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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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

  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. Content type: Research

    Inversion polymorphisms constitute an evolutionary puzzle: they should increase embryo mortality in heterokaryotypic individuals but still they are widespread in some taxa. Some insect species have evolved mec...

    Authors: Ulrich Knief, Georg Hemmrich-Stanisak, Michael Wittig, Andre Franke, Simon C. Griffith, Bart Kempenaers and Wolfgang Forstmeier

    Citation: Genome Biology 2016 17:199

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  21. Content type: Method

    We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific...

    Authors: Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower and Wayne I. Lencer

    Citation: Genome Biology 2016 17:201

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  22. 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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  23. Content type: Research

    Streptococcus pneumoniae, the pneumococcus, is the main etiological agent of pneumonia. Pneumococcal infection is initiated by bacterial adherence to lung epithelial cells. The exact t...

    Authors: Rieza Aprianto, Jelle Slager, Siger Holsappel and Jan-Willem Veening

    Citation: Genome Biology 2016 17:198

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  24. Content type: Research

    DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has bee...

    Authors: Chad E. Niederhuth, Adam J. Bewick, Lexiang Ji, Magdy S. Alabady, Kyung Do Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, John M. Burke, Joshua A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer and Robert J. Schmitz

    Citation: Genome Biology 2016 17:194

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  25. Content type: Research

    Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fa...

    Authors: Nina Koenecke, Jeff Johnston, Bjoern Gaertner, Malini Natarajan and Julia Zeitlinger

    Citation: Genome Biology 2016 17:196

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  26. Content type: Research

    Neuropsychiatric disorders are common forms of disability in humans. Despite recent progress in deciphering the genetics of these disorders, their phenotypic complexity continues to be a major challenge. Mende...

    Authors: Hanan E. Shamseldin, Ikuo Masuho, Ahmed Alenizi, Suad Alyamani, Dipak N. Patil, Niema Ibrahim, Kirill A. Martemyanov and Fowzan S. Alkuraya

    Citation: Genome Biology 2016 17:195

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  27. Content type: Research Highlight

    Schmitz and colleagues recently investigated DNA methylation patterns in diverse flowering plant species, finding substantial variation in the extent and distribution of methylation in angiosperms.

    Authors: Mary Gehring

    Citation: Genome Biology 2016 17:197

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  28. Content type: Research

    Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-...

    Authors: Michelle Beaumont, Julia K. Goodrich, Matthew A. Jackson, Idil Yet, Emily R. Davenport, Sara Vieira-Silva, Justine Debelius, Tess Pallister, Massimo Mangino, Jeroen Raes, Rob Knight, Andrew G. Clark, Ruth E. Ley, Tim D. Spector and Jordana T. Bell

    Citation: Genome Biology 2016 17:189

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  29. Content type: Research

    Advancing age progressively impacts on risk and severity of chronic disease. It also modifies the epigenome, with changes in DNA methylation, due to both random drift and variation within specific functional l...

    Authors: Christopher G. Bell, Yudong Xia, Wei Yuan, Fei Gao, Kirsten Ward, Leonie Roos, Massimo Mangino, Pirro G. Hysi, Jordana Bell, Jun Wang and Timothy D. Spector

    Citation: Genome Biology 2016 17:193

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  30. Content type: Research

    The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade a...

    Authors: Alexie Papanicolaou, Marc F. Schetelig, Peter Arensburger, Peter W. Atkinson, Joshua B. Benoit, Kostas Bourtzis, Pedro Castañera, John P. Cavanaugh, Hsu Chao, Christopher Childers, Ingrid Curril, Huyen Dinh, HarshaVardhan Doddapaneni, Amanda Dolan, Shannon Dugan, Markus Friedrich…

    Citation: Genome Biology 2016 17:192

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    The Erratum to this article has been published in Genome Biology 2017 18:11

  31. Content type: Research

    Epigenetic change is a hallmark of ageing but its link to ageing mechanisms in humans remains poorly understood. While DNA methylation at many CpG sites closely tracks chronological age, DNA methylation change...

    Authors: Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs H. Moed, Hailiang Mei, Michiel van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla J. H. van der Kallen…

    Citation: Genome Biology 2016 17:191

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  32. Content type: Method

    We show that variability in general levels of drug sensitivity in pre-clinical cancer models confounds biomarker discovery. However, using a very large panel of cell lines, each treated with many drugs, we cou...

