Genome Biology | Volume 11 Issue 6

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	Volume 11 Issue 6
	Comment
	Comment Hand-made biology Gregory A Petsko Genome Biology 2010, 11:124 (30 June 2010) Full text \| PDF \| PubMed \| Editor’s summary The genomics era Shelley, Craig Venter, has refocused attention on synthetic biology by creating a bacterium.
	Research highlight Dramatic changes in transcription factor binding over evolutionary time Matthew T Weirauch, Timothy R Hughes Genome Biology 2010, 11:122 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates.
	Research highlight MicroRNA processing without Dicer Anne Dueck, Gunter Meister Genome Biology 2010, 11:123 (21 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microRNA essential for life is processed by Argonaute endonuclease activity.
	Review
	Review Escape from X inactivation in mice and humans Joel B Berletch, Fan Yang, Christine M Disteche Genome Biology 2010, 11:213 (24 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Species-specific differences in X-linked genes that escape inactivation suggest a role in the evolution of sex differences.
	Protein family review A hitchhiker's guide to the MADS world of plants Lydia Gramzow, Guenter Theissen Genome Biology 2010, 11:214 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The MADS-domain transcription factors, a protein family of crucial importance in plant development.
	Report
	Meeting report Genome-wide insights into eukaryotic transcriptional control James A Goodrich, Jennifer F Kugel Genome Biology 2010, 11:305 (7 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium on Dynamics of Eukaryotic Transcription during Development, Big Sky, Montana, USA, 7-12 April 2010.
	Meeting report Genomics through the lens of next-generation sequencing John A Capra, Lucia Carbone, Samantha J Riesenfeld, Jeffrey D Wall Genome Biology 2010, 11:306 (25 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA.
	Research
	Research Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode Shai S Shen-Orr, Yitzhak Pilpel, Craig P Hunter Genome Biology 2010, 11:R58 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of maternal and zygotic transcripts reveals regulatory differences between mammals and egg- laying animals.
	Research The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates Noa Sela, Eddo Kim, Gil Ast Genome Biology 2010, 11:R59 (2 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the influence of transposable elements on non-mammalian vertebrate and invertebrate transcriptomes reveals a link between intron length and exonization.
	Research Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels Maja Klug, Sven Heinz, Claudia Gebhard, Lucia Schwarzfischer, Stefan W Krause, Reinhard Andreesen, Michael Rehli Genome Biology 2010, 11:R63 (18 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Active CpG methylation is demonstrated in the differentiation of human peripheral blood monocytes and shown to correlate with histone modifications but not transcription.
	Research A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes Rossella De Cegli, Antonio Romito, Simona Iacobacci, Lei Mao, Mario Lauria, Anthony O Fedele, Joachim Klose, Christelle Borel, Patrick Descombes, Stylianos E Antonarakis, Diego di Bernardo, Sandro Banfi, Andrea Ballabio, Gilda Cobellis Genome Biology 2010, 11:R64 (22 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mouse embryonic stem cell bank of inducible human chromosome 21 gene expression is shown to be an important resource for investigating trisomy.
	Research Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts Meryem Mekouar, Isabelle Blanc-Lenfle, Christophe Ozanne, Corinne Da Silva, Corinne Cruaud, Patrick Wincker, Claude Gaillardin, Cécile Neuvéglise Genome Biology 2010, 11:R65 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Yarrowia lipolytica genes are intron rich and found to be subject to structural constraints resulting in an unusual gene structure.
	Research Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage Yasuhiro Yamauchi, Jonathan M Riel, Zoia Stoytcheva, Paul S Burgoyne, Monika A Ward Genome Biology 2010, 11:R66 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Defects on the mouse Y chromosome lead to DNA damage in sperm resulting in reduced efficiency of in vitro fertilization
	Research The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle Francisco Ferrezuelo, Neus Colomina, Bruce Futcher, Martí Aldea Genome Biology 2010, 11:R67 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Over-expression of CLN3 and integration with other data sets allows the elucidation of the Cln3 transcriptional network in yeast.
