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	1. 7882 Accesses	Method Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E Mason, Nicholas D Socci, Doron Betel Genome Biology 2013, 14:R95 (10 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An evaluation of differential gene expression analysis methods for RNA-seq data using the SEQC gold standard dataset
	2. 5156 Accesses	Research Reducing assembly complexity of microbial genomes with single-molecule sequencing Sergey Koren, Gregory P Harhay, Timothy PL Smith, James L Bono, Dayna M Harhay, Scott D Mcvey, Diana Radune, Nicholas H Bergman, Adam M Phillippy Genome Biology 2013, 14:R101 (13 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary PacBio sequencing alone is capable of generating finished bacterial genomes in the majority of cases at reasonably low cost
	3. 5051 Accesses	Research Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
	4. 4021 Accesses	Research Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2 Oskar Marin-Bejar, Francesco P Marchese, Alejandro Athie, Yolanda Sanchez, Jovanna Gonzalez, Victor Segura, Lulu Huang, Isabel Moreno, Alfons Navarro, Mariano Monzo, Jesus Garcia-Foncillas, John L Rinn, Shuling Guo, Maite Huarte Genome Biology 2013, 14:R104 (26 September 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel lincRNA, PINT, connects p53 activation with epigenetic silencing by PRC2 and is identified as a candidate tumor suppressor
	5. 3520 Accesses	Comment Crowdfunding genomics and bioinformatics Pamela Cameron, David W Corne, Christopher E Mason, Jeffrey Rosenfeld Genome Biology 2013, 14:134 (30 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How to bypass traditional research funding routes and seek pennies from the people
	6. 3401 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 \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
	7. 3062 Accesses	Research The non-coding snRNA 7SK controls transcriptional termination, poising and bidirectionality in embryonic stem cells Gonçalo Castelo-Branco, Paulo P Amaral, Pär G Engström, Samuel C Robson, Sueli C Marques, Paul Bertone, Tony Kouzarides Genome Biology 2013, 14:r98 (17 September 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary A study in ESCs finds that 7SK promotes transcriptional termination and poising, and regulates bidirectional transcription
	8. 3026 Accesses	Research The mutational landscape of chromatin regulatory factors across 4623 tumor samples Abel Gonzalez-Perez, Alba Jene-Sanz, Nuria Lopez-Bigas Genome Biology 2013, 14:r106 (24 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Identification of mutations in chromatin regulatory factors and their potential role in tumorigenesis
	9. 2847 Accesses	Research Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape Kenneth Day, Lindsay L Waite, Anna Thalacker-Mercer, Andrew West, Marcas M Bamman, James D Brooks, Richard M Myers, Devin Absher Genome Biology 2013, 14:R102 (13 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of DNA methylation changes in four tissues during aging finds both tissue-specific and universal age-associated methylation changes
	10. 2801 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.
	11. 2768 Accesses	Research Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia Jessica Nordlund, Christofer L Bäcklin, Per Wahlberg, Stephan Busche, Eva C Berglund, Maija-Leena Eloranta, Trond Flaegstad, Erik Forestier, Britt-Marie Frost, Arja Harila-Saari, Mats Heyman, Ólafur G Jónsson, Rolf Larsson, Josefine Palle, Lars Rönnblom, Kjeld Schmiegelow, Daniel Sinnett, Stefan Söderhäll, Tomi Pastinen, Mats G Gustafsson, Gudmar Lönnerholm, Ann-Christine Syvänen Genome Biology 2013, 14:r105 (24 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary DNA methylation signatures associated with subtype, relapse and gene expression in pediatric acute lymphoblastic leukemia
	12. 2480 Accesses	Correspondence The advantages of SMRT sequencing Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013) Abstract \| Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
	13. 2406 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
	14. 2206 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 \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed
	15. 2204 Accesses	Research Intraspecific variation of recombination rate in maize Eva Bauer, Matthieu Falque, Hildrun Walter, Cyril Bauland, Christian Camisan, Laura Campo, Nina Meyer, Nicolas Ranc, Renaud Rincent, Wolfgang Schipprack, Thomas Altmann, Pascal Flament, Albrecht E Melchinger, Monica Menz, Jesús Moreno-González, Milena Ouzunova, Pedro Revilla, Alain Charcosset, Olivier C Martin, Chris-Carolin Schön Genome Biology 2013, 14:R103 (19 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A large-scale analysis of recombination rates between 22 European maize inbred lines reveals significant differences in recombination between populations
