Genome Biology | Volume 7 Issue 11

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	Volume 7 Issue 11
	Comment
	Comment Do the math Gregory A Petsko Genome Biology 2006, 7:119 (30 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Statistics is the one branch of mathematics that everybody should be able to grasp - and all biologists should be required to do so.
	Review
	Minireview Koala retrovirus: a genome invasion in real time Jonathan P Stoye Genome Biology 2006, 7:241 (21 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Koalas are currently undergoing a wave of germline retroviral infection, which is spreading throughout Australia.
	Minireview 'Chumanzee' evolution: the urge to diverge and merge Todd R Disotell Genome Biology 2006, 7:240 (24 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative analysis of primate genomes suggests that the divergence between human and chimpanzee lineages around 6 million years ago was initially not a clean split.
	Minireview High-accuracy proteome maps of human body fluids Alexander Schmidt, Ruedi Aebersold Genome Biology 2006, 7:242 (28 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Proteomic analyses of individual body fluids point the way to biomarker discovery.
	Opinion How complete are current yeast and human protein-interaction networks? G Traver Hart, Arun K Ramani, Edward M Marcotte Genome Biology 2006, 7:120 (1 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How can protein-interaction networks can be made more complete?
	Report
	Meeting report Proteomics gets faster and smarter Hannah Johnson, Simon J Gaskell Genome Biology 2006, 7:331 (15 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third annual joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, Hinxton, UK, 12-14 July 2006.
	Research
	Research Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics Klaas Vandepoele, Tineke Casneuf, Yves Van de Peer Genome Biology 2006, 7:R103 (7 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A strategy combining classical motif overrepresentation in co-regulated genes with comparative footprinting is applied to identify 80 transcription factor binding sites and 139 regulatory modules in Arabidopsis thaliana.
	Research Patterns of sequence conservation in presynaptic neural genes Dexter Hadley, Tara Murphy, Otto Valladares, Sridhar Hannenhalli, Lyle Ungar, Junhyong Kim, Maja Bućan Genome Biology 2006, 7:R105 (10 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative sequence analysis and annotation of genomic regions surrounding 150 presynaptic genes identified over 26,000 elements highly conserved in eight vertebrate species; these results are made available in the SynapseDB database.
	Research Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae Birgitte Regenberg, Thomas Grotkjær, Ole Winther, Anders Fausbøll, Mats Åkesson, Christoffer Bro, Lars Hansen, Søren Brunak, Jens Nielsen Genome Biology 2006, 7:R107 (14 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Analysis of S. cerevisiae cultures with generation times varying between 2 and 35 hours shows that the expression of half of all yeast genes is affected by the specific growth rate.
	Research Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans Helga David, Gerald Hofmann, Ana Oliveira, Hanne Jarmer, Jens Nielsen Genome Biology 2006, 7:R108 (15 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide transcription analysis of Aspergillus nidulans grown on different carbon sources and a reconstruction of the complete metabolic network of this filamentous fungi are presented.
	Research Systematic screening of polyphosphate (poly P) levels in yeast mutant cells reveals strong interdependence with primary metabolism Florian M Freimoser, Hans Hürlimann, Claude A Jakob, Thomas P Werner, Nikolaus Amrhein Genome Biology 2006, 7:R109 (15 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of polyphosphate levels in yeast knockout strains for almost every non-essential gene identified 255 genes involved in the maintenance of normal polyphosphate content and provides insights into phosphate homeostasis.
	Research Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome Casey M Bergman, Hadi Quesneville, Dominique Anxolabéhère, Michael Ashburner Genome Biology 2006, 7:R112 (29 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of high-resolution transposable element annotations in Drosophila melanogaster suggests the existence of a global surveillance system against the majority of transposable elements families in the fly.
	Research Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors Margarida Gama-Carvalho, Nuno L Barbosa-Morais, Alexander S Brodsky, Pamela A Silver, Maria Carmo-Fonseca Genome Biology 2006, 7:R113 (30 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome wide identification of mRNAs that were associated with the splicing factor subunit U2AF65 suggests that U2AF65 associates with specific subsets of spliced mRNAs and may be involved in novel cellular functions in addition to splicing.
	Method BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments Lu-yong Wang, Michael Snyder, Mark Gerstein Genome Biology 2006, 7:R102 (1 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary BoCaTFBS, a new method that combines noisy data from ChIP-chip experiments with known binding-site patterns, is described and applied to the ENCODE project.
	Method Predicting domain-domain interactions using a parsimony approach Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka Genome Biology 2006, 7:R104 (9 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new parsimony approach for the prediction of domain-domain interactions is presented and demonstrated to provide improvement in prediction coverage and accuracy.
	Method Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas Nichole L King, Eric W Deutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B Martin, Bong Kim, Hookeun Lee, Brian Raught, Ruedi Aebersold Genome Biology 2006, 7:R106 (13 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The S. cerevisiae PeptideAtlas, composed from 47 diverse experiments and nearly 5 million tandem mass spectra, is described.
	Method ProCAT: a data analysis approach for protein microarrays Xiaowei Zhu, Mark Gerstein, Michael Snyder Genome Biology 2006, 7:R110 (16 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ProCAT, a powerful and flexible new approach for analyzing many types of protein microarrays, is described.
	Software xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features Shannon D Schlueter, Matthew D Wilkerson, Qunfeng Dong, Volker Brendel Genome Biology 2006, 7:R111 (20 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary XGDB, a software infrastructure consisting of integrated tools for the storage, display and analysis of genome features (any property that can be associated with a genomic location, for example spliced alignments) in their genomics context is described.

