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ggbio: an R package for extending the grammar of graphics for genomic data
Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012)
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Editor’s summary
A consistent, robust and versatile software tool for visualizing genomic data
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A computational framework for boosting confidence in high-throughput protein-protein interaction datasets
Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger Genome Biology 2012, 13:R76 (31 August 2012)
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Coev2Net is a method for assigning confidence to high-throughput protein-protein interaction predictions
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The rise of translational bioinformatics
Yves A Lussier, Haiquan Li Genome Biology 2012, 13:319 (31 August 2012)
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A report on the 20th International Conference On Intelligent Systems For Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.
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A modest proposal for an outreach section in scientific publications
Chris Gunter, Anne Osterrieder Genome Biology 2012, 13:168 (31 August 2012)
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By Chris Gunter and Anne Osterrieder
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Turning pipe dreams into reality
Peter Li, Jeremy Goecks, Tin-Lap Lee Genome Biology 2012, 13:318 (30 August 2012)
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The 2012 Galaxy meeting shows how the bioinformatic tools within Galaxy are developing and automating data analysis in the life sciences
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The tomato genome: implications for plant breeding, genomics and evolution
Aashish Ranjan, Yasunori Ichihashi, Neelima R Sinha Genome Biology 2012, 13:167 (30 August 2012)
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The importance of the tomato genome for plant breeding and the future of crop research
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Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012)
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Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
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Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
Hervé Moreau, Bram Verhelst, Arnaud Couloux, Evelyne Derelle, Stephane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F Hohmann-Marriott, Gwenael Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele Genome Biology 2012, 13:R74 (24 August 2012)
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The genome sequence of the marine green alga Bathycoccus prasinos, and a phylogenomic comparison with other Mammiellales species
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Novel origins of copy number variation in the dog genome
Jonas Berglund, Elisa M Nevalainen, Anna-Maja Molin, Michele Perloski, The LUPA Consortium, Catherine André, Michael C Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad-Toh, Hannes Lohi, Matthew T Webster Genome Biology 2012, 13:R73 (23 August 2012)
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CNVs were analyzed in dogs from 17 breeds, and were found to be associated with different features compared to other mammals
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Sequencing and characterization of the FVB/NJ mouse genome
Kim Wong, Suzannah Bumpstead, Louise Van Der Weyden, Laura G Reinholdt, Laurens G Wilming, David J Adams, Thomas M Keane Genome Biology 2012, 13:R72 (23 August 2012)
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The genome of the FVB/NJ mouse is sequenced, revealing variants specific to this strain
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A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers
Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012)
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A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
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The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite
Andrea H Horakova, J Mauro Calabrese, Christine R McLaughlin, Deanna C Tremblay, Terry Magnuson, Brian P Chadwick Genome Biology 2012, 13:R70 (20 August 2012)
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A characterization of the X-linked homogenous tandem repeat DXZ4 in mouse, and a subsequent analysis of conservation across mammals
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Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase
Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian Genome Biology 2012, 13:R69 (17 August 2012)
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Genome-wide mapping of 5-formylcytosine in ES cells reveals an enrichment in promoter and exon CpG islands, and an association with transcription
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Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins
Gary LeRoy, Iouri Chepelev, Peter A DiMaggio, Mario A Blanco, Barry M Zee, Keji Zhao, Benjamin A Garcia Genome Biology 2012, 13:R68 (16 August 2012)
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| F1000 Biology
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A novel proteogenomic strategy links the histone reader proteins Brd3 and Brd4 to HOX gene regulation
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Genomes of extremophile crucifers: new platforms for comparative genomics and beyond
Simon M Dittami, Thierry Tonon Genome Biology 2012, 13:166 (16 August 2012)
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Research Highlight: the genome sequences of extremophile crucifers provide valuable insights into the underlying mechanisms of stress tolerance in plants
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An encyclopedia of mouse DNA elements (Mouse ENCODE)
Mouse ENCODE Consortium, John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al.
Genome Biology 2012, 13:418 (13 August 2012)
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The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome
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Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule Genome Biology 2012, 13:R67 (3 August 2012)
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The CLIP and iCLIP methods are compared for their utility in determining RNA binding protein binding sites
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Autism genetics: searching for specificity and convergence
Jamee M Berg, Daniel H Geschwind Genome Biology 2012, 13:247 (31 July 2012)
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Daniel Geschwind and Jamee Berg review the genes associated with autism spectrum disorders: how might their functions relate to one another?
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The aging epigenome: DNA methylation from the cradle to the grave
Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012)
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Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes
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Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation
Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A Gutowska, Juliane Wolf, Sonja V Bergner, Markus B Schilhabel, Ulrich C Klostermeier, Robert G Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche Genome Biology 2012, 13:R66 (26 July 2012)
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Transcriptomic and proteomic insights into the low-iron tolerance of Thalassoiosira oceanic, an oceanic diatom
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Developmental features of DNA methylation during activation of the embryonic zebrafish genome
Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012)
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DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation
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Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates
Sean Conlan, Lilia A Mijares, NISC Comparative Sequencing Program, Jesse Becker, Robert W Blakesley, Gerard G Bouffard, Shelise Brooks, Holly Coleman, Jyoti Gupta, Natalie Gurson, Morgan Park, Brian Schmidt, Pamela J Thomas, Michael Otto, Heidi H Kong, Patrick R Murray, Julia A Segre Genome Biology 2012, 13:R64 (25 July 2012)
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Comparative genomics of skin commensal and hospital infection-associated isolates uncovers a putative clinical biomarker
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piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense
Allison C Billi, Mallory A Freeberg, John K Kim Genome Biology 2012, 13:164 (20 July 2012)
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John Kim and colleagues discuss transgenerational genome surveillance and the recognition of non-self by the worm piRNA system
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RNA processing in the minimal organism Nanoarchaeum equitans
Lennart Randau Genome Biology 2012, 13:R63 (18 July 2012)
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RNA-seq in the minimal archaeon Nanoarchaeum equitans reveals details of unusual RNA processing such as trans splicing of tRNA molecules
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CIDeR: multifactorial interaction networks in human diseases
Martin Lechner, Veit Höhn, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Gabi Kastenmüller, Brigitte Waegele, Andreas Ruepp Genome Biology 2012, 13:R62 (18 July 2012)
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A database of interactions in neurological and metabolic disorders, with a wide range of search options and graphical outputs
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