Genome Biology | Volume 7 Issue 7

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	Volume 7 Issue 7
	Comment
	Comment Facts and figures Gregory A Petsko Genome Biology 2006, 7:111 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If we had genome sequence information for whole populations coupled with epidemiologic information about health and disease and lifestyle, imagine what we could do with such data.
	Review
	Protein family review The Heterochromatin Protein 1 family Gwen Lomberk, Lori Wallrath, Raul Urrutia Genome Biology 2006, 7:228 (21 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Members of the Heterochromatin Protein 1 (HP1) family contain a chromodomain and a chromoshadow domain and bind to methylated histone H3 as well as to proteins involved in a wide variety of nuclear functions.
	Minireview Targeting Drosophila eye development Jennifer Jemc, Ilaria Rebay Genome Biology 2006, 7:226 (27 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New target genes of Eyeless, a key transcription factor in Drosophila eye development, have been identified.
	Minireview Transcriptional control of dendritic patterning in Drosophila neurons Michel Tassetto, Fen-Biao Gao Genome Biology 2006, 7:225 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An RNA interference screen reveals roles for transcription factors in regulating the outgrowth and branching of the dendrites of Drosophila neurons.
	Minireview Enigma variations: control of sexual fate in nematode germ cells Ronald E Ellis Genome Biology 2006, 7:227 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Spermatogenesis in two species of Caenorhabditis is under quite different genetic controls.
	Opinion Anticipating the $1,000 genome Elaine R Mardis Genome Biology 2006, 7:112 (27 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New technologies will soon enable re-sequencing of human genomes at a much lower cost. The $1,000 human genome is an important goal for research and clinical diagnostics.
	Report
	Meeting report Immunological applications of genomics Silvia Monticelli, Sonia Sharma, Anjana Rao Genome Biology 2006, 7:321 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory meeting 'Gene Expression and Signaling in the Immune System', Cold Spring Harbor, New York, USA, 26-30 April 2006.
	Meeting report Evidence for intelligent (algorithm) design Balaji S Srinivasan, Chuong B Do, Serafim Batzoglou Genome Biology 2006, 7:322 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th annual Research in Computational Molecular Biology (RECOMB) Conference, Venice, Italy, 2-5 April 2006.
	Meeting report An all-round view of eukaryotic transcription Tae Kim, Bing Ren Genome Biology 2006, 7:323 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium 'Regulation of Eukaryotic Transcription: From Chromatin to mRNA', Taos, USA, 21-26 April 2006.
	Research
	Research Comparative genomics of Drosophila and human core promoters Peter C FitzGerald, David Sturgill, Andrey Shyakhtenko, Brian Oliver, Charles Vinson Genome Biology 2006, 7:R53 (7 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of DNA sequence distributions in Drosophila and human promoters suggests that different motifs have distinct functional roles.
	Research Signatures of human regulatory T cells: an encounter with old friends and new players Susanne Pfoertner, Andreas Jeron, Michael Probst-Kepper, Carlos A Guzman, Wiebke Hansen, Astrid M Westendorf, Tanja Toepfer, Andres J Schrader, Anke Franzke, Jan Buer, Robert Geffers Genome Biology 2006, 7:R54 (12 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene expression in human T regulatory cells and naïve cells using a T regulatory cell-specific microarray reveals cell-specific gene signatures.
	Research Design principles of molecular networks revealed by global comparisons and composite motifs Haiyuan Yu, Yu Xia, Valery Trifonov, Mark Gerstein Genome Biology 2006, 7:R55 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A global comparison of the four basic molecular networks in yeast - regulatory, co-expression, interaction and metabolic - reveals general design principles.
	Research Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage Remo Sanges, Eva Kalmar, Pamela Claudiani, Maria D'Amato, Ferenc Muller, Elia Stupka Genome Biology 2006, 7:R56 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Alignment of orthologous vertebrate loci reveals that a significant proportion of conserved cis-regulatory elements have undergone shuffling during evolution.
	Research What makes species unique? The contribution of proteins with obscure features Martin Gollery, Jeff Harper, John Cushman, Taliah Mittler, Thomas Girke, Jian-Kang Zhu, Julia Bailey-Serres, Ron Mittler Genome Biology 2006, 7:R57 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of proteins with obscure features in ten eukaryotic genomes revealed that the majority are species-specific.
	Research The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains Lakshminarayan M Iyer, A Maxwell Burroughs, L Aravind Genome Biology 2006, 7:R60 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history.
	Research Co-evolution of transcription factors and their targets depends on mode of regulation Ruth Hershberg, Hanah Margalit Genome Biology 2006, 7:R62 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of transcription regulatory networks in γ-proteobacteria reveals that repressors co-evolve tightly with their target genes, whereas activators can be lost independently of their targets.
