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	1. 7221 Accesses	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
	2. 4823 Accesses	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
	3. 4541 Accesses	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
	4. 4150 Accesses	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
	5. 3978 Accesses	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
	6. 3894 Accesses	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
	7. 3501 Accesses	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
	8. 2977 Accesses	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
	9. 2970 Accesses	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
	10. 2869 Accesses	Method Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
	11. 2764 Accesses	Software 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
	12. 2657 Accesses	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| 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.
	13. 2559 Accesses	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
	14. 2533 Accesses	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
	15. 2522 Accesses	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
	16. 2443 Accesses	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.
	17. 2396 Accesses	Research The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage H Bradley Shaffer, Patrick Minx, Daniel E Warren, Andrew M Shedlock, Robert C Thomson, Nicole Valenzuela, John Abramyan, Chris T Amemiya, Daleen Badenhorst, Kyle K Biggar, Glen M Borchert, Christopher W Botka, Rachel M Bowden, Edward L Braun, Anne M Bronikowski, Benoit G Bruneau, Leslie T Buck, Blanche Capel, Todd A Castoe, Mike Czerwinski, Kim D Delehaunty, Scott V Edwards, Catrina C Fronick, Matthew K Fujita, Lucinda Fulton, Tina A Graves, Richard E Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernandez et al. Genome Biology 2013, 14:R28 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing
	18. 2341 Accesses	Research Characterizing the admixed African ancestry of African Americans Fouad Zakharia, Analabha Basu, Devin Absher, Themistocles L Assimes, Alan S Go, Mark A Hlatky, Carlos Iribarren, Joshua W Knowles, Jun Li, Balasubramanian Narasimhan, Steven Sidney, Audrey Southwick, Richard M Myers, Thomas Quertermous, Neil Risch, Hua Tang Genome Biology 2009, 10:R141 (22 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide SNP analyses reveal the admixed African genetic ancestry of African Americans.
	19. 2292 Accesses	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
	20. 2242 Accesses	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
	21. 2208 Accesses	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
	22. 2160 Accesses	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
	23. 2126 Accesses	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
	24. 2018 Accesses	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
	25. 1823 Accesses	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