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  1. Content type: Research

    Despite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, a...

    Authors: Irfahan Kassam, Luke Lloyd-Jones, Alexander Holloway, Kerrin S. Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Greg Gibson, Tim D. Spector, Tonu Esko, Grant W. Montgomery, Joseph E. Powell, Jian Yang, Peter M. Visscher and Allan F. McRae

    Citation: Genome Biology 2016 17:248

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  2. Content type: Erratum

    Authors: Etienne Becht, Nicolas A. Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Selves, Pierre Laurent-Puig, Catherine Sautès-Fridman, Wolf H. Fridman and Aurélien de Reyniès

    Citation: Genome Biology 2016 17:249

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    The original article was published in Genome Biology 2016 17:218

  3. Content type: Research

    Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate ...

    Authors: Claartje A. Meddens, Magdalena Harakalova, Noortje A. M. van den Dungen, Hassan Foroughi Asl, Hemme J. Hijma, Edwin P. J. G. Cuppen, Johan L. M. Björkegren, Folkert W. Asselbergs, Edward E. S. Nieuwenhuis and Michal Mokry

    Citation: Genome Biology 2016 17:247

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  4. Content type: Research

    Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients recei...

    Authors: Stefanie Eggers, Simon Sadedin, Jocelyn A. van den Bergen, Gorjana Robevska, Thomas Ohnesorg, Jacqueline Hewitt, Luke Lambeth, Aurore Bouty, Ingrid M. Knarston, Tiong Yang Tan, Fergus Cameron, George Werther, John Hutson, Michele O’Connell, Sonia R. Grover, Yves Heloury…

    Citation: Genome Biology 2016 17:243

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  5. Content type: Research

    The 2’-5’ oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; ye...

    Authors: Aaron J. Sams, Anne Dumaine, Yohann Nédélec, Vania Yotova, Carolina Alfieri, Jerome E. Tanner, Philipp W. Messer and Luis B. Barreiro

    Citation: Genome Biology 2016 17:246

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  6. Content type: Research

    The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were u...

    Authors: Robert VanBuren, Ching Man Wai, Jisen Zhang, Jennifer Han, Jie Arro, Zhicong Lin, Zhenyang Liao, Qingyi Yu, Ming-Li Wang, Francis Zee, Richard C. Moore, Deborah Charlesworth and Ray Ming

    Citation: Genome Biology 2016 17:230

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  7. Content type: Research

    Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge...

    Authors: Ranad Shaheen, Katarzyna Szymanska, Basudha Basu, Nisha Patel, Nour Ewida, Eissa Faqeih, Amal Al Hashem, Nada Derar, Hadeel Alsharif, Mohammed A. Aldahmesh, Anas M. Alazami, Mais Hashem, Niema Ibrahim, Firdous M. Abdulwahab, Rawda Sonbul, Hisham Alkuraya…

    Citation: Genome Biology 2016 17:242

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  8. Content type: Software

    Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely...

    Authors: Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer and Vegard Eldholm

    Citation: Genome Biology 2016 17:238

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    The Erratum to this article has been published in Genome Biology 2016 17:262

  9. Content type: Research

    The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying differe...

    Authors: Michal Malecki, Danny A. Bitton, Maria Rodríguez-López, Charalampos Rallis, Noelia Garcia Calavia, Graeme C. Smith and Jürg Bähler

    Citation: Genome Biology 2016 17:240

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  10. Content type: Opinion

    Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize k...

    Authors: Miten Jain, Hugh E. Olsen, Benedict Paten and Mark Akeson

    Citation: Genome Biology 2016 17:239

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    The Erratum to this article has been published in Genome Biology 2016 17:256

  11. Content type: Research

    Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene–environment interactions. Whole genome sequence analysis of amino acid levels may ...

    Authors: Bing Yu, Paul S. de Vries, Ginger A. Metcalf, Zhe Wang, Elena V. Feofanova, Xiaoming Liu, Donna Marie Muzny, Lynne E. Wagenknecht, Richard A. Gibbs, Alanna C. Morrison and Eric Boerwinkle

    Citation: Genome Biology 2016 17:237

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  12. Content type: Research

    The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign “disease mutations” are difficult to analyze due to their rarity. The Saudi Ara...