	Volume 7 Issue 11
	Comment
	Comment Do the math Gregory A Petsko Genome Biology 2006, 7:119 (30 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Statistics is the one branch of mathematics that everybody should be able to grasp - and all biologists should be required to do so.
	Review
	Minireview Koala retrovirus: a genome invasion in real time Jonathan P Stoye Genome Biology 2006, 7:241 (21 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Koalas are currently undergoing a wave of germline retroviral infection, which is spreading throughout Australia.
	Minireview 'Chumanzee' evolution: the urge to diverge and merge Todd R Disotell Genome Biology 2006, 7:240 (24 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative analysis of primate genomes suggests that the divergence between human and chimpanzee lineages around 6 million years ago was initially not a clean split.
	Minireview High-accuracy proteome maps of human body fluids Alexander Schmidt, Ruedi Aebersold Genome Biology 2006, 7:242 (28 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Proteomic analyses of individual body fluids point the way to biomarker discovery.
	Opinion How complete are current yeast and human protein-interaction networks? G Traver Hart, Arun K Ramani, Edward M Marcotte Genome Biology 2006, 7:120 (1 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How can protein-interaction networks can be made more complete?
	Report
	Meeting report Proteomics gets faster and smarter Hannah Johnson, Simon J Gaskell Genome Biology 2006, 7:331 (15 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third annual joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, Hinxton, UK, 12-14 July 2006.
	Research
	Research Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics Klaas Vandepoele, Tineke Casneuf, Yves Van de Peer Genome Biology 2006, 7:R103 (7 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A strategy combining classical motif overrepresentation in co-regulated genes with comparative footprinting is applied to identify 80 transcription factor binding sites and 139 regulatory modules in Arabidopsis thaliana.
	Research Patterns of sequence conservation in presynaptic neural genes Dexter Hadley, Tara Murphy, Otto Valladares, Sridhar Hannenhalli, Lyle Ungar, Junhyong Kim, Maja Bućan Genome Biology 2006, 7:R105 (10 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative sequence analysis and annotation of genomic regions surrounding 150 presynaptic genes identified over 26,000 elements highly conserved in eight vertebrate species; these results are made available in the SynapseDB database.
	Research Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae Birgitte Regenberg, Thomas Grotkjær, Ole Winther, Anders Fausbøll, Mats Åkesson, Christoffer Bro, Lars Hansen, Søren Brunak, Jens Nielsen Genome Biology 2006, 7:R107 (14 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Analysis of S. cerevisiae cultures with generation times varying between 2 and 35 hours shows that the expression of half of all yeast genes is affected by the specific growth rate.
	Research Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans Helga David, Gerald Hofmann, Ana Oliveira, Hanne Jarmer, Jens Nielsen Genome Biology 2006, 7:R108 (15 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide transcription analysis of Aspergillus nidulans grown on different carbon sources and a reconstruction of the complete metabolic network of this filamentous fungi are presented.
	Research Systematic screening of polyphosphate (poly P) levels in yeast mutant cells reveals strong interdependence with primary metabolism Florian M Freimoser, Hans Hürlimann, Claude A Jakob, Thomas P Werner, Nikolaus Amrhein Genome Biology 2006, 7:R109 (15 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic analysis of polyphosphate levels in yeast knockout strains for almost every non-essential gene identified 255 genes involved in the maintenance of normal polyphosphate content and provides insights into phosphate homeostasis.
	Research Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome Casey M Bergman, Hadi Quesneville, Dominique Anxolabéhère, Michael Ashburner Genome Biology 2006, 7:R112 (29 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of high-resolution transposable element annotations in Drosophila melanogaster suggests the existence of a global surveillance system against the majority of transposable elements families in the fly.
	Research Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors Margarida Gama-Carvalho, Nuno L Barbosa-Morais, Alexander S Brodsky, Pamela A Silver, Maria Carmo-Fonseca Genome Biology 2006, 7:R113 (30 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome wide identification of mRNAs that were associated with the splicing factor subunit U2AF65 suggests that U2AF65 associates with specific subsets of spliced mRNAs and may be involved in novel cellular functions in addition to splicing.
	Method BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments Lu-yong Wang, Michael Snyder, Mark Gerstein Genome Biology 2006, 7:R102 (1 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary BoCaTFBS, a new method that combines noisy data from ChIP-chip experiments with known binding-site patterns, is described and applied to the ENCODE project.
	Method Predicting domain-domain interactions using a parsimony approach Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka Genome Biology 2006, 7:R104 (9 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new parsimony approach for the prediction of domain-domain interactions is presented and demonstrated to provide improvement in prediction coverage and accuracy.
	Method Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas Nichole L King, Eric W Deutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B Martin, Bong Kim, Hookeun Lee, Brian Raught, Ruedi Aebersold Genome Biology 2006, 7:R106 (13 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The S. cerevisiae PeptideAtlas, composed from 47 diverse experiments and nearly 5 million tandem mass spectra, is described.
	Method ProCAT: a data analysis approach for protein microarrays Xiaowei Zhu, Mark Gerstein, Michael Snyder Genome Biology 2006, 7:R110 (16 November 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ProCAT, a powerful and flexible new approach for analyzing many types of protein microarrays, is described.
	Software xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features Shannon D Schlueter, Matthew D Wilkerson, Qunfeng Dong, Volker Brendel Genome Biology 2006, 7:R111 (20 November 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary XGDB, a software infrastructure consisting of integrated tools for the storage, display and analysis of genome features (any property that can be associated with a genomic location, for example spliced alignments) in their genomics context is described.

Explore Genome Biology

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Volume 7 Issue 11

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