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26.
1677 Accesses
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Genomic triumph meets clinical reality
Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013)
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Editor’s summary
A report on the 'Genomic Disorders 2013 - from 60 years of DNA to human genomes in the clinic' meeting, held at Homerton College, Hills Road, Cambridge, UK, April 10-12, 2013.
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27.
1628 Accesses
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CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes
Quan Zhang, Mina Rho, Haixu Tang, Thomas G Doak, Yuzhen Ye Genome Biology 2013, 14:R40 (29 April 2013)
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Editor’s summary
Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements
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28.
1576 Accesses
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Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine
Sean M Cullen, Margaret A Goodell Genome Biology 2013, 14:116 (28 May 2013)
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A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions
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29.
1493 Accesses
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Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry
Alisdair R Fernie, Takayuki Tohge Genome Biology 2013, 14:119 (7 June 2013)
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Editor’s summary
A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes
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30.
1472 Accesses
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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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31.
1424 Accesses
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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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32.
1402 Accesses
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Inactive or moderately active human promoters are enriched for inter-individual epialleles
Carolina Gemma, Sreeram V Ramagopalan, Thomas A Down, Huriya Beyan, Mohammed I Hawa, Michelle L Holland, Paul J Hurd, Gavin Giovannoni, R David Leslie, George C Ebers, Vardhman K Rakyan Genome Biology 2013, 14:R43 (25 May 2013)
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Editor’s summary
Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions
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33.
1386 Accesses
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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)
Abstract | Full text | PDF
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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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34.
1298 Accesses
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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011)
Abstract | Full text | PDF
| PubMed | Cited on BioMed Central
| F1000 Biology
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Editor’s summary
The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias
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35.
1265 Accesses
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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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36.
1244 Accesses
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Improving RNA-Seq expression estimates by correcting for fragment bias
Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011)
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Editor’s summary
An extension to Cufflinks corrects bias in RNA-seq datasets
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37.
1239 Accesses
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu Genome Biology 2008, 9:R137 (17 September 2008)
Abstract | Full text | PDF
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Editor’s summary
MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.
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38.
1190 Accesses
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Comprehensive genotyping of the USA national maize inbred seed bank
Maria C Romay, Mark J Millard, Jeffrey C Glaubitz, Jason A Peiffer, Kelly L Swarts, Terry M Casstevens, Robert J Elshire, Charlotte B Acharya, Sharon E Mitchell, Sherry A Flint-Garcia, Michael D McMullen, James B Holland, Edward S Buckler, Candice A Gardner Genome Biology 2013, 14:R55 (11 June 2013)
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Editor’s summary
Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
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39.
1183 Accesses
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The Transcription Factor Encyclopedia
Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao Cindy Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Bérénice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al.
Genome Biology 2012, 13:R24 (29 March 2012)
Abstract | Full text | PDF
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Editor’s summary
A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system
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40.
1165 Accesses
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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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"The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
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41.
1155 Accesses
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Bioconductor: open software development for computational biology and bioinformatics
Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang Genome Biology 2004, 5:R80 (15 September 2004)
Abstract | Full text | PDF
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Editor’s summary
A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
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42.
1116 Accesses
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Sixty years of genome biology
W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013)
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Editor’s summary
Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
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43.
1123 Accesses
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A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Hoeffner, Marcus Krueger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013)
Abstract | Provisional PDF
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Editor’s summary
A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
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44.
1118 Accesses
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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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45.
1101 Accesses
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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier, Curtis Huttenhower Genome Biology 2012, 13:R79 (26 September 2012)
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Editor’s summary
An analysis of the microbes and microbial metabolism present in intestinal biopsies and stool samples from 231 IBD and healthy subjects
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46.
1105 Accesses
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Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome
María Muñoz-Amatriaín, Steven R Eichten, Thomas Wicker, Todd A Richmond, Martin Mascher, Burkhard Steuernagel, Uwe Scholz, Ruvini Ariyadasa, Manuel Spannagl, Thomas Nussbaumer, Klaus FX Mayer, Stefan Taudien, Matthias Platzer, Jeffrey A Jeddeloh, Nathan M Springer, Gary J Muehlbauer, Nils Stein Genome Biology 2013, 14:R58 (12 June 2013)
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Editor’s summary
An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations
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47.
1100 Accesses
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Functional analysis of transcription factor binding sites in human promoters
Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012)
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Editor’s summary
TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional
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48.
1089 Accesses
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Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids
Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng Genome Biology 2013, 14:R57 (12 June 2013)
Abstract | Provisional PDF
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Editor’s summary
An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
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49.
1064 Accesses
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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)
Abstract | Full text | PDF
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Editor’s summary
Error rates are compared in data from Illumina's HiSeq and GAIIx systems
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50.
1055 Accesses
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Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis
Srikanth Nagalla, Jeff W Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, Lance D Miller Genome Biology 2013, 14:R34 (29 April 2013)
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Editor’s summary
An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
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