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1.
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Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system
Stephen E Von Stetina, Joseph D Watson, Rebecca M Fox, Kellen L Olszewski, W Clay Spencer, Peter J Roy, David M Miller Genome Biology 2007, 8:R135 (5 July 2007)
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Editor’s summary
A novel strategy for profiling Caenorhabditis elegans cells identifies transcripts highly enriched in either the embryonic or larval C. elegans nervous system, including 19 conserved transcripts of unknown function that are also expressed in the mammalian brain.
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2.
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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)
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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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3.
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A Faustian bargain
Gregory A Petsko Genome Biology 2010, 11:138 (31 October 2010)
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Editor’s summary
An open letter to George M Philip, President of the State University of New York At Albany.
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4.
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Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman Genome Biology 2002, 3:research0034-research0034.11 (18 June 2002)
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Editor’s summary
Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested.
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5.
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Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes
Sandip Paul, Sumit K Bag, Sabyasachi Das, Eric T Harvill, Chitra Dutta Genome Biology 2008, 9:R70 (9 April 2008)
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Editor’s summary
A comparative genomic and proteomic study of halophilic and non-halophilic prokaryotes identifies specific genomic and proteomic features typical of halophilic species that are independent from genomic GC-content and taxonomic position.
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6.
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Evaluation of next generation sequencing platforms for population targeted sequencing studies
Olivier Harismendy, Pauline C Ng, Robert L Strausberg, Xiaoyun Wang, Timothy B Stockwell, Karen Y Beeson, Nicholas J Schork, Sarah S Murray, Eric J Topol, Samuel Levy, Kelly A Frazer Genome Biology 2009, 10:R32 (27 March 2009)
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| PubMed | Cited on BioMed Central
| F1000 Biology
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Editor’s summary
Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics.
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7.
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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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Editor’s summary
Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
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8.
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Bioinformatics: alive and kicking
Lincoln D Stein Genome Biology 2008, 9:114 (17 December 2008)
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Editor’s summary
Bioinformatics is alive and well in 2008 concludes Lincoln Stein, despite his earlier prediction of its imminent demise.
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9.
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CellProfiler: image analysis software for identifying and quantifying cell phenotypes
Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Kang, Ola Friman, David A Guertin, Joo Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini Genome Biology 2006, 7:R100 (31 October 2006)
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Editor’s summary
CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.
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10.
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R25 (4 March 2009)
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Editor’s summary
Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
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11.
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A scaling normalization method for differential expression analysis of RNA-seq data
Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010)
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Editor’s summary
A novel and empirical method for normalization of RNA-seq data is presented
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12.
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Having an impact (factor)
Gregory A Petsko Genome Biology 2008, 9:107 (29 July 2008)
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Editor’s summary
A recently departed genome biologist discusses the impact factor of his life with St Peter at the Pearly Gates.
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13.
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Editor's note
Genome Biology 2000, 1:comment0002-comment0002.2 (13 October 2000)
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The fourth issue of GenomeBiology sees the launch of two new article types, the protein family review and the tutorial.
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14.
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A novel and universal method for microRNA RT-qPCR data normalization
Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele Genome Biology 2009, 10:R64 (16 June 2009)
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Editor’s summary
The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments.
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15.
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Searching for SNPs with cloud computing
Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009)
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Editor’s summary
Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.
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16.
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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen Genome Biology 2009, 10:R80 (23 July 2009)
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| PubMed | Cited on BioMed Central
| F1000 Biology
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Editor’s summary
Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.
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17.
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Calling on a million minds for community annotation in WikiProteins
Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert-Jan van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch Genome Biology 2008, 9:R89 (28 May 2008)
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| PubMed | Cited on BioMed Central
| F1000 Biology
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Editor’s summary
WikiProteins is a novel tool that allows community annotation in an open access, wiki-based system.
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18.
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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)
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| 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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19.
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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas, Jacques Izard, Joshua Z Levin, Jonathan Livny, Ashlee M Earl, Dirk Gevers, Doyle V Ward, Chad Nusbaum, Bruce W Birren, Andreas Gnirke Genome Biology 2012, 13:r23 (28 March 2012)
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Editor’s summary
A method is presented for transcriptome sequencing of complex bacterial mixtures or communities
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20.
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Analysis of the platypus genome suggests a transposon origin for mammalian imprinting
Andrew J Pask, Anthony T Papenfuss, Eleanor I Ager, Kaighin A McColl, Terence P Speed, Marilyn B Renfree Genome Biology 2009, 10:R1 (2 January 2009)
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Editor’s summary
Comparisons between the platypus and eutherian mammalian genomes provides new insights into how epigenetic imprinting may have evolved in mammalian genomes.
