Genome Biology | Volume 13 Issue 1

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	Volume 13 Issue 1
	Comment
	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 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 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
	Review
	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
	Report
	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.
	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.
	Research
	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
	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
	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 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 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
	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 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
	Correspondence
	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

	Volume 13 Issue 1
	Comment
	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 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 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
	Review
	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
	Report
	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.
	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.
	Research
	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
	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
	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 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 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
	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 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
	Correspondence
	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

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Volume 13 Issue 1

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