Genome Biology | Volume 8 Issue 2

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	Volume 8 Issue 2
	Comment
	Comment And the second shall be first Gregory A Petsko Genome Biology 2007, 8:103 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The retraction of 5 protein crystal structures has held back an entire sub-field for years due to the inordinately persuasive power of the pretty pictures that structural biology produces. All too often the first report is sketchy, superficial in its analysis, and prone to error. The second report is often more thoughtful, more useful, and is essential to the scientific process of validation and self-correction.
	Review
	Protein family review The Homer family proteins Yoko Shiraishi-Yamaguchi, Teiichi Furuichi Genome Biology 2007, 8:206 (21 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Homer family of proteins act as adapters for many postsynaptic density proteins. They are alternatively spliced into short and long forms; the long forms probably act as protein signaling complexes, whereas short forms might disrupt Homer complexes by competitive binding to target proteins.
	Minireview Expanding the mitochondrial interactome Timothy E Shutt, Gerald S Shadel Genome Biology 2007, 8:203 (23 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The most comprehensive mitochondrial interactome so far has been revealed by integrating many different studies.
	Minireview Decoding dosage compensation Xinxian Deng, Christine M Disteche Genome Biology 2007, 8:204 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In C. elegans, clusters of short DNA motifs have been identified as binding sites for the protein complex that mediates dosage compensation.
	Report
	Meeting report Applying plant genomics to crop improvement Michael Bevan, Robbie Waugh Genome Biology 2007, 8:302 (15 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the European Science Foundation-Wellcome Trust Conference on Crop Genomics, Trait Analysis and Breeding, Hinxton, UK, 8-11 November 2006.
	Research
	Research Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar Genome Biology 2007, 8:R15 (2 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Invertebrate conserved noncoding elements (CNEs) are associated with the same core set of genes as vertebrate CNEs, and may reflect the parallel evolution of enhancers in the gene regulatory networks that define alternative animal body plans.
	Research Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over Penelope R Haddrill, Daniel L Halligan, Dimitris Tomaras, Brian Charlesworth Genome Biology 2007, 8:R18 (6 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Observations from a genome-wide comparison of Drosophila melanogaster and Drosophila yakuba are consistent with a severe reduction in the efficacy of selection in the absence of crossing over, resulting in the accumulation of deleterious mutations in these regions.
	Research Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors? Caroline Deshayes, Emmanuel Perrodou, Sebastien Gallien, Daniel Euphrasie, Christine Schaeffer, Alain Van-Dorsselaer, Olivier Poch, Odile Lecompte, Jean-Marc Reyrat Genome Biology 2007, 8:R20 (12 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The question of whether bacterial interrupted coding sequences (ICDS) should be individually verified to produce an informative genome sequence is raised after bioinformatic, proteomic and sequencing analyses reveal that a significant proportion of ICDSs in the deposited genome sequence of Mycobacterium smegmatis are a result of sequencing errors.
	Research Patterns and rates of intron divergence between humans and chimpanzees Elodie Gazave, Tomàs Marqués-Bonet, Olga Fernando, Brian Charlesworth, Arcadi Navarro Genome Biology 2007, 8:R21 (19 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human-chimpanzee intron divergence shows strong correlations between intron length and divergence and GC-content.
	Research Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake Carleton L Kingsford, Kunmi Ayanbule, Steven L Salzberg Genome Biology 2007, 8:R22 (21 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a novel computational method, an extensive collection of predicted Rho-independent transcription terminators is derived from 343 prokaryotes, offering insight into their relationship to DNA uptake
	Research DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies Iiris Hovatta, Matthew A Zapala, Ron S Broide, Eric E Schadt, Ondrej Libiger, Nicholas J Schork, David J Lockhart, Carrolee Barlow Genome Biology 2007, 8:R25 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression profiles of five brain regions from six inbred mouse strains suggest that many regulatory networks are highly specific to particular brain regions.
	Research A network perspective on the evolution of metabolism by gene duplication Juan Díaz-Mejía, Ernesto Pérez-Rueda, Lorenzo Segovia Genome Biology 2007, 8:R26 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In silico models trying to explain the origin and evolution of metabolism are improved with the inclusion of specific functional constraints, such as the preferential coupling of reactions.
	Research microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder Diana O Perkins, Clark D Jeffries, L Fredrik Jarskog, J Michael Thomson, Keith Woods, Martin A Newman, Joel S Parker, Jianping Jin, Scott M Hammond Genome Biology 2007, 8:R27 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling reveals a possible association between schizophrenia and altered miRNA expression
	Research A genome-wide transcriptional activity survey of rice transposable element-related genes Yuling Jiao, Xing Deng Genome Biology 2007, 8:R28 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide survey of the transcriptional activity of TE-related genes that were associated with fifteen developmental stages and stress conditions revealed clear, albeit low, general transcription of TE-related genes.
	Research RNA-editing-mediated exon evolution Galit Lev-Maor, Rotem Sorek, Erez Y Levanon, Nurit Paz, Eli Eisenberg, Gil Ast Genome Biology 2007, 8:R29 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A primate-specific exon is found to be dependent on RNA editing for its exonization.
	Method DarkHorse: a method for genome-wide prediction of horizontal gene transfer Sheila Podell, Terry Gaasterland Genome Biology 2007, 8:R16 (2 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DarkHorse is a new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins.
	Method Boosting with stumps for predicting transcription start sites Xiaoyue Zhao, Zhenyu Xuan, Michael Q Zhang Genome Biology 2007, 8:R17 (2 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CoreBoost applies a boosting technique to select important features for predicting core promoters with diverse patterns.
	Method qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data Jan Hellemans, Geert Mortier, Anne De Paepe, Frank Speleman, Jo Vandesompele Genome Biology 2007, 8:R19 (9 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary qBase, a free program for the management and automated analysis of qPCR data, is described
	Method Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase Alan M Moses, Jean-Karim Hériché, Richard Durbin Genome Biology 2007, 8:R23 (22 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational strategy is used to predict cyclin-dependent targets by exploiting their propensity for occurring in clusters on substrate proteins.
	Method Quantifying similarity between motifs Shobhit Gupta, John A Stamatoyannopoulos, Timothy L Bailey, William Noble Genome Biology 2007, 8:R24 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tomtom allows for the statistical measurement of similarity between pairs of motifs, thereby enabling searching a motif database with a motif query.
	Correspondence
	Correspondence Systematic overestimation of gene gain through false diagnosis of gene absence Olga Zhaxybayeva, Camilla L Nesbø, W Ford Doolittle Genome Biology 2007, 8:402 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Usual BLAST-based methods for assessing gene presence and absence lead to systematic overestimation of within-species gene gain by lateral transfer.