	16. 2172 Accesses	Method High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing Zhaojie Zhang, Jerome E Lee, Kent Riemondy, Emily M Anderson, Rui Yi Genome Biology 2013, 14:R109 (7 October 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An efficient sRNA cloning method from Rui Yi's lab overcomes ligation biases and enables accurate quantification over a wide dynamic range
	17. 2152 Accesses	Research Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus Laurent AF Frantz, Joshua G Schraiber, Ole Madsen, Hendrik-Jan Megens, Mirte Bosse, Yogesh Paudel, Gono Semiadi, Erik Meijaard, Ning Li, Richard PMA Crooijmans, Alan L Archibald, Montgomery Slatkin, Lawrence B Schook, Greger Larson, Martien AM Groenen Genome Biology 2013, 14:R107 (26 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genome sequencing points to climatic fluctuations and human mediated translocations as factors impacting upon Sus speciation in Southeast Asia
	18. 2145 Accesses	Research A blood based 12-miRNA signature of Alzheimer disease patients Petra Leidinger, Christina Backes, Stephanie Deutscher, Katja Schmitt, Sabine C Mueller, Karen Frese, Jan Haas, Klemens Ruprecht, Friedemann Paul, Cord Stähler, Christoph JG Lang, Benjamin Meder, Tamas Bartfai, Eckart Meese, Andreas Keller Genome Biology 2013, 14:R78 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A 12-miRNA signature in blood samples can be used to detect Alzheimer’s disease and other neurological disorders
	19. 1955 Accesses	Method 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel and empirical method for normalization of RNA-seq data is presented
	20. 1936 Accesses	Research PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation Lorenzo de la Rica, Javier Rodríguez-Ubreva, Mireia García, Abul BMMK Islam, José M Urquiza, Henar Hernando, Jesper Christensen, Kristian Helin, Carmen Gómez-Vaquero, Esteban Ballestar Genome Biology 2013, 14:R99 (12 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tet2 and DNMT3b act in concert with the transcription factor PU.1 to remodel the epigenome during monocyte-to-osteoclast differentiation
	21. 1913 Accesses	Research Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene Mar Gonzàlez-Porta, Adam Frankish, Johan Rung, Jennifer Harrow, Alvis Brazma Genome Biology 2013, 14:R70 (1 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of RNA-seq data across different tissues and cell lines reveals that the majority of genes have a single dominant transcript
	22. 1828 Accesses	Research A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains Michelle M Simon, Simon Greenaway, Jacqueline K White, Helmut Fuchs, Valérie Gailus-Durner, Sara Wells, Tania Sorg, Kim Wong, Elodie Bedu, Elizabeth J Cartwright, Romain Dacquin, Sophia Djebali, Jeanne Estabel, Jochen Graw, Neil J Ingham, Ian J Jackson, Andreas Lengeling, Silvia Mandillo, Jacqueline Marvel, Hamid Meziane, Frédéric Preitner, Oliver Puk, Michel Roux, David J Adams, Sarah Atkins, Abdel Ayadi, Lore Becker, Andrew Blake, Debra Brooker, Heather Cater, Marie-France Champy, Roy Combe, Petr Danecek, Armida di Fenza, Hilary Gates, Anna-Karin Gerdin, Elisabetta Golini, John M Hancock et al. Genome Biology 2013, 14:R82 (31 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A comprehensive genomic and phenotypic analysis identifies significant differences between the widely used C57BL/6J and C57BL/6N mouse strains
	23. 1815 Accesses	Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, 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 \| Full text \| PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
	24. 1656 Accesses	Research Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie C Dunning Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Morgens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2010, 11:R107 (29 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Streptococcus pneumoniae genome analysis reveals that the presence of pathogenicity genes is not sufficient to determine virulence
	25. 1598 Accesses	Software Web Apollo: a web-based genomic annotation editing platform Eduardo Lee, Gregg A Helt, Justin T Reese, Monica C Munoz-Torres, Chris P Childers, Robert M Buels, Lincoln Stein, Ian H Holmes, Christine G Elsik, Suzanna E Lewis Genome Biology 2013, 14:R93 (30 August 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new web-based tool for international collaborations on genome annotations