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		Research Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase Radek Szklarczyk, Bas FJ Wanschers, Thomas D Cuypers, John J Esseling, Moniek Riemersma, Mariël AM van den Brand, Jolein Gloerich, Edwin Lasonder, Lambert P van den Heuvel, Leo G Nijtmans, Martijn A Huynen Genome Biology 2012, 13:R12 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An iterative orthology prediction method identifies previously uncharacterized human orthologs of yeast mitochondrial proteins that are robust to multiple validation approaches
		Research highlight Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Anke Busch, Klemens J Hertel Genome Biology 2012, 13:143 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Anke Busch and Klemens Hertel highlight a recent RNA-seq study demonstrating that alternative tandem acceptor splicing is tissue-specifically regulated
		Research Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells Najeeb U Siddiqui, Xiao Li, Hua Luo, Angelo Karaiskakis, Huayun Hou, Thomas Kislinger, J Timothy Westwood, Quaid Morris, Howard D Lipshitz Genome Biology 2012, 13:R11 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maternal-to-zygotic transition in Drosophila primordial germ cells is delayed relative to the soma and requires the RNA-binding protein Smaug
		Research Autosomal monoallelic expression in the mouse Lillian M Zwemer, Alexander Zak, Benjamin R Thompson, Andrew Kirby, Mark J Daly, Andrew Chess, Alexander A Gimelbrant Genome Biology 2012, 13:R10 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive genome-wide analysis of random monoallelic expression in mouse, and a detailed comparison with human
		Editorial The Research Works Act: a comment Naomi Attar, GB Editorial Team Genome Biology 2012, 13:416 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A bill before Congress aims to skew the market and bar those paying for research (taxpayers) from access to its benefits
		Review Synthetic biology: advancing biological frontiers by building synthetic systems Yvonne Y Chen, Kate E Galloway, Christina D Smolke Genome Biology 2012, 13:240 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Christina Smolke and colleagues review an emerging science, whose frontiers include biomanufacturing, radical therapeutic approaches, and insights into natural biological systems
		Review The genetic basis of alcoholism: multiple phenotypes, many genes, complex networks Tatiana V Morozova, David Goldman, Trudy FC Mackay, Robert RH Anholt Genome Biology 2012, 13:239 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Robert Anholt and colleagues describe the genetics underlying alcohol-related phenotypes emerging from GWAS and work on genetically tractable model organisms
		Method Predicting the effects of frameshifting indels Jing Hu, Pauline C Ng Genome Biology 2012, 13:R9 (9 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SIFT Indel is a method for predicting the effects of frameshifting indels in coding regions
		Research Population-specificity of human DNA methylation Hunter B Fraser, Lucia L Lam, Sarah M Neumann, Michael S Kobor Genome Biology 2012, 13:R8 (9 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Measurement of TSS-proximal DNA methylation in CEU and YRI genomes reveals significant population specificity
		Research Dissecting the regulatory architecture of gene expression QTLs Daniel J Gaffney, Jean-Baptiste Veyrieras, Jacob F Degner, Roger Pique-Regi, Athma A Pai, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard Genome Biology 2012, 13:R7 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of eQTLs located in regulatory elements in the human genome
		Method MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis Leonid Chindelevitch, Sarah Stanley, Deborah Hung, Aviv Regev, Bonnie Berger Genome Biology 2012, 13:r6 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An algorithm that reconciles metabolic network reconstructions into a single model
		Method Uberon, an integrative multi-species anatomy ontology Christopher J Mungall, Carlo Torniai, Georgios V Gkoutos, Suzanna E Lewis, Melissa A Haendel Genome Biology 2012, 13:R5 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A description of the Uberon ontology tool that allows comparisons of genomic information across multiple animal phyla
		Method SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data Mark F Rogers, Julie Thomas, Anireddy SN Reddy, Asa Ben-Hur Genome Biology 2012, 13:R4 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tool that uses a priori information to optimize alternative splicing prediction from RNA-seq data
		Open letter Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes John A St John, Edward L Braun, Sally R Isberg, Lee G Miles, Amanda Y Chong, Jaime Gongora, Pauline Dalzell, Christopher Moran, Bertrand Bed'Hom, Arkhat Abzhanov, Shane C Burgess, Amanda M Cooksey, Todd A Castoe, Nicholas G Crawford, Llewellyn D Densmore, Jennifer C Drew, Scott V Edwards, Brant C Faircloth, Matthew K Fujita, Matthew J Greenwold, Federico G Hoffmann, Jonathan M Howard, Taisen Iguchi, Daniel E Janes, Shahid Khan, Satomi Kohno, AP Jason de Koning, Stacey L Lance, Fiona M McCarthy, John E McCormack et al. Genome Biology 2012, 13:415 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial
		Meeting report Dynamic systems Chris Bakal Genome Biology 2012, 13:312 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011.
