Genome Biology | Volume 9 Issue 9

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	Volume 9 Issue 9
	Comment
	Comment When bubbles burst Gregory A Petsko Genome Biology 2008, 9:110 (29 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the current financial crisis, the house-price 'bubble' has burst with spectacular effects. Big science projects in biology may be on their way to becoming the next scientific bubble.
	Review
	Review The telosome/shelterin complex and its functions Huawei Xin, Dan Liu, Zhou Songyang Genome Biology 2008, 9:232 (18 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The telosome/shelterin protein complex bound to telomeres is essential for maintenance of telomere structure and telomere signaling functions.
	Minireview Transcriptional (dys)regulation and aging in Caenorhabditis elegans Zachary Pincus, Frank J Slack Genome Biology 2008, 9:233 (16 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New work could link laboratory-defined longevity pathways to the process of normal aging.
	Minireview Transcriptome content and dynamics at single-nucleotide resolution Nicole Cloonan, Sean M Grimmond Genome Biology 2008, 9:234 (18 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Massively parallel short-tag 'RNA sequencing' is giving new insights into the complexity of the eukaryotic transcriptome.
	Report
	Meeting report Crops in all shapes and sizes Loreto Holuigue, Jean-Philippe Vielle-Calzada, Rodrigo A Gutiérrez Genome Biology 2008, 9:319 (11 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the joint American Society of Plant Biologists/Sociedad Mexicana De Bioquímica meeting held in Mérida, Mexico, 26 June-1 July 2008.
	Meeting report New insights into tumor suppressors Michelle Marques, Alejandro Sweet-Cordero Genome Biology 2008, 9:320 (19 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory meeting 'Mechanisms and Models of Cancer', Cold Spring Harbor, USA, 13-17 August 2008.
	Meeting report Archaea at St Andrews Andrew T Large, Peter A Lund Genome Biology 2008, 9:321 (30 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Biochemical Society meeting 'The Molecular Biology of Archaea', St Andrews, UK, 19-21 August 2008.
	Research
	Research Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila Enrique Blanco, Miguel Pignatelli, Sergi Beltran, Adrià Punset, Silvia Pérez-Lluch, Florenci Serras, Roderic Guigó, Montserrat Corominas Genome Biology 2008, 9:R134 (10 September 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| f1000 \| Editor’s summary Transcriptional analysis of chromatin regulator mutants in Drosophila melanogaster identified clusters of functionally related genes conserved in other insect species.
	Research Modeling synthetic lethality Nolwenn Le Meur, Robert Gentleman Genome Biology 2008, 9:R135 (12 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Using new computational tools in yeast, multi-protein complexes were identified that share an unusually high number of synthetic genetic interactions.
	Research Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions Evan S Snitkin, Aimée M Dudley, Daniel M Janse, Kaisheen Wong, George M Church, Daniel Segrè Genome Biology 2008, 9:R140 (22 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An iterative approach that integrates high-throughput measurements of yeast deletion mutants and flux balance model predictions improves understanding of both experimental and computational results.
	Research Exon creation and establishment in human genes André Corvelo, Eduardo Eyras Genome Biology 2008, 9:R141 (23 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative genomics study of alternatively spliced exons showing that the relative local abundance of splicing regulatory motifs influences splicing decisions in humans.
	Research Evolutionary rate and gene expression across different brain regions Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2008, 9:R142 (23 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cortically expressed genes are more conserved than sub-cortical ones and gene expression levels exert stronger constraints on sequence evolution in cortical than in sub-cortical regions.
	Research The signature of long-standing balancing selection at the human defensin β-1 promoter Rachele Cagliani, Matteo Fumagalli, Stefania Riva, Uberto Pozzoli, Giacomo P Comi, Giorgia Menozzi, Nereo Bresolin, Manuela Sironi Genome Biology 2008, 9:R143 (25 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the human beta defensin 1 promoter region in six human populations reveals a signature of balancing selection.
	Method Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays Johan Staaf, David Lindgren, Johan Vallon-Christersson, Anders Isaksson, Hanna Göransson, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg, Markus Ringnér Genome Biology 2008, 9:R136 (16 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A strategy is presented for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome SNP genotyping data.
	Method Model-based Analysis of ChIP-Seq (MACS) Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu Genome Biology 2008, 9:R137 (17 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.
	Method Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues Sami Kilpinen, Reija Autio, Kalle Ojala, Kristiina Iljin, Elmar Bucher, Henri Sara, Tommi Pisto, Matti Saarela, Rolf I Skotheim, Mari Björkman, John-Patrick Mpindi, Saija Haapa-Paananen, Paula Vainio, Henrik Edgren, Maija Wolf, Jaakko Astola, Matthias Nees, Sampsa Hautaniemi, Olli Kallioniemi Genome Biology 2008, 9:R139 (19 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for the comparison of mRNA expression levels of most human genes across gene expression array experiments, and a database of the results, are presented.
	Software NetGrep: fast network schema searches in interactomes Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh Genome Biology 2008, 9:R138 (18 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary NetGrep is a system for searching protein interaction networks for matches to user-supplied network schemas.

