Genome Biology | Volume 12 Issue 5

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	Volume 12 Issue 5
	Comment
	Comment In praise of model organisms Gregory A Petsko Genome Biology 2011, 12:115 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Basic research in model organisms is crucial and needs defending against claims that it is irrelevant to human biology and disease.
	Research highlight A mystery unveiled Yves Van de Peer Genome Biology 2011, 12:113 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent phylogenomic study has provided new evidence for two ancient whole genome duplications in plants, with potential importance for the evolution of seed and flowering plants
	Research highlight The volatile microbiome George M Weinstock Genome Biology 2011, 12:114 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary George Weinstock highlights Genome Biology's latest research article on human microbiota
	Review
	Review Mapping of disease-associated variants in admixed populations Daniel Shriner, Adebowale Adeyemo, Edward Ramos, Guanjie Chen, Charles N Rotimi Genome Biology 2011, 12:223 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary High-throughput genotyping and sequencing will enable refined estimation of ancestry, thus enhancing disease loci identification in admixed populations
	Protein family review The lamin protein family Travis A Dittmer, Tom Misteli Genome Biology 2011, 12:222 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lamins are the major architectural proteins of animal nuclear membranes and are involved in a wide range of nuclear functions and human diseases.
	Report
	Meeting report Bright days for yeast research Martin Převorovský, Charalampos Rallis Genome Biology 2011, 12:305 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the British Yeast Group Meeting, Brighton, UK, 23-25 March 2011
	Research
	Research Modulated contact frequencies at gene-rich loci support a statistical helix model for mammalian chromatin organization Franck Court, Julie Miro, Caroline Braem, Marie-Noëlle Lelay-Taha, Audrey Brisebarre, Florian Atger, Thierry Gostan, Michaël Weber, Guy Cathala, Thierry Forné Genome Biology 2011, 12:R42 (10 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene-rich mammalian chromatin is shown by 3C-qPCR and polymer modeling to adopt a helical conformation
	Research Dynamic reprogramming of chromatin accessibility during Drosophila embryo development Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos Genome Biology 2011, 12:R43 (11 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A map of the dynamically changing chromatin landscape throughout Drosophila development.
	Research A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi James K Hane, Thierry Rouxel, Barbara J Howlett, Gert HJ Kema, Stephen B Goodwin, Richard P Oliver Genome Biology 2011, 12:R45 (24 May 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Mesosynteny, in which genes are maintained on the same chromosome but in different orders, is revealed in different ascomycete species
	Research Copy number polymorphisms and anticancer pharmacogenomics Eric R Gamazon, R Stephanie Huang, M Eileen Dolan, Nancy J Cox Genome Biology 2011, 12:R46 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Copy number polymorphisms are shown to significantly contribute to the sensitivity to anticancer drugs
	Research A high resolution map of a cyanobacterial transcriptome Vikram Vijayan, Isha H Jain, Erin K O'Shea Genome Biology 2011, 12:R47 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed transcriptome analysis of the cyanobacterium Synechococcus elongatus reveals widespread non coding transcription and transcript architecture
	Research A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure Andrea Zuccolo, John E Bowers, James C Estill, Zhiyong Xiong, Meizhong Luo, Aswathy Sebastian, José Goicoechea, Kristi Collura, Yeisoo Yu, Yuannian Jiao, Jill Duarte, Haibao Tang, Saravanaraj Ayyampalayam, Steve Rounsley, Dave Kudrna, Andrew H Paterson, J Pires, Andre Chanderbali, Douglas E Soltis, Srikar Chamala, Brad Barbazuk, Pamela S Soltis, Victor A Albert, Hong Ma, Dina Mandoli, Jody Banks, John E Carlson, Jeffrey Tomkins, Claude W dePamphilis, Rod A Wing, Jim Leebens-Mack et al. Genome Biology 2011, 12:R48 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mapping an outlier helps reconstruct the polyploidy timeline in angiosperms
	Research Moving pictures of the human microbiome J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon, Rob Knight Genome Biology 2011, 12:R50 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The dynamism of microbiome populations is seen in daily samples from a landmark multi-body site, multi-individual study
	Research Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths Jacob Enk, Alison Devault, Regis Debruyne, Christine E King, Todd Treangen, Dennis O'Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee, Hendrik Poinar Genome Biology 2011, 12:R51 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A surprising mtDNA phylogeny suggests that North American woolly mammoths bred with the distinct Columbian mammoth species
	Research Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection Omer Gokcumen, Paul L Babb, Rebecca C Iskow, Qihui Zhu, Xinghua Shi, Ryan E Mills, Iuliana Ionita-Laza, Eric J Vallender, Andrew G Clark, Welkin E Johnson, Charles Lee Genome Biology 2011, 12:R52 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Identification of overlapping copy number variation hotspots in chimpanzee, macaque and human
	Method EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield Genome Biology 2011, 12:R44 (19 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Reconstructing full length rRNA sequences from short reads to estimate microbial community structure
	Method Path finding methods accounting for stoichiometry in metabolic networks Jon Pey, Joaquín Prada, John E Beasley, Francisco J Planes Genome Biology 2011, 12:R49 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The incorporation of stoichiometry into path finding improves metabolic network analysis

