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Research   Open Access

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   Open Access

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   Open Access

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   Open Access

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   Open Access

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   Open Access

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   Open Access

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   Open Access

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   Open Access

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   Subscription

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Subscription Highly Accessed

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   Subscription

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   Open Access Highly Accessed

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   Subscription

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   Subscription

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   Open Access Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access

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   Open Access

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   Subscription

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   Subscription

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Subscription Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Subscription Highly Accessed

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   Open Access Highly Accessed

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   Free Highly Accessed

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   Subscription Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Subscription

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   Subscription

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   Subscription Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Subscription Highly Accessed

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   Open Access Highly Accessed

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   Subscription

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   Subscription

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

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