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Page 11 of 125

  1. Content type: Correspondence

    In a recent paper, we described our efforts in search for evidence supporting epigenetic transgenerational inheritance caused by endocrine disrupter chemicals. One aspect of our study was to compare genome-wid...

    Authors: Khursheed Iqbal, Diana A. Tran, Arthur X. Li, Charles Warden, Angela Y. Bai, Purnima Singh, Zach B. Madaj, Mary E. Winn, Xiwei Wu, Gerd P. Pfeifer and Piroska E. Szabó

    Citation: Genome Biology 2016 17:154

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  2. Content type: Research

    A comparison of transcriptional profiles derived from different tissues in a given species or among different species assumes that commonalities reflect evolutionarily conserved programs and that differences r...

    Authors: Alessandra Breschi, Sarah Djebali, Jesse Gillis, Dmitri D. Pervouchine, Alex Dobin, Carrie A. Davis, Thomas R. Gingeras and Roderic Guigó

    Citation: Genome Biology 2016 17:151

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  3. Content type: Research

    Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a n...

    Authors: Vera Pancaldi, Enrique Carrillo-de-Santa-Pau, Biola Maria Javierre, David Juan, Peter Fraser, Mikhail Spivakov, Alfonso Valencia and Daniel Rico

    Citation: Genome Biology 2016 17:152

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  4. Content type: Research

    Dent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. A comparative investigation of ...

    Authors: Sandra Unterseer, Saurabh D. Pophaly, Regina Peis, Peter Westermeier, Manfred Mayer, Michael A. Seidel, Georg Haberer, Klaus F. X. Mayer, Bernardo Ordas, Hubert Pausch, Aurélien Tellier, Eva Bauer and Chris-Carolin Schön

    Citation: Genome Biology 2016 17:137

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  5. Content type: Research

    Chronic inflammation has been recognized as one of the hallmarks of cancer. We recently showed that parainflammation, a unique variant of inflammation between homeostasis and chronic inflammation, strongly pro...

    Authors: Dvir Aran, Audrey Lasry, Adar Zinger, Moshe Biton, Eli Pikarsky, Asaf Hellman, Atul J. Butte and Yinon Ben-Neriah

    Citation: Genome Biology 2016 17:145

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  6. Content type: Research

    The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it ...

    Authors: Maximilian Haeussler, Kai Schönig, Hélène Eckert, Alexis Eschstruth, Joffrey Mianné, Jean-Baptiste Renaud, Sylvie Schneider-Maunoury, Alena Shkumatava, Lydia Teboul, Jim Kent, Jean-Stephane Joly and Jean-Paul Concordet

    Citation: Genome Biology 2016 17:148

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  7. Content type: Method

    Ribosome profiling has emerged as a powerful tool for genome-wide measurements of translation, but library construction requires multiple ligation steps and remains cumbersome relative to more conventional dee...

    Authors: Nicholas Hornstein, Daniela Torres, Sohani Das Sharma, Guomei Tang, Peter Canoll and Peter A. Sims

    Citation: Genome Biology 2016 17:149

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  8. Content type: Research

    Gene expression is controlled at multiple levels, including transcription, stability, translation, and degradation. Over the years, it has become apparent that Plasmodium falciparum exerts limited transcriptional...

    Authors: Evelien M. Bunnik, Gayani Batugedara, Anita Saraf, Jacques Prudhomme, Laurence Florens and Karine G. Le Roch

    Citation: Genome Biology 2016 17:147

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  9. Content type: Research

    Enhancers, not promoters, are the most dynamic in their DNA methylation status throughout development and differentiation. Generally speaking, enhancers that are primed to or actually drive gene expression are...

    Authors: Lucas J. T. Kaaij, Michal Mokry, Meng Zhou, Michael Musheev, Geert Geeven, Adrien S. J. Melquiond, António M. de Jesus Domingues, Wouter de Laat, Christof Niehrs, Andrew D. Smith and René F. Ketting

    Citation: Genome Biology 2016 17:146

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  10. Content type: Erratum

    Authors: Hilda van den Bos, Diana C. J. Spierings, Aaron Taudt, Bjorn Bakker, David Porubský, Ester Falconer, Carolina Novoa, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Victor Guryev, Wilfred F. A. den Dunnen, Floris Foijer, Maria Colomé-Tatché, Hendrikus W. G. M. Boddeke and Peter M. Landsdorp

    Citation: Genome Biology 2016 17:143

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    The original article was published in Genome Biology 2016 17:116

  11. Content type: Research

    Altered metabolism is a hallmark of cancer. However, the role of genomic changes in metabolic genes driving the tumour metabolic shift remains to be elucidated. Here, we have investigated the genomic and trans...

    Authors: Syed Haider, Alan McIntyre, Ruud G. P. M. van Stiphout, Laura M. Winchester, Simon Wigfield, Adrian L. Harris and Francesca M. Buffa

    Citation: Genome Biology 2016 17:140

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  12. Content type: Open Letter

    Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories t...

    Authors: Raúl Catena, Alaz Özcan, Andrea Jacobs, Stephane Chevrier and Bernd Bodenmiller

    Citation: Genome Biology 2016 17:142

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  13. Content type: Research

    Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylc...