	Volume 12 Issue 5
	Comment
	Comment In praise of model organisms Gregory A Petsko Genome Biology 2011, 12:115 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Basic research in model organisms is crucial and needs defending against claims that it is irrelevant to human biology and disease.
	Research highlight A mystery unveiled Yves Van de Peer Genome Biology 2011, 12:113 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent phylogenomic study has provided new evidence for two ancient whole genome duplications in plants, with potential importance for the evolution of seed and flowering plants
	Research highlight The volatile microbiome George M Weinstock Genome Biology 2011, 12:114 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary George Weinstock highlights Genome Biology's latest research article on human microbiota
	Review
	Review Mapping of disease-associated variants in admixed populations Daniel Shriner, Adebowale Adeyemo, Edward Ramos, Guanjie Chen, Charles N Rotimi Genome Biology 2011, 12:223 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary High-throughput genotyping and sequencing will enable refined estimation of ancestry, thus enhancing disease loci identification in admixed populations
	Protein family review The lamin protein family Travis A Dittmer, Tom Misteli Genome Biology 2011, 12:222 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lamins are the major architectural proteins of animal nuclear membranes and are involved in a wide range of nuclear functions and human diseases.
	Report
	Meeting report Bright days for yeast research Martin Převorovský, Charalampos Rallis Genome Biology 2011, 12:305 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the British Yeast Group Meeting, Brighton, UK, 23-25 March 2011
	Research
	Research Modulated contact frequencies at gene-rich loci support a statistical helix model for mammalian chromatin organization Franck Court, Julie Miro, Caroline Braem, Marie-Noëlle Lelay-Taha, Audrey Brisebarre, Florian Atger, Thierry Gostan, Michaël Weber, Guy Cathala, Thierry Forné Genome Biology 2011, 12:R42 (10 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene-rich mammalian chromatin is shown by 3C-qPCR and polymer modeling to adopt a helical conformation
	Research Dynamic reprogramming of chromatin accessibility during Drosophila embryo development Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos Genome Biology 2011, 12:R43 (11 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A map of the dynamically changing chromatin landscape throughout Drosophila development.
	Research A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi James K Hane, Thierry Rouxel, Barbara J Howlett, Gert HJ Kema, Stephen B Goodwin, Richard P Oliver Genome Biology 2011, 12:R45 (24 May 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Mesosynteny, in which genes are maintained on the same chromosome but in different orders, is revealed in different ascomycete species
	Research Copy number polymorphisms and anticancer pharmacogenomics Eric R Gamazon, R Stephanie Huang, M Eileen Dolan, Nancy J Cox Genome Biology 2011, 12:R46 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Copy number polymorphisms are shown to significantly contribute to the sensitivity to anticancer drugs
	Research A high resolution map of a cyanobacterial transcriptome Vikram Vijayan, Isha H Jain, Erin K O'Shea Genome Biology 2011, 12:R47 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed transcriptome analysis of the cyanobacterium Synechococcus elongatus reveals widespread non coding transcription and transcript architecture
	Research A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure Andrea Zuccolo, John E Bowers, James C Estill, Zhiyong Xiong, Meizhong Luo, Aswathy Sebastian, José Goicoechea, Kristi Collura, Yeisoo Yu, Yuannian Jiao, Jill Duarte, Haibao Tang, Saravanaraj Ayyampalayam, Steve Rounsley, Dave Kudrna, Andrew H Paterson, J Pires, Andre Chanderbali, Douglas E Soltis, Srikar Chamala, Brad Barbazuk, Pamela S Soltis, Victor A Albert, Hong Ma, Dina Mandoli, Jody Banks, John E Carlson, Jeffrey Tomkins, Claude W dePamphilis, Rod A Wing, Jim Leebens-Mack et al. Genome Biology 2011, 12:R48 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mapping an outlier helps reconstruct the polyploidy timeline in angiosperms
	Research Moving pictures of the human microbiome J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon, Rob Knight Genome Biology 2011, 12:R50 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The dynamism of microbiome populations is seen in daily samples from a landmark multi-body site, multi-individual study
	Research Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths Jacob Enk, Alison Devault, Regis Debruyne, Christine E King, Todd Treangen, Dennis O'Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee, Hendrik Poinar Genome Biology 2011, 12:R51 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A surprising mtDNA phylogeny suggests that North American woolly mammoths bred with the distinct Columbian mammoth species
	Research Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection Omer Gokcumen, Paul L Babb, Rebecca C Iskow, Qihui Zhu, Xinghua Shi, Ryan E Mills, Iuliana Ionita-Laza, Eric J Vallender, Andrew G Clark, Welkin E Johnson, Charles Lee Genome Biology 2011, 12:R52 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Identification of overlapping copy number variation hotspots in chimpanzee, macaque and human
	Method EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield Genome Biology 2011, 12:R44 (19 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Reconstructing full length rRNA sequences from short reads to estimate microbial community structure
	Method Path finding methods accounting for stoichiometry in metabolic networks Jon Pey, Joaquín Prada, John E Beasley, Francisco J Planes Genome Biology 2011, 12:R49 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The incorporation of stoichiometry into path finding improves metabolic network analysis

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Volume 12 Issue 5

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