	Volume 8 Issue 2
	Comment
	Comment And the second shall be first Gregory A Petsko Genome Biology 2007, 8:103 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The retraction of 5 protein crystal structures has held back an entire sub-field for years due to the inordinately persuasive power of the pretty pictures that structural biology produces. All too often the first report is sketchy, superficial in its analysis, and prone to error. The second report is often more thoughtful, more useful, and is essential to the scientific process of validation and self-correction.
	Review
	Protein family review The Homer family proteins Yoko Shiraishi-Yamaguchi, Teiichi Furuichi Genome Biology 2007, 8:206 (21 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Homer family of proteins act as adapters for many postsynaptic density proteins. They are alternatively spliced into short and long forms; the long forms probably act as protein signaling complexes, whereas short forms might disrupt Homer complexes by competitive binding to target proteins.
	Minireview Expanding the mitochondrial interactome Timothy E Shutt, Gerald S Shadel Genome Biology 2007, 8:203 (23 February 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The most comprehensive mitochondrial interactome so far has been revealed by integrating many different studies.
	Minireview Decoding dosage compensation Xinxian Deng, Christine M Disteche Genome Biology 2007, 8:204 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In C. elegans, clusters of short DNA motifs have been identified as binding sites for the protein complex that mediates dosage compensation.
	Report
	Meeting report Applying plant genomics to crop improvement Michael Bevan, Robbie Waugh Genome Biology 2007, 8:302 (15 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the European Science Foundation-Wellcome Trust Conference on Crop Genomics, Trait Analysis and Breeding, Hinxton, UK, 8-11 November 2006.
	Research
	Research Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar Genome Biology 2007, 8:R15 (2 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Invertebrate conserved noncoding elements (CNEs) are associated with the same core set of genes as vertebrate CNEs, and may reflect the parallel evolution of enhancers in the gene regulatory networks that define alternative animal body plans.
	Research Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over Penelope R Haddrill, Daniel L Halligan, Dimitris Tomaras, Brian Charlesworth Genome Biology 2007, 8:R18 (6 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Observations from a genome-wide comparison of Drosophila melanogaster and Drosophila yakuba are consistent with a severe reduction in the efficacy of selection in the absence of crossing over, resulting in the accumulation of deleterious mutations in these regions.
	Research Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors? Caroline Deshayes, Emmanuel Perrodou, Sebastien Gallien, Daniel Euphrasie, Christine Schaeffer, Alain Van-Dorsselaer, Olivier Poch, Odile Lecompte, Jean-Marc Reyrat Genome Biology 2007, 8:R20 (12 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The question of whether bacterial interrupted coding sequences (ICDS) should be individually verified to produce an informative genome sequence is raised after bioinformatic, proteomic and sequencing analyses reveal that a significant proportion of ICDSs in the deposited genome sequence of Mycobacterium smegmatis are a result of sequencing errors.
	Research Patterns and rates of intron divergence between humans and chimpanzees Elodie Gazave, Tomàs Marqués-Bonet, Olga Fernando, Brian Charlesworth, Arcadi Navarro Genome Biology 2007, 8:R21 (19 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human-chimpanzee intron divergence shows strong correlations between intron length and divergence and GC-content.
	Research Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake Carleton L Kingsford, Kunmi Ayanbule, Steven L Salzberg Genome Biology 2007, 8:R22 (21 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a novel computational method, an extensive collection of predicted Rho-independent transcription terminators is derived from 343 prokaryotes, offering insight into their relationship to DNA uptake