    Authors: Mario Iurlaro, Gordon R. McInroy, Heather E. Burgess, Wendy Dean, Eun-Ang Raiber, Martin Bachman, Dario Beraldi, Shankar Balasubramanian and Wolf Reik

    Citation: Genome Biology 2016 17:141

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  14. Content type: Research

    Cells can be primed by external stimuli to obtain a long-term epigenetic memory. We hypothesize that long-term exposure to elevated blood lipids can prime circulating immune cells through changes in DNA methyl...

    Authors: Koen F. Dekkers, Maarten van Iterson, Roderick C. Slieker, Matthijs H. Moed, Marc Jan Bonder, Michiel van Galen, Hailiang Mei, Daria V. Zhernakova, Leonard H. van den Berg, Joris Deelen, Jenny van Dongen, Diana van Heemst, Albert Hofman, Jouke J. Hottenga, Carla J. H. van der Kallen, Casper G. Schalkwijk…

    Citation: Genome Biology 2016 17:138

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  15. Content type: Research

    Mitochondrial heteroplasmy, the presence of more than one mitochondrial DNA (mtDNA) variant in a cell or individual, is not as uncommon as previously thought. It is mostly due to the high mutation rate of the ...

    Authors: Thomas Rensch, Diego Villar, Julie Horvath, Duncan T. Odom and Paul Flicek

    Citation: Genome Biology 2016 17:139

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  16. Content type: Research

    Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhea...

    Authors: Amelia Cervera, Denisse Urbina and Marcos de la Peña

    Citation: Genome Biology 2016 17:135

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    The Erratum to this article has been published in Genome Biology 2017 18:40

  17. Content type: Research Highlight

    An association between hammerhead ribozymes and non-autonomous, long terminal repeat retrotransposons is uncovered in plants, shedding light on the biological function of genomically encoded ribozymes.

    Authors: Christian Hammann

    Citation: Genome Biology 2016 17:136

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  18. Content type: Erratum

    Authors: Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew N. J. McKenzie, Ruddy Montandon, Kylie R. James…

    Citation: Genome Biology 2016 17:133

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    The original article was published in Genome Biology 2016 17:103

  19. Content type: Software

    Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mas...

    Authors: Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren and Adam M. Phillippy

    Citation: Genome Biology 2016 17:132

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  20. Content type: Research

    PolyA– RNAs have not been widely analyzed in human pre-implantation embryos due to the scarcity of materials. In particular, circular RNA (circRNA), a novel type of polyA– RNA, has not been characterized durin...

    Authors: Yujiao Dang, Liying Yan, Boqiang Hu, Xiaoying Fan, Yixin Ren, Rong Li, Ying Lian, Jie Yan, Qingqing Li, Yan Zhang, Min Li, Xiulian Ren, Jin Huang, Yuqi Wu, Ping Liu, Lu Wen…

    Citation: Genome Biology 2016 17:130

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  21. Content type: Method

    Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the major challenges of cancer research. This challenge is more acute and far from solved for non-coding mutations. Here w...

    Authors: Loris Mularoni, Radhakrishnan Sabarinathan, Jordi Deu-Pons, Abel Gonzalez-Perez and Núria López-Bigas

    Citation: Genome Biology 2016 17:128

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  22. Content type: Method

    Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves ...

    Authors: Jonathan Cairns, Paula Freire-Pritchett, Steven W. Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel Zerbino, Stefan Schoenfelder, Biola-Maria Javierre, Cameron Osborne, Peter Fraser and Mikhail Spivakov

    Citation: Genome Biology 2016 17:127

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  23. Content type: Research

    The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acqu...

    Authors: Sebastian Eves-van den Akker, Dominik R. Laetsch, Peter Thorpe, Catherine J. Lilley, Etienne G. J. Danchin, Martine Da Rocha, Corinne Rancurel, Nancy E. Holroyd, James A. Cotton, Amir Szitenberg, Eric Grenier, Josselin Montarry, Benjamin Mimee, Marc-Olivier Duceppe, Ian Boyes, Jessica M. C. Marvin…

    Citation: Genome Biology 2016 17:124

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  24. Content type: Research

    Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and transcriptomic analyses ...

    Authors: Bruna R. Correa, Patricia Rosa de Araujo, Mei Qiao, Suzanne C. Burns, Chen Chen, Richard Schlegel, Seema Agarwal, Pedro A. F. Galante and Luiz O. F. Penalva

    Citation: Genome Biology 2016 17:125

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  25. Content type: Erratum

    Authors: Maite Mendioroz, Catherine Do, Xiaoling Jiang, Chunhong Liu, Huferesh K. Darbary, Charles F. Lang, John Lin, Anna Thomas, Sayeda Abu-Amero, Philip Stanier, Alexis Temkin, Alexander Yale, Meng-Min Liu, Yang Li, Martha Salas, Kristi Kerkel…

    Citation: Genome Biology 2016 17:123

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    The original article was published in Genome Biology 2015 16:263

  26. Content type: Software

    The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection o...