		Meeting report Low-cost sequencing opens new insights into diverse plant genomes Kenneth D Birnbaum Genome Biology 2012, 13:311 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2011 ?Plant Genomes and Biotechnology: From Genes to Networks? meeting, held at Cold Spring Harbor Laboratory.
		Comment The dog particle Gregory A Petsko Genome Biology 2012, 13:142 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In a big announcement suspiciously soon before their funding is renewed, canine researchers have news about the Briggs Noson
		Research highlight Co-survival of the fittest few: mosaic amplification of receptor tyrosine kinases in glioblastoma Feng Chen, Li Ding Genome Biology 2012, 13:141 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Li Ding highlights recent findings suggesting that tumor cells with different driver mutations may coevolve rather than compete during clonal evolution
		Research highlight Whack-an-E. coli with the morbidostat Ofer Fridman, Amir Goldberg, Nathalie Q Balaban Genome Biology 2012, 13:140 (27 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Nathalie Balaban and colleagues highlight a landmark study of antibiotic resistance evolutionary trajectories, which is centered on a morbidostat
		Research highlight DNA-protein interactions in high definition Eric M Mendenhall, Bradley E Bernstein Genome Biology 2012, 13:139 (27 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mendenhall and Bernstein highlight ChIP-exo, which is an elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors
		Research A genome triplication associated with early diversification of the core eudicots Yuannian Jiao, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E Bowers, Michael R McKain, Joel McNeal, Megan Rolf, Daniel R Ruzicka, Eric Wafula, Norman J Wickett, Xiaolei Wu, Yong Zhang, Jun Wang, Yeting Zhang, Eric J Carpenter, Michael K Deyholos, Toni M Kutchan, Andre S Chanderbali, Pamela S Soltis, Dennis W Stevenson, Richard McCombie, J Pires, Gane Wong, Douglas E Soltis, Claude W dePamphilis Genome Biology 2012, 13:R3 (26 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An investigation of when the gamma polyploidization event occurred in relation to speciation events in angiosperm history
		Research Implications for health and disease in the genetic signature of the Ashkenazi Jewish population Saurav Guha, Jeffrey A Rosenfeld, Anil K Malhotra, Annette T Lee, Peter K Gregersen, John M Kane, Itsik Pe'er, Ariel Darvasi, Todd Lencz Genome Biology 2012, 13:R2 (25 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A population-specific genetic signature, derived from a large genotyping study, helps explain why some diseases are overrepresented in the Ashkenazi population
		Review Transcriptional enhancers in development and disease Noboru Sakabe, Daniel Savic, Marcelo A Nobrega Genome Biology 2012, 13:238 (23 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Distal enhancers are important in development and disease, and genome-wide analyses are now giving greater insights into their function
		Opinion What is complex about complex disorders? Kevin J Mitchell Genome Biology 2012, 13:237 (23 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Complex disorders such as diabetes and schizophrenia are really groups of many distinct genetic disorders caused by rare, recent deleterious mutations
		Research Genetic adaptation to high altitude in the Ethiopian highlands Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Woldemeskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff Genome Biology 2012, 13:R1 (20 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genetics of hypoxia selection in an Ethiopian high-altitude population are distinct from Andean and Tibetan genotypes, suggestive of convergent evolution
		Correction Correction: Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, Ichizo Kobayashi Genome Biology 2011, 12:412 (15 January 2012) Abstract \| Full text \| PDF
		Correction Correction: Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes Carolina Bartolomé, Xabier Bello, Xulio Maside Genome Biology 2011, 12:411 (15 January 2012) Abstract \| Full text \| PDF
		Research Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera Tom A Mendum, Jane Newcombe, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden Genome Biology 2011, 12:R127 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A global screen of mutant fitness in Neisseria meningitidis was used to construct a genome-scale metabolic network
		Research MicroRNAs and their isomiRs function cooperatively to target common biological pathways Nicole Cloonan, Shivangi Wani, Qinying Xu, Jian Gu, Kristi Lea, Sheila Heater, Catalin Barbacioru, Anita L Steptoe, Hilary C Martin, Ehsan Nourbakhsh, Keerthana Krishnan, Brooke Gardiner, Xiaohui Wang, Katia Nones, Jason A Steen, Nicholas A Matigian, David L Wood, Karin S Kassahn, Nic Waddell, Jill Shepherd, Clarence Lee, Jeff Ichikawa, Kevin McKernan, Kelli Bramlett, Scott Kuersten, Sean M Grimmond Genome Biology 2011, 12:R126 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