	Research The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis Joseph F Ryan, Patrick M Burton, Maureen E Mazza, Grace K Kwong, James C Mullikin, John R Finnerty Genome Biology 2006, 7:R64 (24 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first near-complete set of homeodomains from a non-bilaterian animal is described.
	Research Phylogenetically widespread alternative splicing at unusual GYNGYN donors Michael Hiller, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schreiber, Rolf Backofen, Matthias Platzer Genome Biology 2006, 7:R65 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Computational and experimental evidence is given for alternative splicing at the unusual GYNGYN motif in several species, enabling in most cases subtle protein variations.
	Research Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura Stuart J Macdonald, Anthony D Long Genome Biology 2006, 7:R67 (27 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics reveals fine-scale structural variants, including microinversions, distinguishing two diverged Drosophila species
	Method Detecting transcriptionally active regions using genomic tiling arrays Gabor Halasz, Marinus F van Batenburg, Joelle Perusse, Sujun Hua, Xiang-Jun Lu, Kevin P White, Harmen J Bussemaker Genome Biology 2006, 7:R59 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for designing and integrating genomic tiling array data is described and applied to Anopheles and human arrays.
	Method A method for high-throughput gene expression signature analysis David Peck, Emily D Crawford, Kenneth N Ross, Kimberly Stegmaier, Todd R Golub, Justin Lamb Genome Biology 2006, 7:R61 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for cost-effective high-throughput gene expression signature analysis is described.
	Method A strategy for extracting and analyzing large-scale quantitative epistatic interaction data Sean R Collins, Maya Schuldiner, Nevan J Krogan, Jonathan S Weissman Genome Biology 2006, 7:R63 (21 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new technique for analysis of data from synthetic genetic array and E-MAP technology generates high confidence quantitative epistasis scores.
	Software yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes Matthew D Wilkerson, Shannon D Schlueter, Volker Brendel Genome Biology 2006, 7:R58 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary yrGATE is a new web-based tool for community gene and genome annotation.
	Software Analysis of cell-based RNAi screens Michael Boutros, Lígia P Brás, Wolfgang Huber Genome Biology 2006, 7:R66 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary cellHTS is a new method for the analysis and documentation of RNAi screens.

	Volume 7 Issue 7
	Comment
	Comment Facts and figures Gregory A Petsko Genome Biology 2006, 7:111 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If we had genome sequence information for whole populations coupled with epidemiologic information about health and disease and lifestyle, imagine what we could do with such data.
	Review
	Protein family review The Heterochromatin Protein 1 family Gwen Lomberk, Lori Wallrath, Raul Urrutia Genome Biology 2006, 7:228 (21 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Members of the Heterochromatin Protein 1 (HP1) family contain a chromodomain and a chromoshadow domain and bind to methylated histone H3 as well as to proteins involved in a wide variety of nuclear functions.
	Minireview Targeting Drosophila eye development Jennifer Jemc, Ilaria Rebay Genome Biology 2006, 7:226 (27 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New target genes of Eyeless, a key transcription factor in Drosophila eye development, have been identified.
	Minireview Transcriptional control of dendritic patterning in Drosophila neurons Michel Tassetto, Fen-Biao Gao Genome Biology 2006, 7:225 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An RNA interference screen reveals roles for transcription factors in regulating the outgrowth and branching of the dendrites of Drosophila neurons.
	Minireview Enigma variations: control of sexual fate in nematode germ cells Ronald E Ellis Genome Biology 2006, 7:227 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Spermatogenesis in two species of Caenorhabditis is under quite different genetic controls.
	Opinion Anticipating the $1,000 genome Elaine R Mardis Genome Biology 2006, 7:112 (27 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New technologies will soon enable re-sequencing of human genomes at a much lower cost. The $1,000 human genome is an important goal for research and clinical diagnostics.
	Report
	Meeting report Immunological applications of genomics Silvia Monticelli, Sonia Sharma, Anjana Rao Genome Biology 2006, 7:321 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory meeting 'Gene Expression and Signaling in the Immune System', Cold Spring Harbor, New York, USA, 26-30 April 2006.
	Meeting report Evidence for intelligent (algorithm) design Balaji S Srinivasan, Chuong B Do, Serafim Batzoglou Genome Biology 2006, 7:322 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th annual Research in Computational Molecular Biology (RECOMB) Conference, Venice, Italy, 2-5 April 2006.
	Meeting report An all-round view of eukaryotic transcription Tae Kim, Bing Ren Genome Biology 2006, 7:323 (28 July 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium 'Regulation of Eukaryotic Transcription: From Chromatin to mRNA', Taos, USA, 21-26 April 2006.
