Genome Biology | Volume 12 Issue 4

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	Volume 12 Issue 4
	Comment
	Comment The blue marble Gregory A Petsko Genome Biology 2011, 12:112 (28 April 2011) Full text \| PDF \| PubMed \| Editor’s summary A picture speaks a thousand words.
	Research highlight An enigmatic satellite William Amos Genome Biology 2011, 12:110 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A conserved, transcribed X-linked satellite DNA that defies X-inactivation.
	Research highlight Mapping meiotic breaks: Spo11 oligonucleotides precisely mark the spots Patty Hwang, Neil Hunter Genome Biology 2011, 12:111 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mapping double-strand breaks reveals the characteristics of meiotic hotspots.
	Review
	Review Vive la différence: biogenesis and evolution of microRNAs in plants and animals Michael J Axtell, Jakub O Westholm, Eric C Lai Genome Biology 2011, 12:221 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The differences in biogenesis, function and evolution of plant and animal microRNAs contribute to, and are the result of, distinct evolutionary characteristics in the two kingdoms.
	Protein family review The cullin protein family Antonio Sarikas, Thomas Hartmann, Zhen-Qiang Pan Genome Biology 2011, 12:220 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Cullin proteins are molecular scaffolds involved in the posttranslational modification of cellular proteins by ubiquitin.
	Opinion What does biologically meaningful mean? A perspective on gene regulatory network validation Albertha JM Walhout Genome Biology 2011, 12:109 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Deciding whether gene regulatory interactions are biologically meaningful is not as simple as it might seem.
	Report
	Meeting report A top-down view on DNA replication and recombination from 9,000 feet above sea level Erik Johansson, Christian Speck, Andrei Chabes Genome Biology 2011, 12:304 (27 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February - 4 March 2011.
	Research
	Research High recombination rates and hotspots in a Plasmodium falciparum genetic cross Hongying Jiang, Na Li, Vivek Gopalan, Martine M Zilversmit, Sudhir Varma, Vijayaraj Nagarajan, Jian Li, Jianbing Mu, Karen Hayton, Bruce Henschen, Ming Yi, Robert Stephens, Gilean McVean, Philip Awadalla, Thomas E Wellems, Xin-zhuan Su Genome Biology 2011, 12:R33 (4 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification of Plasmodium falciparum recombination rates, hotspots and a potential PRDM9 candidate.
	Research The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin Genome Biology 2011, 12:R34 (7 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromatin accessibility influences the binding of Drosophila transcription factors.
	Research Genome-wide survey of post-meiotic segregation during yeast recombination Eugenio Mancera, Richard Bourgon, Wolfgang Huber, Lars M Steinmetz Genome Biology 2011, 12:R36 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide study of post-meiotic segregation, in which mismatches in heteroduplex DNA are left unrepaired, performed in yeast
	Research Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome Christine R McLaughlin, Brian P Chadwick Genome Biology 2011, 12:R37 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potential roles of the human DXZ4 macrosatellite in CTCF binding and X inactivation are revealed through functional conservation in primates.
	Research Discovery of permuted and recently split transfer RNAs in Archaea Patricia P Chan, Aaron E Cozen, Todd M Lowe Genome Biology 2011, 12:R38 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Discovery of novel split and permuted archaeal tRNAs argues against a single, early origin in Archaea
	Research Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma Christian P Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A Martinez, Irina S Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A Horwitz, Prasun K Mukherjee, Mala Mukherjee, László Kredics, Luis D Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan Deshpande, Hans von Döhren, Daniel J Ebbole, Edgardo U Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Y Gómez-Rodríguez, Sabine Gruber et al. Genome Biology 2011, 12:R40 (18 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of two novel genomes from the biocontrol agent genus Trichoderma
	Method An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations John C Tan, Becky A Miller, Asako Tan, Jigar J Patel, Ian H Cheeseman, Tim JC Anderson, Magnus Manske, Gareth Maslen, Dominic P Kwiatkowski, Michael T Ferdig Genome Biology 2011, 12:R35 (8 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Plasmodium falciparum genotyping array for determining variation in field samples with human DNA contamination.
	Method GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz Genome Biology 2011, 12:R41 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Identification of genes affected by somatic copy number variations that drive human cancer growth.
	Software A quantitative literature-curated gold standard for kinase-substrate pairs Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Young, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2011, 12:R39 (14 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A yeast kinase interaction database is presented, for kinase-gene and kinase-protein interactions
	Correspondence
	Correspondence Observations on shifted cumulative regulation Chao Ye, Ying Liu, Xuegong Zhang Genome Biology 2011, 12:404 (27 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation by F He, J Buer, AP Zeng and R Balling. Genome Biol 2007, 8:R181.
	Correction Correction: Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra C Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2011, 12:403 (19 April 2011) Abstract \| Full text \| PDF \| PubMed