		Correction Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Y Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:414 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
		Correction SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:413 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: A method to detect condition-specific gene expression from microarray data
		Research highlight Making enhancers from spare parts of the genome David Fredman, Xianjun Dong, Boris Lenhard Genome Biology 2011, 12:138 (29 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Boris Lenhard and colleagues on how developmental enhancers form in genomes by the recycling of existing functional elements
		Meeting report Opening sequence: computational genomics in the era of high-throughput sequencing Emily V Chambers, Alida S Kindt, Colin AM Semple Genome Biology 2011, 12:310 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011.
		Review Alu elements: know the SINEs Prescott Deininger Genome Biology 2011, 12:236 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prescott Deininger reviews the contribution of Alu elements to genome evolution, gene regulation and disease
		Review Evolution of biological interaction networks: from models to real data Mark GF Sun, Philip M Kim Genome Biology 2011, 12:235 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sun and Kim review progress in the study of biological network evolution, with a focus on the protein-protein interaction network
		Opinion Genomics in 2011: challenges and opportunities David J Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X Shirley Liu, Chad L Myers, Alicia Oshlack, John L Rinn, Albertha J M Walhout Genome Biology 2011, 12:137 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Several members of the Genome Biology Editorial Board give their views on the state of play in genomics
		Comment The Columnist Manifesto Gregory A Petsko Genome Biology 2011, 12:136 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scientists need to explain to the public what science is and why it needs funding, especially when the economic situation is bad
		Research highlight Games with a scientific purpose Benjamin M Good, Andrew I Su Genome Biology 2011, 12:135 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potent algorithms and solved "unsolvable" structures: are the 230,000 players of the protein folding game Foldit the scientists of the future?
		Research Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights Raluca Gordân, Kevin F Murphy, Rachel P McCord, Cong Zhu, Anastasia Vedenko, Martha L Bulyk Genome Biology 2011, 12:R125 (21 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive resource of DNA binding specificity data for all characterized Saccharomyces cerevisiae transcription factors
		Method Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples
		Research Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism Peter Meister, Sonia Schott, Cécile Bedet, Yu Xiao, Sabine Rohner, Selena Bodennec, Bruno Hudry, Laurent Molin, Florence Solari, Susan M Gasser, Francesca Palladino Genome Biology 2011, 12:R123 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary HPL-2, the C. elegans homolog of heterochromatin protein 1, helps regulate longevity, dauer diapause and lipid metabolism
		Method Accurate proteome-wide protein quantification from high-resolution ¹⁵N mass spectra Zia Khan, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, Saeed Tavazoie Genome Biology 2011, 12:R122 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fast, user-friendly bioinformatic tool for accurate quantification of proteins in 15N mass spectrometry data
		Research Loss of the bloom syndrome helicase increases DNA ligase 4-independent genome rearrangements and tumorigenesis in aging Drosophila Ana Garcia, Robert N Salomon, Alice Witsell, Justine Liepkalns, R Brent Calder, Moonsook Lee, Martha Lundell, Jan Vijg, Mitch McVey Genome Biology 2011, 12:R121 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Drosophila blm mutants show an increase in genome rearrangements which, surprisingly, are independent of DNA ligase 4
		Research The relationship between proteome size, structural disorder and organism complexity Eva Schad, Peter Tompa, Hedi Hegyi Genome Biology 2011, 12:R120 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Complexity is a multi-parametric trait, determined by interaction potential, alternative splicing capacity, protein disorder and, above all, proteome size
		Research RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.) Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse Genome Biology 2011, 12:R119 (2 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization
		Comment Dominoes Gregory A Petsko Genome Biology 2011, 12:134 (30 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If we fund the next big science program, how many smaller research programs will receive no funding as a consequence?
