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	26.	Research The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Pröschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean-Michel Claverie, Igor V Grigoriev, James L Van Etten Genome Biology 2012, 13:R39 (25 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome of a polar eukaryotic microorganism, an alga called Coccomyxa subellipsoidea C-169, reveals universal strategies for cold adaptation
	27.	Research Whole-genome reconstruction and mutational signatures in gastric cancer Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Zang, Fei Yao, Pierre-Étienne Jacques, Audrey SM Teo, Ioana Cutcutache, Zhenshui Zhang, Wah Lee, Yee Sia, Song Gao, Pramila N Ariyaratne, Andrea Ho, Xing Woo, Lavanya Veeravali, Choon Ong, Niantao Deng, Kartiki V Desai, Chiea Khor, Martin L Hibberd, Atif Shahab, Jaideepraj Rao, Mengchu Wu, Ming Teh, Feng Zhu, Sze Chin, Brendan Pang, Jimmy BY So, Guillaume Bourque et al. Genome Biology 2012, 13:R115 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
	28.	Research Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice Falk Hildebrand, Thi Loan Anh Nguyen, Brigitta Brinkman, Roberto Yunta, Benedicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes Genome Biology 2013, 14:R4 (24 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study finds that enterotypes are not only present in mice, but also similar to those in humans
	29.	Research Retrotransposition of gene transcripts leads to structural variation in mammalian genomes Adam D Ewing, Tracy J Ballinger, Dent Earl, Broad Institute Genome Sequencing and Analysis Program and Platform, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
	30.	Research Developmental features of DNA methylation during activation of the embryonic zebrafish genome Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation
	31.	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
	32.	Research The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes Minna-Liisa Änkö, Michaela Müller-McNicoll, Holger Brandl, Tomaz Curk, Crtomir Gorup, Ian Henry, Jernej Ule, Karla M Neugebauer Genome Biology 2012, 13:R17 (21 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA-binding protein SRSF3 is the master regulator of a splicing network, and - together with SRSF4 - mysteriously regulates unsplicable histone transcripts
	33.	Research High levels of RNA-editing site conservation amongst 15 laboratory mouse strains Petr Danecek, Christoffer Nellåker, Rebecca E McIntyre, Jorge E Buendia-Buendia, Suzannah Bumpstead, Chris P Ponting, Jonathan Flint, Richard Durbin, Thomas M Keane, David J Adams Genome Biology 2012, 13:r26 (23 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extensive, genome-wide analysis of RNA editing in the brain transcriptomes of 15 mouse strains
	34.	Research Wound healing and inflammation genes revealed by array analysis of 'macrophageless' PU.1 null mice Lisa Cooper, Claire Johnson, Frank Burslem, Paul Martin Genome Biology 2004, 6:R5 (23 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To define the events in wound healing that are independent of inflammation, gene expression during wound healing was profiled in wild-type mice and PU.1 null mice, which cannot raise the standard inflammatory response but which can repair skin wounds rapidly.
	35.	Comment Science: it's a role model thing Chris Gunter Genome Biology 2013, 14:105 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science
	36.	Research 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 \| PubMed \| Cited on BioMed Central \| Editor’s summary A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
	37.	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
	38.	Minireview Koala retrovirus: a genome invasion in real time Jonathan P Stoye Genome Biology 2006, 7:241 (21 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Koalas are currently undergoing a wave of germline retroviral infection, which is spreading throughout Australia.
	39.	Research A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert S Chapkin Genome Biology 2012, 13:r32 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
	40.	Method A computational framework for boosting confidence in high-throughput protein-protein interaction datasets Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger Genome Biology 2012, 13:R76 (31 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Coev2Net is a method for assigning confidence to high-throughput protein-protein interaction predictions
	41.	Method MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks Edward Vitkin, Tomer Shlomi Genome Biology 2012, 13:R111 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
	42.	Research 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells Hume Stroud, Suhua Feng, Shannon Morey Kinney, Sriharsa Pradhan, Steven E Jacobsen Genome Biology 2011, 12:R54 (20 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide study in hESCs finds that the modified base 5-hydroxymethylcytosine is enriched in enhancer regions and gene bodies
	43.	Research A comparative analysis of exome capture Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer, W Richard McCombie Genome Biology 2011, 12:R97 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The coverage of two solution exome capture kits is compared
	44.	Software MetAMOS: a modular and open source metagenomic assembly and analysis pipeline Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya, Brian Ondov, Aaron E Darling, Adam M Phillippy, Mihai Pop Genome Biology 2013, 14:R2 (15 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A modular, metagenomic analysis and assembly pipeline that inputs next-generation sequencing reads to generate genomic scaffolds and open reading frames
	45.	Correspondence Do-it-yourself genetic testing Steven L Salzberg, Mihaela Pertea Genome Biology 2010, 11:404 (7 October 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary How to test your BRCA status and why we need to prepare for the personal genomics age.
	46.	Research Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes Cecilia Alsmark, Peter G Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T Martin Embley, Robert P Hirt Genome Biology 2013, 14:R19 (25 February 2013) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes
	47.	Research Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional chinese medicine Peng Zheng, Yongliang Xia, Guohua Xiao, Chenghui Xiong, Xiao Hu, Siwei Zhang, Huajun Zheng, Yin Huang, Yan Zhou, Shengyue Wang, Guo-Ping Zhao, Xingzhong Liu, Raymond J St Leger, Chengshu Wang Genome Biology 2011, 12:R116 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome and transcriptome sequences of Cordyceps militaris, a fungal pathogen of insects that is used in traditional Chinese medicine
	48.	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
	49.	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
	50.	Research Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.