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Page 10 of 125

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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

  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. Content type: Erratum

    Authors: Claire Morandin, Mandy M. Y. Tin, Sílvia Abril, Crisanto Gómez, Luigi Pontieri, Morten Schiøtt, Liselotte Sundstrom, Kazuki Tsuji, Jes Søe Pedersen, Heikki Helantera and Alexander S. Mikheyev

    Citation: Genome Biology 2016 17:179

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    The original article was published in Genome Biology 2016 17:43

  24. Content type: METHOD

    Subclonal mutations reveal important features of the genetic architecture of tumors. However, accurate detection of mutations in genetically heterogeneous tumor cell populations using next-generation sequencin...

    Authors: Yu Fan, Liu Xi, Daniel S. T. Hughes, Jianjun Zhang, Jianhua Zhang, P. Andrew Futreal, David A. Wheeler and Wenyi Wang

    Citation: Genome Biology 2016 17:178

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  25. Content type: Comment

    The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that appr...

    Authors: Mark Ziemann, Yotam Eren and Assam El-Osta

    Citation: Genome Biology 2016 17:177

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  26. Content type: Research

    Understanding the interactions between tumor and the host immune system is critical to finding prognostic biomarkers, reducing drug resistance, and developing new therapies. Novel computational methods are nee...

    Authors: Bo Li, Eric Severson, Jean-Christophe Pignon, Haoquan Zhao, Taiwen Li, Jesse Novak, Peng Jiang, Hui Shen, Jon C. Aster, Scott Rodig, Sabina Signoretti, Jun S. Liu and X. Shirley Liu

    Citation: Genome Biology 2016 17:174

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  27. Content type: Research Highlight

    Understanding a tumor’s complex cellular heterogeneity will be crucial for the development of better treatment strategies. A new study suggests a novel method for the in silico dissociation of solid tumors and...

    Authors: Dvir Aran and Atul J. Butte

    Citation: Genome Biology 2016 17:175

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  28. Content type: Research

    Human pluripotent stem cells offer the best available model to study the underlying cellular and molecular mechanisms of human embryonic lineage specification. However, it is not fully understood how individua...

    Authors: Li-Fang Chu, Ning Leng, Jue Zhang, Zhonggang Hou, Daniel Mamott, David T. Vereide, Jeea Choi, Christina Kendziorski, Ron Stewart and James A. Thomson

    Citation: Genome Biology 2016 17:173

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  29. Content type: Research

    Epigenetic biomarkers of aging (the “epigenetic clock”) have the potential to address puzzling findings surrounding mortality rates and incidence of cardio-metabolic disease such as: (1) women consistently exh...

    Authors: Steve Horvath, Michael Gurven, Morgan E. Levine, Benjamin C. Trumble, Hillard Kaplan, Hooman Allayee, Beate R. Ritz, Brian Chen, Ake T. Lu, Tammy M. Rickabaugh, Beth D. Jamieson, Dianjianyi Sun, Shengxu Li, Wei Chen, Lluis Quintana-Murci, Maud Fagny…

    Citation: Genome Biology 2016 17:171

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  30. Content type: Research

    Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM). In plants, canonical RdDM functions through RNA poly...

    Authors: Kaushik Panda, Lexiang Ji, Drexel A. Neumann, Josquin Daron, Robert J. Schmitz and R. Keith Slotkin

    Citation: Genome Biology 2016 17:170

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  31. Content type: Research

    The Mouse Genomes Project is an ongoing collaborative effort to sequence the genomes of the common laboratory mouse strains. In 2011, the initial analysis of sequence variation across 17 strains found 56.7 M u...

    Authors: Anthony G. Doran, Kim Wong, Jonathan Flint, David J. Adams, Kent W. Hunter and Thomas M. Keane

    Citation: Genome Biology 2016 17:167

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  32. Content type: Research

    Examples of heterozygote advantage in humans are scarce and limited to protein-coding sequences. Here, we attempt a genome-wide functional inference of advantageous heterozygosity at cis-regulatory regions.

    Authors: Min Kyung Sung, Juneil Jang, Kang Seon Lee, Cheol-Min Ghim and Jung Kyoon Choi

    Citation: Genome Biology 2016 17:164

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  33. Content type: Research

    The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonom...

    Authors: Guoqin Yu, Mitchell H. Gail, Dario Consonni, Michele Carugno, Michael Humphrys, Angela C. Pesatori, Neil E. Caporaso, James J. Goedert, Jacques Ravel and Maria Teresa Landi

    Citation: Genome Biology 2016 17:163

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  34. Content type: Research

    Germline stem cells play an essential role in establishing the fertility of an organism. Although extensively characterized, the regulatory mechanisms that govern the fundamental properties of mammalian female...

    Authors: Xiao-Li Zhang, Jun Wu, Jian Wang, Tingting Shen, Hua Li, Jun Lu, Yunzhao Gu, Yani Kang, Chee-Hong Wong, Chew Yee Ngan, Zhifeng Shao, Ji Wu and Xiaodong Zhao

    Citation: Genome Biology 2016 17:162

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  35. Content type: Research

    Our understanding of the factors influencing the emergence, dissemination and global distribution of epidemic clones of bacteria is limited. ST59 is a major epidemic clone of community-associated MRSA in East ...

    Authors: Melissa J. Ward, Mariya Goncheva, Emily Richardson, Paul R. McAdam, Emma Raftis, Angela Kearns, Robert S. Daum, Michael Z. David, Tsai Ling Lauderdale, Giles F. Edwards, Graeme R. Nimmo, Geoffrey W. Coombs, Xander Huijsdens, Mark E. J. Woolhouse and J. Ross Fitzgerald

    Citation: Genome Biology 2016 17:160

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  36. Content type: Research

    Histone modification H4K20me3 and its methyltransferase SUV420H2 have been implicated in suppression of tumorigenesis. The underlying mechanism is unclear, although H4K20me3 abundance increases during cellular...

    Authors: David M. Nelson, Farah Jaber-Hijazi, John J. Cole, Neil A. Robertson, Jeffrey S. Pawlikowski, Kevin T. Norris, Steven W. Criscione, Nikolay A. Pchelintsev, Desiree Piscitello, Nicholas Stong, Taranjit Singh Rai, Tony McBryan, Gabriel L. Otte, Colin Nixon, William Clark, Harold Riethman…

    Citation: Genome Biology 2016 17:158

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  37. Content type: Open Letter

    An important application of modern genomics is diagnosing genetic disorders. We use the largest publicly available exome sequence database to show that this key clinical service can currently be performed much...

    Authors: Slavé Petrovski and David B. Goldstein

    Citation: Genome Biology 2016 17:157

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