	Volume 9 Issue 9
	Comment
	Comment When bubbles burst Gregory A Petsko Genome Biology 2008, 9:110 (29 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the current financial crisis, the house-price 'bubble' has burst with spectacular effects. Big science projects in biology may be on their way to becoming the next scientific bubble.
	Review
	Review The telosome/shelterin complex and its functions Huawei Xin, Dan Liu, Zhou Songyang Genome Biology 2008, 9:232 (18 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The telosome/shelterin protein complex bound to telomeres is essential for maintenance of telomere structure and telomere signaling functions.
	Minireview Transcriptional (dys)regulation and aging in Caenorhabditis elegans Zachary Pincus, Frank J Slack Genome Biology 2008, 9:233 (16 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New work could link laboratory-defined longevity pathways to the process of normal aging.
	Minireview Transcriptome content and dynamics at single-nucleotide resolution Nicole Cloonan, Sean M Grimmond Genome Biology 2008, 9:234 (18 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Massively parallel short-tag 'RNA sequencing' is giving new insights into the complexity of the eukaryotic transcriptome.
	Report
	Meeting report Crops in all shapes and sizes Loreto Holuigue, Jean-Philippe Vielle-Calzada, Rodrigo A Gutiérrez Genome Biology 2008, 9:319 (11 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the joint American Society of Plant Biologists/Sociedad Mexicana De Bioquímica meeting held in Mérida, Mexico, 26 June-1 July 2008.
	Meeting report New insights into tumor suppressors Michelle Marques, Alejandro Sweet-Cordero Genome Biology 2008, 9:320 (19 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory meeting 'Mechanisms and Models of Cancer', Cold Spring Harbor, USA, 13-17 August 2008.
	Meeting report Archaea at St Andrews Andrew T Large, Peter A Lund Genome Biology 2008, 9:321 (30 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Biochemical Society meeting 'The Molecular Biology of Archaea', St Andrews, UK, 19-21 August 2008.
	Research
	Research Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila Enrique Blanco, Miguel Pignatelli, Sergi Beltran, Adrià Punset, Silvia Pérez-Lluch, Florenci Serras, Roderic Guigó, Montserrat Corominas Genome Biology 2008, 9:R134 (10 September 2008) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| f1000 \| Editor’s summary Transcriptional analysis of chromatin regulator mutants in Drosophila melanogaster identified clusters of functionally related genes conserved in other insect species.
	Research Modeling synthetic lethality Nolwenn Le Meur, Robert Gentleman Genome Biology 2008, 9:R135 (12 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Using new computational tools in yeast, multi-protein complexes were identified that share an unusually high number of synthetic genetic interactions.
	Research Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions Evan S Snitkin, Aimée M Dudley, Daniel M Janse, Kaisheen Wong, George M Church, Daniel Segrè Genome Biology 2008, 9:R140 (22 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An iterative approach that integrates high-throughput measurements of yeast deletion mutants and flux balance model predictions improves understanding of both experimental and computational results.
	Research Exon creation and establishment in human genes André Corvelo, Eduardo Eyras Genome Biology 2008, 9:R141 (23 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative genomics study of alternatively spliced exons showing that the relative local abundance of splicing regulatory motifs influences splicing decisions in humans.
	Research Evolutionary rate and gene expression across different brain regions Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2008, 9:R142 (23 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cortically expressed genes are more conserved than sub-cortical ones and gene expression levels exert stronger constraints on sequence evolution in cortical than in sub-cortical regions.
	Research The signature of long-standing balancing selection at the human defensin β-1 promoter Rachele Cagliani, Matteo Fumagalli, Stefania Riva, Uberto Pozzoli, Giacomo P Comi, Giorgia Menozzi, Nereo Bresolin, Manuela Sironi Genome Biology 2008, 9:R143 (25 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the human beta defensin 1 promoter region in six human populations reveals a signature of balancing selection.
	Method Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays Johan Staaf, David Lindgren, Johan Vallon-Christersson, Anders Isaksson, Hanna Göransson, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg, Markus Ringnér Genome Biology 2008, 9:R136 (16 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A strategy is presented for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome SNP genotyping data.
	Method Model-based Analysis of ChIP-Seq (MACS) Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu Genome Biology 2008, 9:R137 (17 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.
	Method Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues Sami Kilpinen, Reija Autio, Kalle Ojala, Kristiina Iljin, Elmar Bucher, Henri Sara, Tommi Pisto, Matti Saarela, Rolf I Skotheim, Mari Björkman, John-Patrick Mpindi, Saija Haapa-Paananen, Paula Vainio, Henrik Edgren, Maija Wolf, Jaakko Astola, Matthias Nees, Sampsa Hautaniemi, Olli Kallioniemi Genome Biology 2008, 9:R139 (19 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for the comparison of mRNA expression levels of most human genes across gene expression array experiments, and a database of the results, are presented.
	Software NetGrep: fast network schema searches in interactomes Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh Genome Biology 2008, 9:R138 (18 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary NetGrep is a system for searching protein interaction networks for matches to user-supplied network schemas.

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Volume 9 Issue 9

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