10. Research

    Strong epistatic and additive effects of linked candidate SNPs for Drosophila pigmentation have implications for analysis of genome-wide association studies results

    The mapping resolution of genome-wide association studies (GWAS) is limited by historic recombination events and effects are often assigned to haplotype blocks rather than individual SNPs. It is not clear how ...

    Jean-Michel Gibert, Jorge Blanco, Marlies Dolezal, Viola Nolte, Frédérique Peronnet and Christian Schlötterer

    Genome Biology 2017 18:126

    Published on: 3 July 2017

  11. Method

    NicE-seq: high resolution open chromatin profiling

    Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell...

    V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf and Sriharsa Pradhan

    Genome Biology 2017 18:122

    Published on: 28 June 2017

  12. 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

  13. Method

    Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

    Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, i...

    Louise Harewood, Kamal Kishore, Matthew D. Eldridge, Steven Wingett, Danita Pearson, Stefan Schoenfelder, V. Peter Collins and Peter Fraser

    Genome Biology 2017 18:125

    Published on: 27 June 2017

  14. 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

  15. 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

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