		Research highlight BRD4 jump-starts transcription after mitotic silencing Philipp Voigt, Danny Reinberg Genome Biology 2011, 12:133 (29 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Voigt and Danny Reinberg highlight BRD4's role in gene bookmarking during mitosis, and how this might be exploited in chemotherapy
		Research Hundreds of putatively functional small open reading frames in Drosophila Emmanuel Ladoukakis, Vini Pereira, Emile G Magny, Adam Eyre-Walker, Juan Pablo Couso Genome Biology 2011, 12:R118 (25 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Drosophila genome contains hundreds of small open reading frames with putative functionality
		Meeting report Human genetics in full resolution Alicia Schiavi, Nicholas Light, Veronique Adoue, Stephan Busche, Tomi Pastinen Genome Biology 2011, 12:309 (24 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 12th International Congress of Human Genetics, and the annual American Society of Human Genetics conference, October 2011
		Research Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism Rajesh Pandey, Amit K Mandal, Vineet Jha, Mitali Mukerji Genome Biology 2011, 12:R117 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary HSF binding to conserved sites in Alu repeats initiates an antisense transcript-mediated response to heat shock

	All
		Research Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase Radek Szklarczyk, Bas FJ Wanschers, Thomas D Cuypers, John J Esseling, Moniek Riemersma, Mariël AM van den Brand, Jolein Gloerich, Edwin Lasonder, Lambert P van den Heuvel, Leo G Nijtmans, Martijn A Huynen Genome Biology 2012, 13:R12 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An iterative orthology prediction method identifies previously uncharacterized human orthologs of yeast mitochondrial proteins that are robust to multiple validation approaches
		Research highlight Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Anke Busch, Klemens J Hertel Genome Biology 2012, 13:143 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Anke Busch and Klemens Hertel highlight a recent RNA-seq study demonstrating that alternative tandem acceptor splicing is tissue-specifically regulated
		Research Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells Najeeb U Siddiqui, Xiao Li, Hua Luo, Angelo Karaiskakis, Huayun Hou, Thomas Kislinger, J Timothy Westwood, Quaid Morris, Howard D Lipshitz Genome Biology 2012, 13:R11 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maternal-to-zygotic transition in Drosophila primordial germ cells is delayed relative to the soma and requires the RNA-binding protein Smaug
		Research Autosomal monoallelic expression in the mouse Lillian M Zwemer, Alexander Zak, Benjamin R Thompson, Andrew Kirby, Mark J Daly, Andrew Chess, Alexander A Gimelbrant Genome Biology 2012, 13:R10 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive genome-wide analysis of random monoallelic expression in mouse, and a detailed comparison with human
		Editorial The Research Works Act: a comment Naomi Attar, GB Editorial Team Genome Biology 2012, 13:416 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A bill before Congress aims to skew the market and bar those paying for research (taxpayers) from access to its benefits
		Review Synthetic biology: advancing biological frontiers by building synthetic systems Yvonne Y Chen, Kate E Galloway, Christina D Smolke Genome Biology 2012, 13:240 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Christina Smolke and colleagues review an emerging science, whose frontiers include biomanufacturing, radical therapeutic approaches, and insights into natural biological systems