	Research DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies Iiris Hovatta, Matthew A Zapala, Ron S Broide, Eric E Schadt, Ondrej Libiger, Nicholas J Schork, David J Lockhart, Carrolee Barlow Genome Biology 2007, 8:R25 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression profiles of five brain regions from six inbred mouse strains suggest that many regulatory networks are highly specific to particular brain regions.
	Research A network perspective on the evolution of metabolism by gene duplication Juan Díaz-Mejía, Ernesto Pérez-Rueda, Lorenzo Segovia Genome Biology 2007, 8:R26 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In silico models trying to explain the origin and evolution of metabolism are improved with the inclusion of specific functional constraints, such as the preferential coupling of reactions.
	Research microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder Diana O Perkins, Clark D Jeffries, L Fredrik Jarskog, J Michael Thomson, Keith Woods, Martin A Newman, Joel S Parker, Jianping Jin, Scott M Hammond Genome Biology 2007, 8:R27 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling reveals a possible association between schizophrenia and altered miRNA expression
	Research A genome-wide transcriptional activity survey of rice transposable element-related genes Yuling Jiao, Xing Deng Genome Biology 2007, 8:R28 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide survey of the transcriptional activity of TE-related genes that were associated with fifteen developmental stages and stress conditions revealed clear, albeit low, general transcription of TE-related genes.
	Research RNA-editing-mediated exon evolution Galit Lev-Maor, Rotem Sorek, Erez Y Levanon, Nurit Paz, Eli Eisenberg, Gil Ast Genome Biology 2007, 8:R29 (27 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A primate-specific exon is found to be dependent on RNA editing for its exonization.
	Method DarkHorse: a method for genome-wide prediction of horizontal gene transfer Sheila Podell, Terry Gaasterland Genome Biology 2007, 8:R16 (2 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DarkHorse is a new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins.
	Method Boosting with stumps for predicting transcription start sites Xiaoyue Zhao, Zhenyu Xuan, Michael Q Zhang Genome Biology 2007, 8:R17 (2 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CoreBoost applies a boosting technique to select important features for predicting core promoters with diverse patterns.
	Method qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data Jan Hellemans, Geert Mortier, Anne De Paepe, Frank Speleman, Jo Vandesompele Genome Biology 2007, 8:R19 (9 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary qBase, a free program for the management and automated analysis of qPCR data, is described
	Method Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase Alan M Moses, Jean-Karim Hériché, Richard Durbin Genome Biology 2007, 8:R23 (22 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational strategy is used to predict cyclin-dependent targets by exploiting their propensity for occurring in clusters on substrate proteins.
	Method Quantifying similarity between motifs Shobhit Gupta, John A Stamatoyannopoulos, Timothy L Bailey, William Noble Genome Biology 2007, 8:R24 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tomtom allows for the statistical measurement of similarity between pairs of motifs, thereby enabling searching a motif database with a motif query.
	Correspondence
	Correspondence Systematic overestimation of gene gain through false diagnosis of gene absence Olga Zhaxybayeva, Camilla L Nesbø, W Ford Doolittle Genome Biology 2007, 8:402 (26 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Usual BLAST-based methods for assessing gene presence and absence lead to systematic overestimation of within-species gene gain by lateral transfer.

Explore Genome Biology

Articles

Volume 8 Issue 2

Comment

Review

Report

Research

Correspondence