	Research
	Research Comparative genomics of Drosophila and human core promoters Peter C FitzGerald, David Sturgill, Andrey Shyakhtenko, Brian Oliver, Charles Vinson Genome Biology 2006, 7:R53 (7 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of DNA sequence distributions in Drosophila and human promoters suggests that different motifs have distinct functional roles.
	Research Signatures of human regulatory T cells: an encounter with old friends and new players Susanne Pfoertner, Andreas Jeron, Michael Probst-Kepper, Carlos A Guzman, Wiebke Hansen, Astrid M Westendorf, Tanja Toepfer, Andres J Schrader, Anke Franzke, Jan Buer, Robert Geffers Genome Biology 2006, 7:R54 (12 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene expression in human T regulatory cells and naïve cells using a T regulatory cell-specific microarray reveals cell-specific gene signatures.
	Research Design principles of molecular networks revealed by global comparisons and composite motifs Haiyuan Yu, Yu Xia, Valery Trifonov, Mark Gerstein Genome Biology 2006, 7:R55 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A global comparison of the four basic molecular networks in yeast - regulatory, co-expression, interaction and metabolic - reveals general design principles.
	Research Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage Remo Sanges, Eva Kalmar, Pamela Claudiani, Maria D'Amato, Ferenc Muller, Elia Stupka Genome Biology 2006, 7:R56 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Alignment of orthologous vertebrate loci reveals that a significant proportion of conserved cis-regulatory elements have undergone shuffling during evolution.
	Research What makes species unique? The contribution of proteins with obscure features Martin Gollery, Jeff Harper, John Cushman, Taliah Mittler, Thomas Girke, Jian-Kang Zhu, Julia Bailey-Serres, Ron Mittler Genome Biology 2006, 7:R57 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of proteins with obscure features in ten eukaryotic genomes revealed that the majority are species-specific.
	Research The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains Lakshminarayan M Iyer, A Maxwell Burroughs, L Aravind Genome Biology 2006, 7:R60 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history.
	Research Co-evolution of transcription factors and their targets depends on mode of regulation Ruth Hershberg, Hanah Margalit Genome Biology 2006, 7:R62 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of transcription regulatory networks in γ-proteobacteria reveals that repressors co-evolve tightly with their target genes, whereas activators can be lost independently of their targets.
	Research The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis Joseph F Ryan, Patrick M Burton, Maureen E Mazza, Grace K Kwong, James C Mullikin, John R Finnerty Genome Biology 2006, 7:R64 (24 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first near-complete set of homeodomains from a non-bilaterian animal is described.
	Research Phylogenetically widespread alternative splicing at unusual GYNGYN donors Michael Hiller, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schreiber, Rolf Backofen, Matthias Platzer Genome Biology 2006, 7:R65 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Computational and experimental evidence is given for alternative splicing at the unusual GYNGYN motif in several species, enabling in most cases subtle protein variations.
	Research Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura Stuart J Macdonald, Anthony D Long Genome Biology 2006, 7:R67 (27 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics reveals fine-scale structural variants, including microinversions, distinguishing two diverged Drosophila species
	Method Detecting transcriptionally active regions using genomic tiling arrays Gabor Halasz, Marinus F van Batenburg, Joelle Perusse, Sujun Hua, Xiang-Jun Lu, Kevin P White, Harmen J Bussemaker Genome Biology 2006, 7:R59 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for designing and integrating genomic tiling array data is described and applied to Anopheles and human arrays.
	Method A method for high-throughput gene expression signature analysis David Peck, Emily D Crawford, Kenneth N Ross, Kimberly Stegmaier, Todd R Golub, Justin Lamb Genome Biology 2006, 7:R61 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for cost-effective high-throughput gene expression signature analysis is described.
	Method A strategy for extracting and analyzing large-scale quantitative epistatic interaction data Sean R Collins, Maya Schuldiner, Nevan J Krogan, Jonathan S Weissman Genome Biology 2006, 7:R63 (21 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new technique for analysis of data from synthetic genetic array and E-MAP technology generates high confidence quantitative epistasis scores.
	Software yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes Matthew D Wilkerson, Shannon D Schlueter, Volker Brendel Genome Biology 2006, 7:R58 (19 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary yrGATE is a new web-based tool for community gene and genome annotation.
	Software Analysis of cell-based RNAi screens Michael Boutros, Lígia P Brás, Wolfgang Huber Genome Biology 2006, 7:R66 (25 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary cellHTS is a new method for the analysis and documentation of RNAi screens.

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Volume 7 Issue 7

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