		Review The genetic basis of alcoholism: multiple phenotypes, many genes, complex networks Tatiana V Morozova, David Goldman, Trudy FC Mackay, Robert RH Anholt Genome Biology 2012, 13:239 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Robert Anholt and colleagues describe the genetics underlying alcohol-related phenotypes emerging from GWAS and work on genetically tractable model organisms
		Method Predicting the effects of frameshifting indels Jing Hu, Pauline C Ng Genome Biology 2012, 13:R9 (9 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SIFT Indel is a method for predicting the effects of frameshifting indels in coding regions
		Research Population-specificity of human DNA methylation Hunter B Fraser, Lucia L Lam, Sarah M Neumann, Michael S Kobor Genome Biology 2012, 13:R8 (9 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Measurement of TSS-proximal DNA methylation in CEU and YRI genomes reveals significant population specificity
		Research Dissecting the regulatory architecture of gene expression QTLs Daniel J Gaffney, Jean-Baptiste Veyrieras, Jacob F Degner, Roger Pique-Regi, Athma A Pai, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard Genome Biology 2012, 13:R7 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of eQTLs located in regulatory elements in the human genome
		Method MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis Leonid Chindelevitch, Sarah Stanley, Deborah Hung, Aviv Regev, Bonnie Berger Genome Biology 2012, 13:r6 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An algorithm that reconciles metabolic network reconstructions into a single model
		Method Uberon, an integrative multi-species anatomy ontology Christopher J Mungall, Carlo Torniai, Georgios V Gkoutos, Suzanna E Lewis, Melissa A Haendel Genome Biology 2012, 13:R5 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A description of the Uberon ontology tool that allows comparisons of genomic information across multiple animal phyla
		Method SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data Mark F Rogers, Julie Thomas, Anireddy SN Reddy, Asa Ben-Hur Genome Biology 2012, 13:R4 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tool that uses a priori information to optimize alternative splicing prediction from RNA-seq data
		Open letter Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes John A St John, Edward L Braun, Sally R Isberg, Lee G Miles, Amanda Y Chong, Jaime Gongora, Pauline Dalzell, Christopher Moran, Bertrand Bed'Hom, Arkhat Abzhanov, Shane C Burgess, Amanda M Cooksey, Todd A Castoe, Nicholas G Crawford, Llewellyn D Densmore, Jennifer C Drew, Scott V Edwards, Brant C Faircloth, Matthew K Fujita, Matthew J Greenwold, Federico G Hoffmann, Jonathan M Howard, Taisen Iguchi, Daniel E Janes, Shahid Khan, Satomi Kohno, AP Jason de Koning, Stacey L Lance, Fiona M McCarthy, John E McCormack et al. Genome Biology 2012, 13:415 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial
		Meeting report Dynamic systems Chris Bakal Genome Biology 2012, 13:312 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011.
		Meeting report Low-cost sequencing opens new insights into diverse plant genomes Kenneth D Birnbaum Genome Biology 2012, 13:311 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2011 ?Plant Genomes and Biotechnology: From Genes to Networks? meeting, held at Cold Spring Harbor Laboratory.