    Authors: Mohamed Abouelhoda, Tariq Faquih, Mohamed El-Kalioby and Fowzan S. Alkuraya

    Citation: Genome Biology 2016 17:235

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  13. Content type: Research

    Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their eff...

    Authors: Lorenzo de la Rica, Özgen Deniz, Kevin C. L. Cheng, Christopher D. Todd, Cristina Cruz, Jonathan Houseley and Miguel R. Branco

    Citation: Genome Biology 2016 17:234

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  14. Content type: Research

    Tumor-infiltrating immune cells have been linked to prognosis and response to immunotherapy; however, the levels of distinct immune cell subsets and the signals that draw them into a tumor, such as the express...

    Authors: 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…

    Citation: Genome Biology 2016 17:231

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    The Erratum to this article has been published in Genome Biology 2017 18:46

  15. Content type: Opinion

    Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare,...

    Authors: Nicholas Katsanis

    Citation: Genome Biology 2016 17:233

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  16. Content type: METHOD

    Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a p...

    Authors: Kai Wei, Maxwell W. Libbrecht, Jeffrey A. Bilmes and William Stafford Noble

    Citation: Genome Biology 2016 17:229

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  17. Content type: Research

    Autism spectrum disorder (ASD) is a common neurodevelopmental disorder that tends to co-occur with other diseases, including asthma, inflammatory bowel disease, infections, cerebral palsy, dilated cardiomyopat...

    Authors: Sumaiya Nazeen, Nathan P. Palmer, Bonnie Berger and Isaac S. Kohane

    Citation: Genome Biology 2016 17:228

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  18. Content type: Research

    Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes,...

    Authors: Duane D. McKenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung-Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla…

    Citation: Genome Biology 2016 17:227

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  19. Content type: Research

    There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to ...

    Authors: Soonok Kim, Yun Sung Cho, Hak-Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim…

    Citation: Genome Biology 2016 17:211

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  20. Content type: Research

    The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potentia...

    Authors: Amanda McGovern, Stefan Schoenfelder, Paul Martin, Jonathan Massey, Kate Duffus, Darren Plant, Annie Yarwood, Arthur G. Pratt, Amy E. Anderson, John D. Isaacs, Julie Diboll, Nishanthi Thalayasingam, Caroline Ospelt, Anne Barton, Jane Worthington, Peter Fraser…

    Citation: Genome Biology 2016 17:212

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  21. Content type: Method

    Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approa...

    Authors: Javier Sánchez-Martín, Burkhard Steuernagel, Sreya Ghosh, Gerhard Herren, Severine Hurni, Nikolai Adamski, Jan Vrána, Marie Kubaláková, Simon G. Krattinger, Thomas Wicker, Jaroslav Doležel, Beat Keller and Brande B. H. Wulff

    Citation: Genome Biology 2016 17:221

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  22. Content type: Research

    Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The...

    Authors: Anthony J. Studer, James C. Schnable, Sarit Weissmann, Allison R. Kolbe, Michael R. McKain, Ying Shao, Asaph B. Cousins, Elizabeth A. Kellogg and Thomas P. Brutnell

    Citation: Genome Biology 2016 17:223

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  23. Content type: METHOD

    The ability to quantify cellular heterogeneity is a major advantage of single-cell technologies. However, statistical methods often treat cellular heterogeneity as a nuisance. We present a novel method to char...

    Authors: Keegan D. Korthauer, Li-Fang Chu, Michael A. Newton, Yuan Li, James Thomson, Ron Stewart and Christina Kendziorski

    Citation: Genome Biology 2016 17:222

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  24. Content type: Research

    Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous rep...

    Authors: Mansoureh Tajaddod, Andrea Tanzer, Konstantin Licht, Michael T. Wolfinger, Stefan Badelt, Florian Huber, Oliver Pusch, Sandy Schopoff, Michael Janisiw, Ivo Hofacker and Michael F. Jantsch

    Citation: Genome Biology 2016 17:220

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  25. Content type: Research

    In order to become functionally competent but harmless mediators of the immune system, T cells undergo a strict educational program in the thymus, where they learn to discriminate between self and non-self. Th...

