Genome Biology | Volume 7 Issue 8

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	Volume 7 Issue 8
	Comment
	Comment Senior moments Gregory A Petsko Genome Biology 2006, 7:113 (1 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The problem with reaching 'senior faculty' status is the feeling that you have nothing much to contribute except experience, but the recently announced Neanderthal Genome Project might put things into perspective.
	Review
	Protein family review The peptidoglycan recognition proteins (PGRPs) Roman Dziarski, Dipika Gupta Genome Biology 2006, 7:232 (23 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Peptidoglycan recognition proteins (PGRPs) are found in insects, mollusks, echinoderms, and vertebrates, and they protect animals against infections. The four mammalian family members are either bactericidal proteins or amidases that hydrolyze bacterial peptidoglycan.
	Minireview Protein-protein interaction networks in the spinocerebellar ataxias David C Rubinsztein Genome Biology 2006, 7:229 (10 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A large yeast two-hybrid study shows that some proteins mutated in different spinocerebellar ataxias have interacting protein partners in common.
	Minireview Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi Ola Snøve, John J Rossi Genome Biology 2006, 7:231 (29 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A popular method of RNA interference shows levels of toxicity in mice that could limit its therapeutic potential.
	Minireview Unraveling the transcriptional network controlling ES cell pluripotency Sridhar Rao, Stuart H Orkin Genome Biology 2006, 7:230 (30 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Separate transcriptional pathways have been delineated for the maintenance of the undifferentiated state and for self-renewal in embryonic stem cells.
	Opinion Fast, cheap and somewhat in control Adam P Arkin, Daniel A Fletcher Genome Biology 2006, 7:114 (30 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Various practical challenges involved in controlling living organisms must be surmounted if synthetic biology is to be productive.
	Report
	Meeting report The future is genome-wide Samuel Deutsch, Alexandre Reymond Genome Biology 2006, 7:324 (24 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the annual meeting of the European Society of Human Genetics, Amsterdam, 6-9 May 2006.
	Meeting report Advances in the genetics and epigenetics of gene regulation and human disease Kristine Kleivi Genome Biology 2006, 7:325 (24 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Human Genome Organisation (HUGO) 11th Human Genome Meeting, Helsinki, Finland, 31 May-3 June 2006.
	Meeting report Genomics - from Neanderthals to high-throughput sequencing Matthew John Wakefield Genome Biology 2006, 7:326 (24 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on 'The Biology of Genomes' meeting, Cold Spring Harbor, USA, 10-14 May 2006.
	Research
	Research Primate-specific evolution of an LDLR enhancer Qian-fei Wang, Shyam Prabhakar, Qianben Wang, Alan M Moses, Sumita Chanan, Myles Brown, Michael B Eisen, Jan-Fang Cheng, Edward M Rubin, Dario Boffelli Genome Biology 2006, 7:R68 (2 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of primate-specific evolution of the LDL receptor enhancer demonstrates a molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions.
	Research Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution Julia Tischler, Ben Lehner, Nansheng Chen, Andrew G Fraser Genome Biology 2006, 7:R69 (2 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary High-throughput combinatorial RNAi demonstrates that many duplicated genes in C. elegans can retain redundant functions for more than 80 million years
	Research Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae Guo-Cheng Yuan, Ping Ma, Wenxuan Zhong, Jun S Liu Genome Biology 2006, 7:R70 (2 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of genome-wide histone acetylation data using a few complementary statistical models gives support to a cumulative effect model for global histone acetylation.
	Research Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors Gustavo A de Souza, Lyris MF de Godoy, Matthias Mann Genome Biology 2006, 7:R72 (10 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A proteomic analysis of the tear fluid suggests that an interplay between proteases and protease inhibitors, and between oxidative reactions, is an important feature of the ocular environment.
	Research A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population Valeria Mattiangeli, Anthony W Ryan, Ross McManus, Daniel G Bradley Genome Biology 2006, 7:R74 (11 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A single population test applied in a genomic context reveals evidence of selection on three biologically interesting genes in the Irish population.
	Research Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species Makedonka Mitreva, Michael C Wendl, John Martin, Todd Wylie, Yong Yin, Allan Larson, John Parkinson, Robert H Waterston, James P McCarter Genome Biology 2006, 7:R75 (14 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A codon usage table for 32 nematode species is presented and suggests that total genomic GC content drives codon usage.
	Research Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes Yves Gibon, Bjoern Usadel, Oliver E Blaesing, Beate Kamlage, Melanie Hoehne, Richard Trethewey, Mark Stitt Genome Biology 2006, 7:R76 (17 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the temporal dynamics of metabolite and transcript levels, as well as enzyme activity, of 137 metabolites during diurnal cycles in Arabidopsis leaves
	Research Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters Jasmina Ponjavic, Boris Lenhard, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Albin Sandelin Genome Biology 2006, 7:R78 (17 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Investigations of the spacing between TATA box and transcription start site in mouse core promoters reveals a coupling of spacing to tissue specificity.
	Research Sex-specific expression of alternative transcripts in Drosophila Lauren M McIntyre, Lisa M Bono, Anne Genissel, Rick Westerman, Damion Junk, Marina Telonis-Scott, Larry Harshman, Marta L Wayne, Artyom Kopp, Sergey V Nuzhdin Genome Biology 2006, 7:R79 (25 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide microarray analysis of sex-specific expression of alternative transcripts in Drosophila shows sexual dimorphism in transcript abundance for 53% of the genes.
	Method Zebrafish promoter microarrays identify actively transcribed embryonic genes Fiona C Wardle, Duncan T Odom, George W Bell, Bingbing Yuan, Timothy W Danford, Elizabeth L Wiellette, Elizabeth Herbolsheimer, Hazel L Sive, Richard A Young, James C Smith Genome Biology 2006, 7:R71 (4 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The development and verification of a genomic microarray for ChIP-chip analysis of zebrafish genes is described.
	Method Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts Florian Hahne, Dorit Arlt, Mamatha Sauermann, Meher Majety, Annemarie Poustka, Stefan Wiemann, Wolfgang Huber Genome Biology 2006, 7:R77 (17 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A software tool for the analysis of high-throughput cell-based assays is presented.
	Software UniPep - a database for human N-linked glycosites: a resource for biomarker discovery Hui Zhang, Paul Loriaux, Jimmy Eng, David Campbell, Andrew Keller, Pat Moss, Richard Bonneau, Ning Zhang, Yong Zhou, Bernd Wollscheid, Kelly Cooke, Eugene C Yi, Hookeun Lee, Elaine R Peskind, Jing Zhang, Richard D Smith, Ruedi Aebersold Genome Biology 2006, 7:R73 (10 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary UniPep, a database of human N-linked glycosites is presented as a resource for biomarker discovery
	Correspondence
	Correspondence Feature-level exploration of a published Affymetrix GeneChip control dataset Rafael A Irizarry, Leslie M Cope, Zhijin Wu Genome Biology 2006, 7:404 (1 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16
	Correction Correction: Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress Anthony D Aragon, Gabriel A Quiñones, Edward V Thomas, Sushmita Roy, Margaret Werner-Washburne Genome Biology 2006, 7:403 (23 August 2006) Abstract \| Full text \| PDF