		Comment The dog particle Gregory A Petsko Genome Biology 2012, 13:142 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In a big announcement suspiciously soon before their funding is renewed, canine researchers have news about the Briggs Noson
		Research highlight Co-survival of the fittest few: mosaic amplification of receptor tyrosine kinases in glioblastoma Feng Chen, Li Ding Genome Biology 2012, 13:141 (30 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Li Ding highlights recent findings suggesting that tumor cells with different driver mutations may coevolve rather than compete during clonal evolution
		Research highlight Whack-an-E. coli with the morbidostat Ofer Fridman, Amir Goldberg, Nathalie Q Balaban Genome Biology 2012, 13:140 (27 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Nathalie Balaban and colleagues highlight a landmark study of antibiotic resistance evolutionary trajectories, which is centered on a morbidostat
		Research highlight DNA-protein interactions in high definition Eric M Mendenhall, Bradley E Bernstein Genome Biology 2012, 13:139 (27 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mendenhall and Bernstein highlight ChIP-exo, which is an elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors
		Research A genome triplication associated with early diversification of the core eudicots Yuannian Jiao, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E Bowers, Michael R McKain, Joel McNeal, Megan Rolf, Daniel R Ruzicka, Eric Wafula, Norman J Wickett, Xiaolei Wu, Yong Zhang, Jun Wang, Yeting Zhang, Eric J Carpenter, Michael K Deyholos, Toni M Kutchan, Andre S Chanderbali, Pamela S Soltis, Dennis W Stevenson, Richard McCombie, J Pires, Gane Wong, Douglas E Soltis, Claude W dePamphilis Genome Biology 2012, 13:R3 (26 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An investigation of when the gamma polyploidization event occurred in relation to speciation events in angiosperm history
		Research Implications for health and disease in the genetic signature of the Ashkenazi Jewish population Saurav Guha, Jeffrey A Rosenfeld, Anil K Malhotra, Annette T Lee, Peter K Gregersen, John M Kane, Itsik Pe'er, Ariel Darvasi, Todd Lencz Genome Biology 2012, 13:R2 (25 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A population-specific genetic signature, derived from a large genotyping study, helps explain why some diseases are overrepresented in the Ashkenazi population
		Review Transcriptional enhancers in development and disease Noboru Sakabe, Daniel Savic, Marcelo A Nobrega Genome Biology 2012, 13:238 (23 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Distal enhancers are important in development and disease, and genome-wide analyses are now giving greater insights into their function
		Opinion What is complex about complex disorders? Kevin J Mitchell Genome Biology 2012, 13:237 (23 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Complex disorders such as diabetes and schizophrenia are really groups of many distinct genetic disorders caused by rare, recent deleterious mutations
		Research Genetic adaptation to high altitude in the Ethiopian highlands Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Woldemeskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff Genome Biology 2012, 13:R1 (20 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genetics of hypoxia selection in an Ethiopian high-altitude population are distinct from Andean and Tibetan genotypes, suggestive of convergent evolution
		Correction Correction: Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, Ichizo Kobayashi Genome Biology 2011, 12:412 (15 January 2012) Abstract \| Full text \| PDF
		Correction Correction: Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes Carolina Bartolomé, Xabier Bello, Xulio Maside Genome Biology 2011, 12:411 (15 January 2012) Abstract \| Full text \| PDF
		Research Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera Tom A Mendum, Jane Newcombe, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden Genome Biology 2011, 12:R127 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A global screen of mutant fitness in Neisseria meningitidis was used to construct a genome-scale metabolic network
		Research MicroRNAs and their isomiRs function cooperatively to target common biological pathways Nicole Cloonan, Shivangi Wani, Qinying Xu, Jian Gu, Kristi Lea, Sheila Heater, Catalin Barbacioru, Anita L Steptoe, Hilary C Martin, Ehsan Nourbakhsh, Keerthana Krishnan, Brooke Gardiner, Xiaohui Wang, Katia Nones, Jason A Steen, Nicholas A Matigian, David L Wood, Karin S Kassahn, Nic Waddell, Jill Shepherd, Clarence Lee, Jeff Ichikawa, Kevin McKernan, Kelli Bramlett, Scott Kuersten, Sean M Grimmond Genome Biology 2011, 12:R126 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
		Correction Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Y Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:414 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology
		Correction SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:413 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: A method to detect condition-specific gene expression from microarray data
		Research highlight Making enhancers from spare parts of the genome David Fredman, Xianjun Dong, Boris Lenhard Genome Biology 2011, 12:138 (29 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Boris Lenhard and colleagues on how developmental enhancers form in genomes by the recycling of existing functional elements
		Meeting report Opening sequence: computational genomics in the era of high-throughput sequencing Emily V Chambers, Alida S Kindt, Colin AM Semple Genome Biology 2011, 12:310 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011.