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21.
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The ethics of characterizing difference: guiding principles on using racial categories in human genetics
Sandra Lee, Joanna Mountain, Barbara Koenig, Russ Altman, Melissa Brown, Albert Camarillo, Luca Cavalli-Sforza, Mildred Cho, Jennifer Eberhardt, Marcus Feldman, Richard Ford, Henry Greely, Roy King, Hazel Markus, Debra Satz, Matthew Snipp, Claude Steele, Peter Underhill Genome Biology 2008, 9:404 (15 July 2008)
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Editor’s summary
We are a multidisciplinary group of Stanford faculty who propose ten principles to guide the use of racial and ethnic categories when characterizing group differences in research into human genetic variation.
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22.
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The 14-3-3s
Robert J Ferl, Michael S Manak, Matthew F Reyes Genome Biology 2002, 3:reviews3010-reviews3010.7 (27 June 2002)
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Editor’s summary
The major native forms of 14-3-3s are homo- and hetero-dimers, the biological functions of which are to interact physically with specific client proteins and thereby effect a change in the client. As a result, 14-3-3s are involved in a vast array of processes such as the response to stress, cell-cycle control, and apoptosis, serving as adapters, activators, and repressors. There are currently 133 full-length sequences available.
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23.
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Categorization of humans in biomedical research: genes, race and disease
Neil Risch, Esteban Burchard, Elad Ziv, Hua Tang Genome Biology 2002, 3:comment2007-comment2007.12 (1 July 2002)
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Editor’s summary
A debate has arisen regarding the validity of racial/ethnic categories for biomedical and genetic research. An epidemiologic perspective on the issue of human categorization in biomedical and genetic research strongly supports the continued use of self-identified race and ethnicity.
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24.
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Metabolic changes in schizophrenia and human brain evolution
Philipp Khaitovich, Helen E Lockstone, Matthew T Wayland, Tsz M Tsang, Samantha D Jayatilaka, Arfu J Guo, Jie Zhou, Mehmet Somel, Laura W Harris, Elaine Holmes, Svante Pääbo, Sabine Bahn Genome Biology 2008, 9:R124 (5 August 2008)
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Editor’s summary
Human cognitive evolution involved genes implicated in energy metabolism and energy-expensive brain functions that are also altered in schizophrenia, suggesting that human brains may have reached their metabolic limit, with schizophrenia as a costly by-product.
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25.
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De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones Genome Biology 2009, 10:R94 (11 September 2009)
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Editor’s summary
A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data
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26.
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Community-wide analysis of microbial genome sequence signatures
Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009)
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Editor’s summary
Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members.
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27.
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Genome-wide prediction of transcription factor binding sites using an integrated model
Kyoung-Jae Won, Bing Ren, Wei Wang Genome Biology 2010, 11:R7 (22 January 2010)
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Editor’s summary
A new approach for genome-wide transcription factor binding site prediction is presented that integrates sequence and chromatin modification data.
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28.
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Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009)
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Editor’s summary
The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.
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29.
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Sniper: improved SNP discovery by multiply mapping deep sequenced reads
Daniel F Simola, Junhyong Kim Genome Biology 2011, 12:R55 (20 June 2011)
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Editor’s summary
A method for improved SNP discovery in next-generation sequencing data
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30.
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A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
Desmond S Lun, Ashley Sherrid, Brian Weiner, David R Sherman, James E Galagan Genome Biology 2009, 10:R142 (22 December 2009)
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Editor’s summary
CSdeconv is a novel method for determining the location of transcription factor binding from ChIP-seq data that discriminates closely-spaced sites.
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31.
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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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Editor’s summary
The Human Microbiome Project's analysis of ten sites in the digestive tract of healthy human adults
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32.
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Implications for health and disease in the genetic signature of the Ashkenazi Jewish population
Saurav Guha, Jeffrey A Rosenfeld, Anil K Malhotra, Annette T Lee, Peter K Gregersen, John M Kane, Itsik Pe'er, Ariel Darvasi, Todd Lencz Genome Biology 2012, 13:R2 (25 January 2012)
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Editor’s summary
A population-specific genetic signature, derived from a large genotyping study, helps explain why some diseases are overrepresented in the Ashkenazi population
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33.
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Proteomic analysis of the secretome of Leishmania donovani
J Maxwell Silverman, Simon K Chan, Dale P Robinson, Dennis M Dwyer, Devki Nandan, Leonard J Foster, Neil E Reiner Genome Biology 2008, 9:R35 (18 February 2008)
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Editor’s summary
Analysis of Leishmania-conditioned medium resulted in the identification of 151 proteins apparently secreted by the parasitic protozoan Leishmania donovani and suggested a vesicle-based secretion system.
