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		Research Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization Sara Schaarschmidt, Peter M Gresshoff, Bettina Hause Genome Biology 2013, 14:R62 (18 June 2013) Abstract \| Provisional PDF \| Editor’s summary A transcriptomic analysis of changes in soybean gene expression in response to mycorrhization identifies GmNF-YA1a/b as positive regulators of arbuscular mycorrhization
		Method User guide for mapping-by-sequencing in Arabidopsis Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel, Korbinian Schneeberger Genome Biology 2013, 14:R61 (17 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Method for mapping-by-sequencing in Arabidopsis, using the Pop-seq software, and application to barley and rice as well
		Research Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch, Nikolai V Ivanov Genome Biology 2013, 14:R60 (17 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genome sequencing and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis show that differences in alkaloid production may regulate insect resistance
		Research Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann Genome Biology 2013, 14:R59 (14 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations
		Research 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 \| PubMed \| Editor’s summary An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
		Research Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis Veronica Gregis, Fernando Andrés, Alice Sessa, Rosalinda F Guerra, Sara Simonini, Julieta L Mateos, Stefano Torti, Federico Zambelli, Gian Marco Prazzoli, Katrine N Bjerkan, Paul E Grini, Giulio Pavesi, Lucia Colombo, George Coupland, Martin M Kater Genome Biology 2013, 14:R56 (11 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of SVP-regulated pathways that control vegetative and floral meristem development
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
		Research The plasticity of the grapevine berry transcriptome Silvia Dal Santo, Giovanni Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti Genome Biology 2013, 14:r54 (7 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A transcriptomic and metabolomic analysis of the plasticity of grapevine berry gene expression in response to development and the environment
		Research highlight 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes
		Research The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida, David N Kuhn et al. Genome Biology 2013, 14:R53 (3 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color
		Method Integrated analysis of recurrent properties of cancer genes to identify novel drivers Matteo D'Antonio, Francesca D Ciccarelli Genome Biology 2013, 14:R52 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A method to detect rare driver genes through integrated analysis of expression profiles, mutation effects and properties of known cancer genes
		Research Characterizing and measuring bias in sequence data Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe Genome Biology 2013, 14:R51 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed
		Review Machine learning and genome annotation: a match meant to be? Kevin Y Yip, Chao Cheng, Mark Gerstein Genome Biology 2013, 14:205 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Gerstein, Kevin Yip and Chao Cheng present a beginner's guide to machine learning for genome annotation
		Research highlight Deep C diving: mapping the low-abundance modifications of the DNA demethylation pathway John P Thomson, Jennifer M Hunter, Richard R Meehan Genome Biology 2013, 14:118 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Richard Meehan and colleagues highlight recent insights into the 5th, 6th, 7th and 8th DNA bases: 5mC, 5hmC, 5fC and 5caC
		Research DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus Lucas JT Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, Rene F Ketting Genome Biology 2013, 14:R50 (28 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation
		Meeting report Genomic triumph meets clinical reality Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| 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.
		Research highlight 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions
		Research Mutations within lncRNAs are effectively selected against in fruitfly but not in human Wilfried Haerty, Chris P Ponting Genome Biology 2013, 14:R49 (27 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of lncRNA conservation in fruitfly and humans shows that these elements are well conserved in insects, but not in mammals
		Research Genome-wide analysis of functional sirtuin chromatin targets in yeast Mingguang Li, Veena Valsakumar, Kunal Poorey, Stefan Bekiranov, Jeffrey S Smith Genome Biology 2013, 14:R48 (27 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Sirtuins regulate both glycolytic gene expression and condensin/cohesin deposition, suggesting a mechanistic link between metabolism and chromatin architecture
		Software 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new user-friendly software tool for genome assembly evaluation
		Research 5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes Maja Klug, Sandra Schmidhofer, Claudia Gebhard, Reinhard Andreesen, Michael Rehli Genome Biology 2013, 14:R46 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation
		Research Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs
		Research Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles Nicole YP Souren, Pavlo Lutsik, Gilles Gasparoni, Sascha Tierling, Jasmin Gries, Matthias Riemenschneider, Jean-Pierre Fryns, Catherine Derom, Maurice P Zeegers, Jörn Walter Genome Biology 2013, 14:R44 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Monozygotic twins discordant for birth weight have very similar DNA methylation profiles
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions
		Meeting report Epigenetics and transgenerational inheritance Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.
