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  1. Q & A

    Heroes of peer review: Robert Lowe

    In the second of our series of articles celebrating peer reviewers, we talk to Robert Lowe, who is a Lecturer in computational biology at Queen Mary University of London, UK, and a valued reviewer for Genome Biol...

    Robert Lowe

    Genome Biology 2017 18:72

    Published on: 19 April 2017

  2. Research

    The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy

    Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates ...

    Andrej Trauner, Qingyun Liu, Laura E. Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England…

    Genome Biology 2017 18:71

    Published on: 19 April 2017

  3. Research

    Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort

    The gut microbiome is a complex and metabolically active community that directly influences host phenotypes. In this study, we profile gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finni...

    Elin Org, Yuna Blum, Silva Kasela, Margarete Mehrabian, Johanna Kuusisto, Antti J. Kangas, Pasi Soininen, Zeneng Wang, Mika Ala-Korpela, Stanley L. Hazen, Markku Laakso and Aldons J. Lusis

    Genome Biology 2017 18:70

    Published on: 13 April 2017

  4. Research

    Multi-tissue DNA methylation age predictor in mouse

    DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an un...

    Thomas M. Stubbs, Marc Jan Bonder, Anne-Katrien Stark, Felix Krueger, Ferdinand von Meyenn, Oliver Stegle and Wolf Reik

    Genome Biology 2017 18:68

    Published on: 11 April 2017

  5. Method

    DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

    Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methyl...

    Christof Angermueller, Heather J. Lee, Wolf Reik and Oliver Stegle

    Genome Biology 2017 18:67

    Published on: 11 April 2017

    The Erratum to this article has been published in Genome Biology 2017 18:90

  6. Method

    SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling

    Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues...

    Grace O. Silva, Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou and Mengjie Chen

    Genome Biology 2017 18:66

    Published on: 8 April 2017

  7. Opinion

    Structuring supplemental materials in support of reproducibility

    Supplements are increasingly important to the scientific record, particularly in genomics. However, they are often underutilized. Optimally, supplements should make results findable, accessible, interoperable,...

    Dov Greenbaum, Joel Rozowsky, Victoria Stodden and Mark Gerstein

    Genome Biology 2017 18:64

    Published on: 5 April 2017

  8. Q & A

    Coming out: the experience of LGBT+ people in STEM

    Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three openly LGBT+ researchers on their experiences in biology.

    Ben Barres, Beth Montague-Hellen and Jeremy Yoder

    Genome Biology 2017 18:62

    Published on: 4 April 2017

  9. Erratum

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

    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 18:63

    Published on: 4 April 2017

    The original article was published in Genome Biology 2017 18:27

  10. Research

    Functional implications of Neandertal introgression in modern humans

    Admixture between early modern humans and Neandertals approximately 50,000–60,000 years ago has resulted in 1.5–4% Neandertal ancestry in the genomes of present-day non-Africans. Evidence is accumulating that ...

    Michael Dannemann, Kay Prüfer and Janet Kelso

    Genome Biology 2017 18:61

    Published on: 3 April 2017

  11. Research

    Genomic history of the origin and domestication of common bean unveils its closest sister species

    Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domest...

    Martha Rendón-Anaya, Josaphat M. Montero-Vargas, Soledad Saburido-Álvarez, Anna Vlasova, Salvador Capella-Gutierrez, José Juan Ordaz-Ortiz, O. Mario Aguilar, Rosana P. Vianello-Brondani, Marta Santalla, Luis Delaye, Toni Gabaldón, Paul Gepts, Robert Winkler, Roderic Guigó, Alfonso Delgado-Salinas and Alfredo Herrera-Estrella

    Genome Biology 2017 18:60

    Published on: 29 March 2017

  12. Research

    Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment

    Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can a...

    Tina Wang, Brian Tsui, Jason F. Kreisberg, Neil A. Robertson, Andrew M. Gross, Michael Ku Yu, Hannah Carter, Holly M. Brown-Borg, Peter D. Adams and Trey Ideker

    Genome Biology 2017 18:57

    Published on: 28 March 2017

  13. Research

    Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism

    Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse species, including rodents. However, the mechanisms by w...

    Oliver Hahn, Sebastian Grönke, Thomas M. Stubbs, Gabriella Ficz, Oliver Hendrich, Felix Krueger, Simon Andrews, Qifeng Zhang, Michael J. Wakelam, Andreas Beyer, Wolf Reik and Linda Partridge

    Genome Biology 2017 18:56

    Published on: 28 March 2017

  14. Research

    Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions

    Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging “clock”, a robust biomarker of aging. However, while genetic, dietary and d...

    John J. Cole, Neil A. Robertson, Mohammed Iqbal Rather, John P. Thomson, Tony McBryan, Duncan Sproul, Tina Wang, Claire Brock, William Clark, Trey Ideker, Richard R. Meehan, Richard A. Miller, Holly M. Brown-Borg and Peter D. Adams

    Genome Biology 2017 18:58

    Published on: 28 March 2017

  15. Method

    CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA

    We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously inf...

    Shuli Kang, Qingjiao Li, Quan Chen, Yonggang Zhou, Stacy Park, Gina Lee, Brandon Grimes, Kostyantyn Krysan, Min Yu, Wei Wang, Frank Alber, Fengzhu Sun, Steven M. Dubinett, Wenyuan Li and Xianghong Jasmine Zhou

    Genome Biology 2017 18:53

    Published on: 24 March 2017

  16. Method

    cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes

    It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitativ...

    Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A. Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S. Liu and Junwen Wang

    Genome Biology 2017 18:52

    Published on: 16 March 2017

  17. Software

    IRFinder: assessing the impact of intron retention on mammalian gene expression

    Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing dat...

    Robert Middleton, Dadi Gao, Aubin Thomas, Babita Singh, Amy Au, Justin J-L Wong, Alexandra Bomane, Bertrand Cosson, Eduardo Eyras, John E. J. Rasko and William Ritchie

    Genome Biology 2017 18:51

    Published on: 15 March 2017

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