	Volume 7 Issue 8
	Comment
	Comment Senior moments Gregory A Petsko Genome Biology 2006, 7:113 (1 September 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The problem with reaching 'senior faculty' status is the feeling that you have nothing much to contribute except experience, but the recently announced Neanderthal Genome Project might put things into perspective.
	Review
	Protein family review The peptidoglycan recognition proteins (PGRPs) Roman Dziarski, Dipika Gupta Genome Biology 2006, 7:232 (23 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Peptidoglycan recognition proteins (PGRPs) are found in insects, mollusks, echinoderms, and vertebrates, and they protect animals against infections. The four mammalian family members are either bactericidal proteins or amidases that hydrolyze bacterial peptidoglycan.
	Minireview Protein-protein interaction networks in the spinocerebellar ataxias David C Rubinsztein Genome Biology 2006, 7:229 (10 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A large yeast two-hybrid study shows that some proteins mutated in different spinocerebellar ataxias have interacting protein partners in common.
	Minireview Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi Ola Snøve, John J Rossi Genome Biology 2006, 7:231 (29 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A popular method of RNA interference shows levels of toxicity in mice that could limit its therapeutic potential.
	Minireview Unraveling the transcriptional network controlling ES cell pluripotency Sridhar Rao, Stuart H Orkin Genome Biology 2006, 7:230 (30 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Separate transcriptional pathways have been delineated for the maintenance of the undifferentiated state and for self-renewal in embryonic stem cells.
	Opinion Fast, cheap and somewhat in control Adam P Arkin, Daniel A Fletcher Genome Biology 2006, 7:114 (30 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Various practical challenges involved in controlling living organisms must be surmounted if synthetic biology is to be productive.
	Report
	Meeting report The future is genome-wide Samuel Deutsch, Alexandre Reymond Genome Biology 2006, 7:324 (24 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the annual meeting of the European Society of Human Genetics, Amsterdam, 6-9 May 2006.
	Meeting report Advances in the genetics and epigenetics of gene regulation and human disease Kristine Kleivi Genome Biology 2006, 7:325 (24 August 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Human Genome Organisation (HUGO) 11th Human Genome Meeting, Helsinki, Finland, 31 May-3 June 2006.
	Meeting report Genomics - from Neanderthals to high-throughput sequencing Matthew John Wakefield Genome Biology 2006, 7:326 (24 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on 'The Biology of Genomes' meeting, Cold Spring Harbor, USA, 10-14 May 2006.
	Research
	Research Primate-specific evolution of an LDLR enhancer Qian-fei Wang, Shyam Prabhakar, Qianben Wang, Alan M Moses, Sumita Chanan, Myles Brown, Michael B Eisen, Jan-Fang Cheng, Edward M Rubin, Dario Boffelli Genome Biology 2006, 7:R68 (2 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of primate-specific evolution of the LDL receptor enhancer demonstrates a molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions.
	Research Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution Julia Tischler, Ben Lehner, Nansheng Chen, Andrew G Fraser Genome Biology 2006, 7:R69 (2 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary High-throughput combinatorial RNAi demonstrates that many duplicated genes in C. elegans can retain redundant functions for more than 80 million years
	Research Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae Guo-Cheng Yuan, Ping Ma, Wenxuan Zhong, Jun S Liu Genome Biology 2006, 7:R70 (2 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of genome-wide histone acetylation data using a few complementary statistical models gives support to a cumulative effect model for global histone acetylation.