    Authors: Miri Danan-Gotthold, Clotilde Guyon, Matthieu Giraud, Erez Y. Levanon and Jakub Abramson

    Citation: Genome Biology 2016 17:219

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  26. Content type: Method

    We introduce the Microenvironment Cell Populations-counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneo...

    Authors: Etienne Becht, Nicolas A. Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Selves, Pierre Laurent-Puig, Catherine Sautès-Fridman, Wolf H. Fridman and Aurélien de Reyniès

    Citation: Genome Biology 2016 17:218

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    The Erratum to this article has been published in Genome Biology 2016 17:249

  27. Content type: Review

    Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect size...

    Authors: Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez and Rob Knight

    Citation: Genome Biology 2016 17:217

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  28. Content type: Review

    Chromosome conformation capture (3C)-based techniques have revolutionized the field of nuclear organization, partly replacing DNA FISH as the method of choice for studying three-dimensional chromosome architec...

    Authors: Luca Giorgetti and Edith Heard

    Citation: Genome Biology 2016 17:215

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  29. Content type: METHOD

    We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on ...

    Authors: Kevin A. McGoff, Xin Guo, Anastasia Deckard, Christina M. Kelliher, Adam R. Leman, Lauren J. Francey, John B. Hogenesch, Steven B. Haase and John L. Harer

    Citation: Genome Biology 2016 17:214

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  30. Content type: Research Highlight

    A new mitotic clock and mathematical approach that incorporates DNA methylation biology common among human cell types provides a new tool for cancer epigenetics research.

    Authors: Brock C. Christensen and Karl T. Kelsey

    Citation: Genome Biology 2016 17:216

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  31. Content type: Research

    The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contain...

    Authors: Björn Pietzenuk, Catarine Markus, Hervé Gaubert, Navratan Bagwan, Aldo Merotto, Etienne Bucher and Ales Pecinka

    Citation: Genome Biology 2016 17:209

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  32. Content type: Research

    In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements...

    Authors: Ruth Pidsley, Elena Zotenko, Timothy J. Peters, Mitchell G. Lawrence, Gail P. Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker and Susan J. Clark

    Citation: Genome Biology 2016 17:208

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  33. Content type: Research

    Gestational age is often used as a proxy for developmental maturity by clinicians and researchers alike. DNA methylation has previously been shown to be associated with age and has been used to accurately esti...

    Authors: Anna K. Knight, Jeffrey M. Craig, Christiane Theda, Marie Bækvad-Hansen, Jonas Bybjerg-Grauholm, Christine S. Hansen, Mads V. Hollegaard, David M. Hougaard, Preben B. Mortensen, Shantel M. Weinsheimer, Thomas M. Werge, Patricia A. Brennan, Joseph F. Cubells, D. Jeffrey Newport, Zachary N. Stowe, Jeanie L. Y. Cheong…

    Citation: Genome Biology 2016 17:206

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  34. Content type: Research

    We explored the association between gestational age and cord blood DNA methylation at birth and whether DNA methylation could be effective in predicting gestational age due to limitations with the presently us...

    Authors: J. Bohlin, S. E. Håberg, P. Magnus, S. E. Reese, H. K. Gjessing, M. C. Magnus, C. L. Parr, C. M. Page, S. J. London and W. Nystad

    Citation: Genome Biology 2016 17:207

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  35. Content type: Research

    Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be...

    Authors: Zhen Yang, Andrew Wong, Diana Kuh, Dirk S. Paul, Vardhman K. Rakyan, R. David Leslie, Shijie C. Zheng, Martin Widschwendter, Stephan Beck and Andrew E. Teschendorff

    Citation: Genome Biology 2016 17:205

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  36. Content type: Q and A

    Peer reviewers are the unsung heroes of science. We celebrate reviewers through a series of interviews with people who have made particularly strong recent contributions to Genome Biology as reviewers. The first ...

    Authors: Hyongbum Kim

    Citation: Genome Biology 2016 17:200

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