		Review Alu elements: know the SINEs Prescott Deininger Genome Biology 2011, 12:236 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prescott Deininger reviews the contribution of Alu elements to genome evolution, gene regulation and disease
		Review Evolution of biological interaction networks: from models to real data Mark GF Sun, Philip M Kim Genome Biology 2011, 12:235 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sun and Kim review progress in the study of biological network evolution, with a focus on the protein-protein interaction network
		Opinion Genomics in 2011: challenges and opportunities David J Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X Shirley Liu, Chad L Myers, Alicia Oshlack, John L Rinn, Albertha J M Walhout Genome Biology 2011, 12:137 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Several members of the Genome Biology Editorial Board give their views on the state of play in genomics
		Comment The Columnist Manifesto Gregory A Petsko Genome Biology 2011, 12:136 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scientists need to explain to the public what science is and why it needs funding, especially when the economic situation is bad
		Research highlight Games with a scientific purpose Benjamin M Good, Andrew I Su Genome Biology 2011, 12:135 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potent algorithms and solved "unsolvable" structures: are the 230,000 players of the protein folding game Foldit the scientists of the future?
		Research Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights Raluca Gordân, Kevin F Murphy, Rachel P McCord, Cong Zhu, Anastasia Vedenko, Martha L Bulyk Genome Biology 2011, 12:R125 (21 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive resource of DNA binding specificity data for all characterized Saccharomyces cerevisiae transcription factors
		Method Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples
		Research Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism Peter Meister, Sonia Schott, Cécile Bedet, Yu Xiao, Sabine Rohner, Selena Bodennec, Bruno Hudry, Laurent Molin, Florence Solari, Susan M Gasser, Francesca Palladino Genome Biology 2011, 12:R123 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary HPL-2, the C. elegans homolog of heterochromatin protein 1, helps regulate longevity, dauer diapause and lipid metabolism
		Method Accurate proteome-wide protein quantification from high-resolution ¹⁵N mass spectra Zia Khan, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, Saeed Tavazoie Genome Biology 2011, 12:R122 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fast, user-friendly bioinformatic tool for accurate quantification of proteins in 15N mass spectrometry data
		Research Loss of the bloom syndrome helicase increases DNA ligase 4-independent genome rearrangements and tumorigenesis in aging Drosophila Ana Garcia, Robert N Salomon, Alice Witsell, Justine Liepkalns, R Brent Calder, Moonsook Lee, Martha Lundell, Jan Vijg, Mitch McVey Genome Biology 2011, 12:R121 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Drosophila blm mutants show an increase in genome rearrangements which, surprisingly, are independent of DNA ligase 4
		Research The relationship between proteome size, structural disorder and organism complexity Eva Schad, Peter Tompa, Hedi Hegyi Genome Biology 2011, 12:R120 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Complexity is a multi-parametric trait, determined by interaction potential, alternative splicing capacity, protein disorder and, above all, proteome size
		Research RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.) Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse Genome Biology 2011, 12:R119 (2 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization
		Comment Dominoes Gregory A Petsko Genome Biology 2011, 12:134 (30 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If we fund the next big science program, how many smaller research programs will receive no funding as a consequence?
		Research highlight BRD4 jump-starts transcription after mitotic silencing Philipp Voigt, Danny Reinberg Genome Biology 2011, 12:133 (29 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Voigt and Danny Reinberg highlight BRD4's role in gene bookmarking during mitosis, and how this might be exploited in chemotherapy
		Research Hundreds of putatively functional small open reading frames in Drosophila Emmanuel Ladoukakis, Vini Pereira, Emile G Magny, Adam Eyre-Walker, Juan Pablo Couso Genome Biology 2011, 12:R118 (25 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Drosophila genome contains hundreds of small open reading frames with putative functionality
		Meeting report Human genetics in full resolution Alicia Schiavi, Nicholas Light, Veronique Adoue, Stephan Busche, Tomi Pastinen Genome Biology 2011, 12:309 (24 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 12th International Congress of Human Genetics, and the annual American Society of Human Genetics conference, October 2011
		Research Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism Rajesh Pandey, Amit K Mandal, Vineet Jha, Mitali Mukerji Genome Biology 2011, 12:R117 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary HSF binding to conserved sites in Alu repeats initiates an antisense transcript-mediated response to heat shock