    Authors: William McLaren, Laurent Gil, Sarah E. Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek and Fiona Cunningham

    Citation: Genome Biology 2016 17:122

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  27. Content type: Method

    Predicting dynamics of host-microbial ecosystems is crucial for the rational design of bacteriotherapies. We present MDSINE, a suite of algorithms for inferring dynamical systems models from microbiome time-se...

    Authors: Vanni Bucci, Belinda Tzen, Ning Li, Matt Simmons, Takeshi Tanoue, Elijah Bogart, Luxue Deng, Vladimir Yeliseyev, Mary L. Delaney, Qing Liu, Bernat Olle, Richard R. Stein, Kenya Honda, Lynn Bry and Georg K. Gerber

    Citation: Genome Biology 2016 17:121

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  28. Content type: Research

    For many genes, RNA polymerase II stably pauses before transitioning to productive elongation. Although polymerase II pausing has been shown to be a mechanism for regulating transcriptional activation, the ext...

    Authors: Daniel S. Day, Bing Zhang, Sean M. Stevens, Francesco Ferrari, Erica N. Larschan, Peter J. Park and William T. Pu

    Citation: Genome Biology 2016 17:120

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  29. Content type: Software

    The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file ...

    Authors: Brent S. Pedersen, Ryan M. Layer and Aaron R. Quinlan

    Citation: Genome Biology 2016 17:118

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  30. Content type: Research

    Alzheimer’s disease (AD) is a neurodegenerative disease of the brain and the most common form of dementia in the elderly. Aneuploidy, a state in which cells have an abnormal number of chromosomes, has been pro...

    Authors: Hilda van den Bos, Diana C. J. Spierings, Aaron Taudt, Bjorn Bakker, David Porubský, Ester Falconer, Carolina Novoa, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Victor Guryev, Wilfred F. A. den Dunnen, Floris Foijer, Maria Colomé-Tatché, Hendrikus W. G. M. Boddeke and Peter M. Lansdorp

    Citation: Genome Biology 2016 17:116

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    The Erratum to this article has been published in Genome Biology 2016 17:143

  31. Content type: Research

    Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accel...

    Authors: Bjorn Bakker, Aaron Taudt, Mirjam E. Belderbos, David Porubsky, Diana C. J. Spierings, Tristan V. de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S. J. M. de Bont, Anke van den Berg, Victor Guryev, Peter M. Lansdorp, Maria Colomé-Tatché and Floris Foijer

    Citation: Genome Biology 2016 17:115

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  32. Content type: METHOD

    Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dime...

    Authors: Alireza Fotuhi Siahpirani, Ferhat Ay and Sushmita Roy

    Citation: Genome Biology 2016 17:114

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  33. Content type: Software

    High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies h...

    Authors: Steven Flygare, Keith Simmon, Chase Miller, Yi Qiao, Brett Kennedy, Tonya Di Sera, Erin H. Graf, Keith D. Tardif, Aurélie Kapusta, Shawn Rynearson, Chris Stockmann, Krista Queen, Suxiang Tong, Karl V. Voelkerding, Anne Blaschke, Carrie L. Byington…

    Citation: Genome Biology 2016 17:111

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  34. Content type: METHOD

    Current approaches to single-cell transcriptomic analysis are computationally intensive and require assay-specific modeling, which limits their scope and generality. We propose a novel method that compares and...

    Authors: Vasilis Ntranos, Govinda M. Kamath, Jesse M. Zhang, Lior Pachter and David N. Tse

    Citation: Genome Biology 2016 17:112

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  35. Content type: Research Highlight

    Computational methods have been developed to reconstruct evolutionary lineages from tumors using single-cell genomic data. The resulting tumor trees have important applications in cancer research and clinical ...

    Authors: Alexander Davis and Nicholas E. Navin

    Citation: Genome Biology 2016 17:113

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  36. Content type: Research

    Soluble protein and lipid mediators play essential roles in the tumor environment, but their cellular origins, targets, and clinical relevance are only partially known. We have addressed this question for the ...

    Authors: Silke Reinartz, Florian Finkernagel, Till Adhikary, Verena Rohnalter, Tim Schumann, Yvonne Schober, W. Andreas Nockher, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller-Brüsselbach and Rolf Müller

    Citation: Genome Biology 2016 17:108

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  37. Content type: Method

    Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We i...

    Authors: Qi Zhao, Arion I. Stettner, Ed Reznik, Ioannis Ch. Paschalidis and Daniel Segrè

    Citation: Genome Biology 2016 17:109

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  38. Content type: Research Highlight

    Genome-scale models require an objective function representing what an organism strives for. A method has been developed to infer this fundamental biological function from data.

    Authors: Adam M. Feist and Bernhard O. Palsson

    Citation: Genome Biology 2016 17:110

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  39. Content type: Research Highlight

    A new study shows how RNA-induced silencing complex (RISC)-mediated posttranscriptional regulation of chromatin remodelers allows for tight control of the naïve-to-primed pluripotency transition.

    Authors: Diana Guallar and Jianlong Wang

    Citation: Genome Biology 2016 17:104

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