		Research highlight New gene expression pipelines gush lncRNAs Jiashi Wang, Bronwyn A Lucas, Lynne E Maquat Genome Biology 2013, 14:117 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The characterization of lncRNA expression during neuronal development is a useful resource for elucidating the functions of non-coding transcripts
		Research 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 Jin Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
		Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
		Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements
		Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
		Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sündüz Kele Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Provisional PDF \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
		Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
		Comment How to evaluate a graduate studentship, or choosing the right doctoral advisor Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Duncan Odom has some sage advice for those considering PhD options
		Method TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg Genome Biology 2013, 14:R36 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A major update to TopHat, the popular Bowtie-based spliced aligner
		Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
		Opinion 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) Abstract \| Full text \| PDF \| PubMed \| 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
		Research DNA binding specificities of the long zinc-finger recombination protein PRDM9 Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
		Research Systematic biases in DNA copy number originate from isolation procedures Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
		Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
		Meeting report Single-cell biology meeting marks rebirth of an old science Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013
		Review Neurogenomics of speech and language disorders: the road ahead Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders
		Research p53 induces transcriptional and translational programs to suppress cell proliferation and growth Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
		Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
		Research highlight The fractured genome of HeLa cells David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome
		Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
		Meeting report Clinical applications of sequencing take center stage Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
		Review Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes

	All
		Research Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization Sara Schaarschmidt, Peter M Gresshoff, Bettina Hause Genome Biology 2013, 14:R62 (18 June 2013) Abstract \| Provisional PDF \| Editor’s summary A transcriptomic analysis of changes in soybean gene expression in response to mycorrhization identifies GmNF-YA1a/b as positive regulators of arbuscular mycorrhization
		Method User guide for mapping-by-sequencing in Arabidopsis Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel, Korbinian Schneeberger Genome Biology 2013, 14:R61 (17 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Method for mapping-by-sequencing in Arabidopsis, using the Pop-seq software, and application to barley and rice as well
		Research Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch, Nikolai V Ivanov Genome Biology 2013, 14:R60 (17 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genome sequencing and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis show that differences in alkaloid production may regulate insect resistance
		Research Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann Genome Biology 2013, 14:R59 (14 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations
		Research 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 \| PubMed \| Editor’s summary An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids
		Research Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis Veronica Gregis, Fernando Andrés, Alice Sessa, Rosalinda F Guerra, Sara Simonini, Julieta L Mateos, Stefano Torti, Federico Zambelli, Gian Marco Prazzoli, Katrine N Bjerkan, Paul E Grini, Giulio Pavesi, Lucia Colombo, George Coupland, Martin M Kater Genome Biology 2013, 14:R56 (11 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of SVP-regulated pathways that control vegetative and floral meristem development
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
		Research The plasticity of the grapevine berry transcriptome Silvia Dal Santo, Giovanni Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti Genome Biology 2013, 14:r54 (7 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A transcriptomic and metabolomic analysis of the plasticity of grapevine berry gene expression in response to development and the environment
		Research highlight 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes
		Research The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida, David N Kuhn et al. Genome Biology 2013, 14:R53 (3 June 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color
		Method Integrated analysis of recurrent properties of cancer genes to identify novel drivers Matteo D'Antonio, Francesca D Ciccarelli Genome Biology 2013, 14:R52 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A method to detect rare driver genes through integrated analysis of expression profiles, mutation effects and properties of known cancer genes
		Research Characterizing and measuring bias in sequence data Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe Genome Biology 2013, 14:R51 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed
		Review Machine learning and genome annotation: a match meant to be? Kevin Y Yip, Chao Cheng, Mark Gerstein Genome Biology 2013, 14:205 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Gerstein, Kevin Yip and Chao Cheng present a beginner's guide to machine learning for genome annotation
		Research highlight Deep C diving: mapping the low-abundance modifications of the DNA demethylation pathway John P Thomson, Jennifer M Hunter, Richard R Meehan Genome Biology 2013, 14:118 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Richard Meehan and colleagues highlight recent insights into the 5th, 6th, 7th and 8th DNA bases: 5mC, 5hmC, 5fC and 5caC
		Research DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus Lucas JT Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, Rene F Ketting Genome Biology 2013, 14:R50 (28 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation
		Meeting report Genomic triumph meets clinical reality Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| 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.
		Research highlight 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions
		Research Mutations within lncRNAs are effectively selected against in fruitfly but not in human Wilfried Haerty, Chris P Ponting Genome Biology 2013, 14:R49 (27 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of lncRNA conservation in fruitfly and humans shows that these elements are well conserved in insects, but not in mammals
		Research Genome-wide analysis of functional sirtuin chromatin targets in yeast Mingguang Li, Veena Valsakumar, Kunal Poorey, Stefan Bekiranov, Jeffrey S Smith Genome Biology 2013, 14:R48 (27 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Sirtuins regulate both glycolytic gene expression and condensin/cohesin deposition, suggesting a mechanistic link between metabolism and chromatin architecture
		Software 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new user-friendly software tool for genome assembly evaluation
		Research 5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes Maja Klug, Sandra Schmidhofer, Claudia Gebhard, Reinhard Andreesen, Michael Rehli Genome Biology 2013, 14:R46 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation
		Research Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs
		Research Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles Nicole YP Souren, Pavlo Lutsik, Gilles Gasparoni, Sascha Tierling, Jasmin Gries, Matthias Riemenschneider, Jean-Pierre Fryns, Catherine Derom, Maurice P Zeegers, Jörn Walter Genome Biology 2013, 14:R44 (26 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Monozygotic twins discordant for birth weight have very similar DNA methylation profiles
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions
		Meeting report Epigenetics and transgenerational inheritance Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.
		Research highlight New gene expression pipelines gush lncRNAs Jiashi Wang, Bronwyn A Lucas, Lynne E Maquat Genome Biology 2013, 14:117 (24 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The characterization of lncRNA expression during neuronal development is a useful resource for elucidating the functions of non-coding transcripts
		Research 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 Jin Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
		Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
		Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements
		Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
		Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sündüz Kele Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Provisional PDF \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
		Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
		Comment How to evaluate a graduate studentship, or choosing the right doctoral advisor Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Duncan Odom has some sage advice for those considering PhD options
		Method TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg Genome Biology 2013, 14:R36 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A major update to TopHat, the popular Bowtie-based spliced aligner
		Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
		Opinion 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) Abstract \| Full text \| PDF \| PubMed \| 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
		Research DNA binding specificities of the long zinc-finger recombination protein PRDM9 Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
		Research Systematic biases in DNA copy number originate from isolation procedures Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
		Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
		Meeting report Single-cell biology meeting marks rebirth of an old science Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013
		Review Neurogenomics of speech and language disorders: the road ahead Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders
		Research p53 induces transcriptional and translational programs to suppress cell proliferation and growth Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
		Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
		Research highlight The fractured genome of HeLa cells David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome
		Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
		Meeting report Clinical applications of sequencing take center stage Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
		Review Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes