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		Method Predicting the effects of frameshifting indels Jing Hu, Pauline C Ng Genome Biology 2012, 13:R9 (9 February 2012) Abstract \| Provisional PDF \| 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 Lam, Sarah Neumann, Michael S Kobor Genome Biology 2012, 13:R8 (9 February 2012) Abstract \| Provisional PDF \| Editor’s summary Measurement of TSS-proximal DNA methylation in CEU and YRI genomes reveals significant population specificity
		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 Genome Biology 2012, 13:415 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial
		Research Dissecting the regulatory architecture of gene expression QTLs Daniel J Gaffney, Jean-Baptiste Veyrieras, Jacob F Degner, Pique-Regi Roger, Athma A Pai, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard Genome Biology 2012, 13:R7 (31 January 2012) Abstract \| Provisional PDF \| PubMed \| 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 \| Provisional PDF \| PubMed \| 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 \| Provisional PDF \| PubMed \| 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 \| Provisional PDF \| PubMed \| Editor’s summary A tool that uses a priori information to optimize alternative splicing prediction from RNA-seq data
		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
		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.
		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 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 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, Chris J Pires, Gane KA-SHU Wong, Douglas E Soltis, Claude W dePamphilis Genome Biology 2012, 13:R3 (26 January 2012) Abstract \| Provisional PDF \| PubMed \| 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 \| Provisional 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
		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
		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 \| Editor’s summary Distal enhancers are important in development and disease, and genome-wide analyses are now giving greater insights into their function
		Research Genetic adaptation to high altitude in the Ethiopian highlands Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Wolde Meskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff Genome Biology 2012, 13:R1 (20 January 2012) Abstract \| Provisional PDF \| PubMed \| 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 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
		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 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
		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 A Kierzek, Johnjoe McFadden Genome Biology 2011, 12:R127 (30 December 2011) Abstract \| Provisional 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, Nick Matigan, 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 \| Provisional PDF \| PubMed \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
		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
		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
		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 \| Editor’s summary A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011.

	All
		Method Predicting the effects of frameshifting indels Jing Hu, Pauline C Ng Genome Biology 2012, 13:R9 (9 February 2012) Abstract \| Provisional PDF \| 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 Lam, Sarah Neumann, Michael S Kobor Genome Biology 2012, 13:R8 (9 February 2012) Abstract \| Provisional PDF \| Editor’s summary Measurement of TSS-proximal DNA methylation in CEU and YRI genomes reveals significant population specificity
		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 Genome Biology 2012, 13:415 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial
		Research Dissecting the regulatory architecture of gene expression QTLs Daniel J Gaffney, Jean-Baptiste Veyrieras, Jacob F Degner, Pique-Regi Roger, Athma A Pai, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard Genome Biology 2012, 13:R7 (31 January 2012) Abstract \| Provisional PDF \| PubMed \| 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 \| Provisional PDF \| PubMed \| 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 \| Provisional PDF \| PubMed \| 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 \| Provisional PDF \| PubMed \| Editor’s summary A tool that uses a priori information to optimize alternative splicing prediction from RNA-seq data
		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
		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.
		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 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 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, Chris J Pires, Gane KA-SHU Wong, Douglas E Soltis, Claude W dePamphilis Genome Biology 2012, 13:R3 (26 January 2012) Abstract \| Provisional PDF \| PubMed \| 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 \| Provisional 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
		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
		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 \| Editor’s summary Distal enhancers are important in development and disease, and genome-wide analyses are now giving greater insights into their function
		Research Genetic adaptation to high altitude in the Ethiopian highlands Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Wolde Meskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff Genome Biology 2012, 13:R1 (20 January 2012) Abstract \| Provisional PDF \| PubMed \| 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 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
		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 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
		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 A Kierzek, Johnjoe McFadden Genome Biology 2011, 12:R127 (30 December 2011) Abstract \| Provisional 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, Nick Matigan, 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 \| Provisional PDF \| PubMed \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
		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
		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
		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 \| Editor’s summary A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011.