	Research Molecular evolution of genes in avian genomes Kiwoong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen BW Wolf, Niclas Backström, Axel Künstner, Christopher N Balakrishnan, Andreas Heger, Chris P Ponting, David F Clayton, Hans Ellegren Genome Biology 2010, 11:R68 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evolutionary analysis of the gene content of the chicken and zebrafinch genomes relative to other vertebrate lineages reveals avian specific patterns of evolution.
	Method Global fitness profiling of fission yeast deletion strains by barcode sequencing Tian Han, Xing-Ya Xu, Mei-Jun Zhang, Xu Peng, Li-Lin Du Genome Biology 2010, 11:R60 (10 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The barcode sequences used in creating the Schizosaccharomyces pombe deletion collection are reported.
	Method Whole exome capture in solution with 3 Gbp of data Matthew N Bainbridge, Min Wang, Daniel L Burgess, Christie Kovar, Matthew J Rodesch, Mark D'Ascenzo, Jacob Kitzman, Yuan-Qing Wu, Irene Newsham, Todd A Richmond, Jeffrey A Jeddeloh, Donna Muzny, Thomas J Albert, Richard A Gibbs Genome Biology 2010, 11:R62 (17 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for whole exome capture, using just 3Gbp of raw sequence data. Rare coding alleles can be identified in large-scale studies.
	Method Estimating enrichment of repetitive elements from high-throughput sequence data Daniel S Day, Lovelace J Luquette, Peter J Park, Peter V Kharchenko Genome Biology 2010, 11:R69 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors present a method for estimating repetitive sequence content in high-throughput sequencing data, including from ChIP-seq experiments
	Software Design and evaluation of genome-wide libraries for RNA interference screens Thomas Horn, Thomas Sandmann, Michael Boutros Genome Biology 2010, 11:R61 (15 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary NEXT-RNAi allows the design and evaluation of genome-wide RNAi screens in any organism.
	Correspondence
	Correction Correction: Diatom genomes come of age Assaf Vardi, Kimberlee Thamatrakoln, Kay D Bidle, Paul G Falkowski Genome Biology 2010, 11:401 (4 June 2010) Full text \| PDF \| PubMed

	Volume 11 Issue 6
	Comment
	Comment Hand-made biology Gregory A Petsko Genome Biology 2010, 11:124 (30 June 2010) Full text \| PDF \| PubMed \| Editor’s summary The genomics era Shelley, Craig Venter, has refocused attention on synthetic biology by creating a bacterium.
	Research highlight Dramatic changes in transcription factor binding over evolutionary time Matthew T Weirauch, Timothy R Hughes Genome Biology 2010, 11:122 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates.
	Research highlight MicroRNA processing without Dicer Anne Dueck, Gunter Meister Genome Biology 2010, 11:123 (21 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microRNA essential for life is processed by Argonaute endonuclease activity.
	Review
	Review Escape from X inactivation in mice and humans Joel B Berletch, Fan Yang, Christine M Disteche Genome Biology 2010, 11:213 (24 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Species-specific differences in X-linked genes that escape inactivation suggest a role in the evolution of sex differences.
	Protein family review A hitchhiker's guide to the MADS world of plants Lydia Gramzow, Guenter Theissen Genome Biology 2010, 11:214 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The MADS-domain transcription factors, a protein family of crucial importance in plant development.
	Report
	Meeting report Genome-wide insights into eukaryotic transcriptional control James A Goodrich, Jennifer F Kugel Genome Biology 2010, 11:305 (7 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium on Dynamics of Eukaryotic Transcription during Development, Big Sky, Montana, USA, 7-12 April 2010.
	Meeting report Genomics through the lens of next-generation sequencing John A Capra, Lucia Carbone, Samantha J Riesenfeld, Jeffrey D Wall Genome Biology 2010, 11:306 (25 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA.
	Research
	Research Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode Shai S Shen-Orr, Yitzhak Pilpel, Craig P Hunter Genome Biology 2010, 11:R58 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of maternal and zygotic transcripts reveals regulatory differences between mammals and egg- laying animals.
	Research The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates Noa Sela, Eddo Kim, Gil Ast Genome Biology 2010, 11:R59 (2 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the influence of transposable elements on non-mammalian vertebrate and invertebrate transcriptomes reveals a link between intron length and exonization.
