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ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011)
Abstract | Full text | PDF
| PubMed | Cited on BioMed Central
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Editor’s summary
ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
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2.
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Sequestration: inadvertently killing biomedical research to score political points
Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013)
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Editor’s summary
Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction
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3.
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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome
Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grützner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013)
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| PubMed
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Editor’s summary
A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
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4.
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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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| PubMed | Cited on BioMed Central
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Editor’s summary
A consistent, robust and versatile software tool for visualizing genomic data
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5.
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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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| PubMed | Cited on BioMed Central
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Editor’s summary
A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
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6.
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Aging effects on DNA methylation modules in human brain and blood tissue
Steve Horvath, Yafeng Zhang, Peter Langfelder, René S Kahn, Marco PM Boks, Kristel van Eijk, Leonard H van den Berg, Roel A Ophoff Genome Biology 2012, 13:R97 (3 October 2012)
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| PubMed | Cited on BioMed Central
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Editor’s summary
An age-related co-methylation module in human brain and blood tissue includes genes associated with Alzheimer's disease
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7.
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The GENCODE pseudogene resource
Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard, Jennifer Harrow, Mark B Gerstein Genome Biology 2012, 13:R51 (5 September 2012)
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| PubMed | Cited on BioMed Central
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Editor’s summary
The GENCODE pseudogene resource includes evidence for dead genes undergoing resurrection
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8.
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Raymond Gosling: the man who crystallized genes
Naomi Attar Genome Biology 2013, 14:402 (25 April 2013)
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| PubMed | Cited on BioMed Central |
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Editor’s summary
"The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
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9.
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Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda Genome Biology 2013, 14:R31 (17 April 2013)
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| PubMed
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Editor’s summary
Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
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10.
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From RNA-seq reads to differential expression results
Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010)
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| PubMed | Cited on BioMed Central
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Editor’s summary
Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
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11.
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Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery
Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013)
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Editor’s summary
A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
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12.
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The advantages of SMRT sequencing
Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013)
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Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
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13.
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REAPR: a universal tool for genome assembly evaluation
Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto Genome Biology 2013, 14:R47 (27 May 2013)
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Editor’s summary
A new user-friendly software tool for genome assembly evaluation
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14.
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Modeling gene expression using chromatin features in various cellular contexts
Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012)
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| PubMed | Cited on BioMed Central
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Editor’s summary
Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
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15.
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Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
Nicola Segata, Susan Haake, Peter Mannon, Katherine P Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard Genome Biology 2012, 13:R42 (14 June 2012)
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| PubMed | Cited on BioMed Central
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Editor’s summary
The Human Microbiome Project's analysis of ten sites in the digestive tract of healthy human adults
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16.
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A blood based 12-miRNA signature of Alzheimer disease patients
Petra Leidinger, Christina Backes, Stephanie Deutscher, Katja Schmitt, Sabine C Muller, Karen Frese, Jan Haas, Klemens Ruprecht, Friedemann Paul, Cord Stahler, Christoph JG Lang, Benjamin Meder, Tamas Bartfai, Eckart Meese, Andreas Keller Genome Biology 2013, 14:R78 (29 July 2013)
Abstract | Provisional PDF
| PubMed
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Editor’s summary
A 12-miRNA signature in blood samples can be used to detect Alzheimer’s disease and other neurological disorders
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17.
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Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance
David Martino, Yuk Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013)
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Editor’s summary
A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
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18.
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Ray Meta: scalable de novo metagenome assembly and profiling
Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012)
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| PubMed | Cited on BioMed Central
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Editor’s summary
A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
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19.
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FOCAL: an experimental design tool for systematizing metabolic discoveries and model
development
Christopher J Tervo, Jennifer L Reed Genome Biology 2012, 13:R116 (13 December 2012)
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Editor’s summary
A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
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20.
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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason Genome Biology 2012, 13:R87 (3 October 2012)
Abstract | Full text | PDF
| PubMed | Cited on BioMed Central
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Editor’s summary
An R package (incorporating multiple analysis tools) automates and simplifies the characterization of methylation datasets
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21.
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Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells
Ishita S Mehta, Christopher H Eskiw, Halime D Arican, Ian R Kill, Joanna M Bridger Genome Biology 2011, 12:R74 (12 August 2011)
Abstract | Full text | PDF
| PubMed | Cited on BioMed Central
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Editor’s summary
Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics
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22.
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How to evaluate a graduate studentship, or choosing the right doctoral advisor
Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013)
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Editor’s summary
Duncan Odom has some sage advice for those considering PhD options
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23.
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A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans
Anna C Need, Dalia Kasperavičiūtė, Elizabeth T Cirulli, David B Goldstein Genome Biology 2009, 10:R7 (22 January 2009)
Abstract | Full text | PDF
| PubMed | Cited on BioMed Central
| F1000 Biology
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Editor’s summary
A principal components analysis of genomic information showed that individuals with full Jewish ancestry formed a clearly distinct cluster from those individuals with no Jewish ancestry.
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24.
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EpiExplorer: live exploration and global analysis of large epigenomic datasets
Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer, Christoph Bock Genome Biology 2012, 13:R96 (3 October 2012)
Abstract | Full text | PDF
| PubMed | Cited on BioMed Central
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Editor’s summary
A text indexing algorithm enables extremely rapid, global analysis of large epigenomic datasets
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25.
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Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum
Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss Genome Biology 2012, 13:R108 (26 November 2012)
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Editor’s summary
A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
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