	Volume 12 Issue 4
	Comment
	Comment The blue marble Gregory A Petsko Genome Biology 2011, 12:112 (28 April 2011) Full text \| PDF \| PubMed \| Editor’s summary A picture speaks a thousand words.
	Research highlight An enigmatic satellite William Amos Genome Biology 2011, 12:110 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A conserved, transcribed X-linked satellite DNA that defies X-inactivation.
	Research highlight Mapping meiotic breaks: Spo11 oligonucleotides precisely mark the spots Patty Hwang, Neil Hunter Genome Biology 2011, 12:111 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mapping double-strand breaks reveals the characteristics of meiotic hotspots.
	Review
	Review Vive la différence: biogenesis and evolution of microRNAs in plants and animals Michael J Axtell, Jakub O Westholm, Eric C Lai Genome Biology 2011, 12:221 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The differences in biogenesis, function and evolution of plant and animal microRNAs contribute to, and are the result of, distinct evolutionary characteristics in the two kingdoms.
	Protein family review The cullin protein family Antonio Sarikas, Thomas Hartmann, Zhen-Qiang Pan Genome Biology 2011, 12:220 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Cullin proteins are molecular scaffolds involved in the posttranslational modification of cellular proteins by ubiquitin.
	Opinion What does biologically meaningful mean? A perspective on gene regulatory network validation Albertha JM Walhout Genome Biology 2011, 12:109 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Deciding whether gene regulatory interactions are biologically meaningful is not as simple as it might seem.
	Report
	Meeting report A top-down view on DNA replication and recombination from 9,000 feet above sea level Erik Johansson, Christian Speck, Andrei Chabes Genome Biology 2011, 12:304 (27 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February - 4 March 2011.
	Research
	Research High recombination rates and hotspots in a Plasmodium falciparum genetic cross Hongying Jiang, Na Li, Vivek Gopalan, Martine M Zilversmit, Sudhir Varma, Vijayaraj Nagarajan, Jian Li, Jianbing Mu, Karen Hayton, Bruce Henschen, Ming Yi, Robert Stephens, Gilean McVean, Philip Awadalla, Thomas E Wellems, Xin-zhuan Su Genome Biology 2011, 12:R33 (4 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification of Plasmodium falciparum recombination rates, hotspots and a potential PRDM9 candidate.
	Research The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin Genome Biology 2011, 12:R34 (7 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromatin accessibility influences the binding of Drosophila transcription factors.
	Research Genome-wide survey of post-meiotic segregation during yeast recombination Eugenio Mancera, Richard Bourgon, Wolfgang Huber, Lars M Steinmetz Genome Biology 2011, 12:R36 (11 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genome-wide study of post-meiotic segregation, in which mismatches in heteroduplex DNA are left unrepaired, performed in yeast
	Research Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome Christine R McLaughlin, Brian P Chadwick Genome Biology 2011, 12:R37 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potential roles of the human DXZ4 macrosatellite in CTCF binding and X inactivation are revealed through functional conservation in primates.
	Research Discovery of permuted and recently split transfer RNAs in Archaea Patricia P Chan, Aaron E Cozen, Todd M Lowe Genome Biology 2011, 12:R38 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Discovery of novel split and permuted archaeal tRNAs argues against a single, early origin in Archaea
	Research Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma Christian P Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A Martinez, Irina S Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A Horwitz, Prasun K Mukherjee, Mala Mukherjee, László Kredics, Luis D Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan Deshpande, Hans von Döhren, Daniel J Ebbole, Edgardo U Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Y Gómez-Rodríguez, Sabine Gruber et al. Genome Biology 2011, 12:R40 (18 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of two novel genomes from the biocontrol agent genus Trichoderma
	Method An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations John C Tan, Becky A Miller, Asako Tan, Jigar J Patel, Ian H Cheeseman, Tim JC Anderson, Magnus Manske, Gareth Maslen, Dominic P Kwiatkowski, Michael T Ferdig Genome Biology 2011, 12:R35 (8 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Plasmodium falciparum genotyping array for determining variation in field samples with human DNA contamination.
	Method GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz Genome Biology 2011, 12:R41 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Identification of genes affected by somatic copy number variations that drive human cancer growth.
	Software A quantitative literature-curated gold standard for kinase-substrate pairs Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Young, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2011, 12:R39 (14 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A yeast kinase interaction database is presented, for kinase-gene and kinase-protein interactions
	Correspondence
	Correspondence Observations on shifted cumulative regulation Chao Ye, Ying Liu, Xuegong Zhang Genome Biology 2011, 12:404 (27 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation by F He, J Buer, AP Zeng and R Balling. Genome Biol 2007, 8:R181.
	Correction Correction: Closing gaps in the human genome using sequencing by synthesis Manuel Garber, Michael C Zody, Harindra C Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2011, 12:403 (19 April 2011) Abstract \| Full text \| PDF \| PubMed

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Volume 12 Issue 4

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Review

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Research

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