	Research Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors Gustavo A de Souza, Lyris MF de Godoy, Matthias Mann Genome Biology 2006, 7:R72 (10 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A proteomic analysis of the tear fluid suggests that an interplay between proteases and protease inhibitors, and between oxidative reactions, is an important feature of the ocular environment.
	Research A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population Valeria Mattiangeli, Anthony W Ryan, Ross McManus, Daniel G Bradley Genome Biology 2006, 7:R74 (11 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A single population test applied in a genomic context reveals evidence of selection on three biologically interesting genes in the Irish population.
	Research Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species Makedonka Mitreva, Michael C Wendl, John Martin, Todd Wylie, Yong Yin, Allan Larson, John Parkinson, Robert H Waterston, James P McCarter Genome Biology 2006, 7:R75 (14 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A codon usage table for 32 nematode species is presented and suggests that total genomic GC content drives codon usage.
	Research Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes Yves Gibon, Bjoern Usadel, Oliver E Blaesing, Beate Kamlage, Melanie Hoehne, Richard Trethewey, Mark Stitt Genome Biology 2006, 7:R76 (17 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the temporal dynamics of metabolite and transcript levels, as well as enzyme activity, of 137 metabolites during diurnal cycles in Arabidopsis leaves
	Research Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters Jasmina Ponjavic, Boris Lenhard, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Albin Sandelin Genome Biology 2006, 7:R78 (17 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Investigations of the spacing between TATA box and transcription start site in mouse core promoters reveals a coupling of spacing to tissue specificity.
	Research Sex-specific expression of alternative transcripts in Drosophila Lauren M McIntyre, Lisa M Bono, Anne Genissel, Rick Westerman, Damion Junk, Marina Telonis-Scott, Larry Harshman, Marta L Wayne, Artyom Kopp, Sergey V Nuzhdin Genome Biology 2006, 7:R79 (25 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide microarray analysis of sex-specific expression of alternative transcripts in Drosophila shows sexual dimorphism in transcript abundance for 53% of the genes.
	Method Zebrafish promoter microarrays identify actively transcribed embryonic genes Fiona C Wardle, Duncan T Odom, George W Bell, Bingbing Yuan, Timothy W Danford, Elizabeth L Wiellette, Elizabeth Herbolsheimer, Hazel L Sive, Richard A Young, James C Smith Genome Biology 2006, 7:R71 (4 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The development and verification of a genomic microarray for ChIP-chip analysis of zebrafish genes is described.
	Method Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts Florian Hahne, Dorit Arlt, Mamatha Sauermann, Meher Majety, Annemarie Poustka, Stefan Wiemann, Wolfgang Huber Genome Biology 2006, 7:R77 (17 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A software tool for the analysis of high-throughput cell-based assays is presented.
	Software UniPep - a database for human N-linked glycosites: a resource for biomarker discovery Hui Zhang, Paul Loriaux, Jimmy Eng, David Campbell, Andrew Keller, Pat Moss, Richard Bonneau, Ning Zhang, Yong Zhou, Bernd Wollscheid, Kelly Cooke, Eugene C Yi, Hookeun Lee, Elaine R Peskind, Jing Zhang, Richard D Smith, Ruedi Aebersold Genome Biology 2006, 7:R73 (10 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary UniPep, a database of human N-linked glycosites is presented as a resource for biomarker discovery
	Correspondence
	Correspondence Feature-level exploration of a published Affymetrix GeneChip control dataset Rafael A Irizarry, Leslie M Cope, Zhijin Wu Genome Biology 2006, 7:404 (1 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16
	Correction Correction: Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress Anthony D Aragon, Gabriel A Quiñones, Edward V Thomas, Sushmita Roy, Margaret Werner-Washburne Genome Biology 2006, 7:403 (23 August 2006) Abstract \| Full text \| PDF

Explore Genome Biology

Articles

Volume 7 Issue 8

Comment

Review

Report

Research

Correspondence