	Research Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels Maja Klug, Sven Heinz, Claudia Gebhard, Lucia Schwarzfischer, Stefan W Krause, Reinhard Andreesen, Michael Rehli Genome Biology 2010, 11:R63 (18 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Active CpG methylation is demonstrated in the differentiation of human peripheral blood monocytes and shown to correlate with histone modifications but not transcription.
	Research A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes Rossella De Cegli, Antonio Romito, Simona Iacobacci, Lei Mao, Mario Lauria, Anthony O Fedele, Joachim Klose, Christelle Borel, Patrick Descombes, Stylianos E Antonarakis, Diego di Bernardo, Sandro Banfi, Andrea Ballabio, Gilda Cobellis Genome Biology 2010, 11:R64 (22 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mouse embryonic stem cell bank of inducible human chromosome 21 gene expression is shown to be an important resource for investigating trisomy.
	Research Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts Meryem Mekouar, Isabelle Blanc-Lenfle, Christophe Ozanne, Corinne Da Silva, Corinne Cruaud, Patrick Wincker, Claude Gaillardin, Cécile Neuvéglise Genome Biology 2010, 11:R65 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Yarrowia lipolytica genes are intron rich and found to be subject to structural constraints resulting in an unusual gene structure.
	Research Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage Yasuhiro Yamauchi, Jonathan M Riel, Zoia Stoytcheva, Paul S Burgoyne, Monika A Ward Genome Biology 2010, 11:R66 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Defects on the mouse Y chromosome lead to DNA damage in sperm resulting in reduced efficiency of in vitro fertilization
	Research The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle Francisco Ferrezuelo, Neus Colomina, Bruce Futcher, Martí Aldea Genome Biology 2010, 11:R67 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Over-expression of CLN3 and integration with other data sets allows the elucidation of the Cln3 transcriptional network in yeast.
	Research Molecular evolution of genes in avian genomes Kiwoong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen BW Wolf, Niclas Backström, Axel Künstner, Christopher N Balakrishnan, Andreas Heger, Chris P Ponting, David F Clayton, Hans Ellegren Genome Biology 2010, 11:R68 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evolutionary analysis of the gene content of the chicken and zebrafinch genomes relative to other vertebrate lineages reveals avian specific patterns of evolution.
	Method Global fitness profiling of fission yeast deletion strains by barcode sequencing Tian Han, Xing-Ya Xu, Mei-Jun Zhang, Xu Peng, Li-Lin Du Genome Biology 2010, 11:R60 (10 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The barcode sequences used in creating the Schizosaccharomyces pombe deletion collection are reported.
	Method Whole exome capture in solution with 3 Gbp of data Matthew N Bainbridge, Min Wang, Daniel L Burgess, Christie Kovar, Matthew J Rodesch, Mark D'Ascenzo, Jacob Kitzman, Yuan-Qing Wu, Irene Newsham, Todd A Richmond, Jeffrey A Jeddeloh, Donna Muzny, Thomas J Albert, Richard A Gibbs Genome Biology 2010, 11:R62 (17 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for whole exome capture, using just 3Gbp of raw sequence data. Rare coding alleles can be identified in large-scale studies.
	Method Estimating enrichment of repetitive elements from high-throughput sequence data Daniel S Day, Lovelace J Luquette, Peter J Park, Peter V Kharchenko Genome Biology 2010, 11:R69 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors present a method for estimating repetitive sequence content in high-throughput sequencing data, including from ChIP-seq experiments
	Software Design and evaluation of genome-wide libraries for RNA interference screens Thomas Horn, Thomas Sandmann, Michael Boutros Genome Biology 2010, 11:R61 (15 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary NEXT-RNAi allows the design and evaluation of genome-wide RNAi screens in any organism.
	Correspondence
	Correction Correction: Diatom genomes come of age Assaf Vardi, Kimberlee Thamatrakoln, Kay D Bidle, Paul G Falkowski Genome Biology 2010, 11:401 (4 June 2010) Full text \| PDF \| PubMed

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Volume 11 Issue 6

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