    Authors: Paul Geeleher, Nancy J. Cox and R. Stephanie Huang

    Citation: Genome Biology 2016 17:190

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  33. Content type: Method

    We present a scalable, integrated strategy for coupled protein and RNA detection from single cells. Our approach leverages the DNA polymerase activity of reverse transcriptase to simultaneously perform proximi...

    Authors: Alex S Genshaft, Shuqiang Li, Caroline J. Gallant, Spyros Darmanis, Sanjay M. Prakadan, Carly G. K. Ziegler, Martin Lundberg, Simon Fredriksson, Joyce Hong, Aviv Regev, Kenneth J. Livak, Ulf Landegren and Alex K. Shalek

    Citation: Genome Biology 2016 17:188

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  34. Content type: Method

    Engineered endonucleases are a powerful tool for editing DNA. However, sequence preferences may limit their application. We engineer a structure-guided endonuclease (SGN) composed of flap endonuclease-1 (FEN-1...

    Authors: Shu Xu, Shasha Cao, Bingjie Zou, Yunyun Yue, Chun Gu, Xin Chen, Pei Wang, Xiaohua Dong, Zheng Xiang, Kai Li, Minsheng Zhu, Qingshun Zhao and Guohua Zhou

    Citation: Genome Biology 2016 17:186

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  35. Content type: Research

    The APOBEC3 family of cytidine deaminases mutate the cancer genome in a range of cancer types. Although many studies have documented the downstream effects of APOBEC3 activity through next-generation sequencin...

    Authors: Nnennaya Kanu, Maria Antonietta Cerone, Gerald Goh, Lykourgos-Panagiotis Zalmas, Jirina Bartkova, Michelle Dietzen, Nicholas McGranahan, Rebecca Rogers, Emily K. Law, Irina Gromova, Maik Kschischo, Michael I. Walton, Olivia W. Rossanese, Jiri Bartek, Reuben S. Harris, Subramanian Venkatesan…

    Citation: Genome Biology 2016 17:185

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  36. Content type: Research Highlight

    The search for novel ways to target and alter the genomes of living organisms accelerated rapidly this decade with the discovery of CRISPR/Cas9. Since the initial discovery, efforts to find alternative methods...

    Authors: Gaurav K. Varshney and Shawn M. Burgess

    Citation: Genome Biology 2016 17:187

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  37. Content type: Research

    A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their rel...

    Authors: Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, Daniel D’Andrea, Rosalba Lepore, Christopher S. Funk, Indika Kahanda, Karin M. Verspoor, Asa Ben-Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin…

    Citation: Genome Biology 2016 17:184

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  38. Content type: Review

    We are entering an era of epigenome engineering. The precision manipulation of chromatin and epigenetic modifications provides new ways to interrogate their influence on genome and cell function and to harness...

    Authors: Minhee Park, Albert J. Keung and Ahmad S. Khalil

    Citation: Genome Biology 2016 17:183

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  39. Content type: Research

    Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and ...

    Authors: Liis Uusküla-Reimand, Huayun Hou, Payman Samavarchi-Tehrani, Matteo Vietri Rudan, Minggao Liang, Alejandra Medina-Rivera, Hisham Mohammed, Dominic Schmidt, Petra Schwalie, Edwin J. Young, Jüri Reimand, Suzana Hadjur, Anne-Claude Gingras and Michael D. Wilson

    Citation: Genome Biology 2016 17:182

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  40. Content type: Research

    Schizophrenia is a highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia,...

    Authors: Eilis Hannon, Emma Dempster, Joana Viana, Joe Burrage, Adam R. Smith, Ruby Macdonald, David St Clair, Colette Mustard, Gerome Breen, Sebastian Therman, Jaakko Kaprio, Timothea Toulopoulou, Hilleke E. Hulshoff Pol, Marc M. Bohlken, Rene S. Kahn, Igor Nenadic…

    Citation: Genome Biology 2016 17:176

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  41. Content type: Method

    Duplex sequencing was originally developed to detect rare nucleotide polymorphisms normally obscured by the noise of high-throughput sequencing. Here we describe a new, streamlined, reference-free approach for...

    Authors: Nicholas Stoler, Barbara Arbeithuber, Wilfried Guiblet, Kateryna D. Makova and Anton Nekrutenko

    Citation: Genome Biology 2016 17:180

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