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34.
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Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity
Corneliu Henegar, Joan Tordjman, Vincent Achard, Danièle Lacasa, Isabelle Cremer, Michèle Guerre-Millo, Christine Poitou, Arnaud Basdevant, Vladimir Stich, Nathalie Viguerie, Dominique Langin, Pierre Bedossa, Jean-Daniel Zucker, Karine Clement Genome Biology 2008, 9:R14 (21 January 2008)
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Editor’s summary
Analysis of the transcriptomic signature of white adipose tissue in obese human subjects revealed increased interstitial fibrosis and an infiltration of inflammatory cells into the tissue.
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35.
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Constructing a fish metabolic network model
Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010)
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Editor’s summary
The first genome-wide fish metabolic model, MetaFishNet, is presented.
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36.
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The draft genome and transcriptome of Cannabis sativa
Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011)
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| F1000 Biology
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Editor’s summary
The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
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37.
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PyCogent: a toolkit for making sense from sequence
Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying, Gavin A Huttley Genome Biology 2007, 8:R171 (21 August 2007)
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Editor’s summary
The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python.
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38.
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Many LINE1 elements contribute to the transcriptome of human somatic cells
Sanjida H Rangwala, Lili Zhang, Haig H Kazazian Genome Biology 2009, 10:R100 (22 September 2009)
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Editor’s summary
Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome.
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39.
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Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium
Richard A Stabler, Miao He, Lisa Dawson, Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor D Lawley, Mohammed Sebaihia, Michael A Quail, Graham Rose, Dale N Gerding, Maryse Gibert, Michel R Popoff, Julian Parkhill, Gordon Dougan, Brendan W Wren Genome Biology 2009, 10:R102 (25 September 2009)
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Editor’s summary
A genome comparison of non-epidemic and epidemic strains of Clostridium difficile reveals gene gains that could explain how a hypervirulent strain has emerged
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40.
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Closing gaps in the human genome using sequencing by synthesis
Manuel Garber, Michael C Zody, Harindra M Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2009, 10:R60 (2 June 2009)
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Editor’s summary
A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.
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41.
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The case for cloud computing in genome informatics
Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010)
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Editor’s summary
With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.
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42.
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Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
André E Minoche, Juliane C Dohm, Heinz Himmelbauer Genome Biology 2011, 12:R112 (8 November 2011)
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Editor’s summary
Error rates are compared in data from Illumina's HiSeq and GAIIx systems
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43.
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Genetic determinants of phenotypic diversity in humans
Nazli G Rahim, Olivier Harismendy, Eric J Topol, Kelly A Frazer Genome Biology 2008, 9:215 (24 April 2008)
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Editor’s summary
New techniques are enabling the identification of genetic variants underlying complex diseases and phenotypic traits.
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44.
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A simple, fast, and accurate method of phylogenomic inference
Martin Wu, Jonathan A Eisen Genome Biology 2008, 9:R151 (13 October 2008)
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| PubMed | Cited on BioMed Central
| F1000 Biology
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Editor’s summary
An automated pipeline for phylogenomic analysis (AMPHORA) is presented that overcomes existing limits to large-scale protein phylogenetic inference.
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45.
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Phylogenetic assessment of alignments reveals neglected tree signal in gaps
Christophe Dessimoz, Manuel Gil Genome Biology 2010, 11:R37 (6 April 2010)
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Editor’s summary
Tree-based tests of alignment methods enable the evaluation of the effect of gap placement on the inference of phylogenetic relationships.
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46.
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KEGG spider: interpretation of genomics data in the context of the global gene metabolic network
Alexey V Antonov, Sabine Dietmann, Hans W Mewes Genome Biology 2008, 9:R179 (18 December 2008)
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Editor’s summary
A web-based tool for interpretation of experimentally-derived gene lists that provides global models uniting genes from different metabolic pathways.
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47.
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Preferential regulation of duplicated genes by microRNAs in mammals
Jingjing Li, Gabriel Musso, Zhaolei Zhang Genome Biology 2008, 9:R132 (26 August 2008)
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Editor’s summary
Analysis of duplicate genes and predicted microRNA targets in human and mouse shows that microRNAs are important in how the regulatory patterns of mammalian paralogs have evolved.
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48.
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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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49.
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Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing
Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011)
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Editor’s summary
An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples
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50.
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Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases
Monika Ray, Jianhua Ruan, Weixiong Zhang Genome Biology 2008, 9:R148 (8 October 2008)
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Editor’s summary
Analysis of microarray data reveals extensive links between Alzheimer’s disease and cardiovascular diseases.
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