Genome Biology | Volume 7 Issue 1

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	Volume 7 Issue 1
	Comment
	Comment Let's get our priorities straight Gregory A Petsko Genome Biology 2006, 7:101 (1 February 2006) Abstract \| Full text \| PDF \| Editor’s summary Supplementary material is one of the worst ideas in the history of bad ideas. It's the scientific publishing equivalent of fighting a land war in Asia.
	Review
	Review Attacking pathogens through their hosts Paul Kellam Genome Biology 2006, 7:201 (30 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions.
	Minireview Functional genomics of early cortex patterning David Chambers, Gord Fishell Genome Biology 2006, 7:202 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study has sought to unravel the underlying genetic control of pattern formation in the cortex by elucidating the transcriptional profile of discrete neocortical regions.
	Minireview Where is the difference between the genomes of humans and annelids? Alexei Fedorov, Larisa Fedorova Genome Biology 2006, 7:203 (1 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The first systematic investigation of an annelid genome has revealed that the genes of the marine worm Platynereis dumerilii are more closely related to those of vertebrates than to those of insects or nematodes.
	Opinion On the evolution of the standard amino-acid alphabet Yi Lu, Stephen Freeland Genome Biology 2006, 7:102 (1 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fresh insights into the origin of the amino-acid alphabet are now emerging from disciplines as diverse as astrobiology, biochemical engineering and bioinformatics.
	Report
	Meeting report Interactome networks: the state of the science Guy J Warner, Yeyejide A Adeleye, Trey Ideker Genome Biology 2006, 7:301 (23 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Cold Spring Harbor/Wellcome Trust Meeting 'Interactome Networks', Hinxton, UK, 31 August-4 September 2005.
	Meeting report Epigenetic regulation: DNA confers identity but is not enough to maintain it Raymond A Poot, Richard Festenstein Genome Biology 2006, 7:302 (27 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the conference 'Epigenetics and the dynamic genome', 30 June-2 July 2005, Babraham, Cambridge, UK.
	Meeting report Bioinformatics meets systems biology Carlos Salazar, Jana Schütze, Oliver Ebenhöh Genome Biology 2006, 7:303 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Fifth International Workshop on Bioinformatics and Systems Biology, Berlin, Germany, 22-25 August 2005.
	Meeting report Towards the visualization of genome activity at nanoscale dimensions Joan Politz Genome Biology 2006, 7:304 (1 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Fifth Annual Nanostructural Genomics meeting, Bar Harbor, USA, 7-10 September 2005.
	Research
	Research A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones Clare Gooding, Francis Clark, Matthew C Wollerton, Sushma-Nagaraja Grellscheid, Harriet Groom, Christopher WJ Smith Genome Biology 2006, 7:R1 (13 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exons with predicted branch points were identified from a large dataset of human exons and the importance of these branch points for splicing was verified.
	Research Variable window binding for mutually exclusive alternative splicing Dimitris Anastassiou, Hairuo Liu, Vinay Varadan Genome Biology 2006, 7:R2 (13 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A mechanism called Variable Window Binding for mutually exclusive alternative splicing is described for exon 6 of the Drosophila Dscam gene, which represents an extreme case of alternative splicing.
	Research Challenging the spliceosome machine Michael Weir, Matthew Eaton, Michael Rice Genome Biology 2006, 7:R3 (17 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of a set of almost 25,000 donor and acceptor splice sites in Drosophila shows that information content increases near splice sites flanking very long of very short introns and exons.
	Research Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference Ben Lehner, Andrea Calixto, Catriona Crombie, Julia Tischler, Angelo Fortunato, Martin Chalfie, Andrew G Fraser Genome Biology 2006, 7:R4 (20 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mutations in lin-35, the worm ortholog of a mammalian tumor suppressor gene, and other synMuv B genes result in an increased sensitivity to RNAi and enhanced somatic transgene silencing.
	Research Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases Alistair RR Forrest, Darrin F Taylor, Mark L Crowe, Alistair M Chalk, Nic J Waddell, Gabriel Kolle, Geoffrey J Faulkner, Rimantas Kodzius, Shintaro Katayama, Christine Wells, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Sean M Grimmond Genome Biology 2006, 7:R5 (26 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic study of the transcript variants of all protein kinase- and phosphatase-like loci in mouse shows that at least 75% of them generate alternative transcripts, many of which encode different domain structures.
	Method Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes Rammohan Narayanaswamy, Wei Niu, Alexander D Scouras, G Traver Hart, Jonathan Davies, Andrew D Ellington, Vishwanath R Iyer, Edward M Marcotte Genome Biology 2006, 7:R6 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Spotted cell microarrays were developed for measuring cellular phenotypes on a large scale and used to identify genes involved in the response of yeast to mating pheromone.
	Method Identifying repeat domains in large genomes Degui Zhi, Benjamin J Raphael, Alkes L Price, Haixu Tang, Pavel A Pevzner Genome Biology 2006, 7:R7 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A graph-based method for the analysis of repeat families in a repeat library is presented that helps elucidating the evolutionary history of repeats.
	Method A gold standard set of mechanistically diverse enzyme superfamilies Shoshana D Brown, John A Gerlt, Jennifer L Seffernick, Patricia C Babbitt Genome Biology 2006, 7:R8 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A gold standard set of enzyme superfamilies, clustered according to sequence, structure and functional criteria, is presented.

	Volume 7 Issue 1
	Comment
	Comment Let's get our priorities straight Gregory A Petsko Genome Biology 2006, 7:101 (1 February 2006) Abstract \| Full text \| PDF \| Editor’s summary Supplementary material is one of the worst ideas in the history of bad ideas. It's the scientific publishing equivalent of fighting a land war in Asia.
	Review
	Review Attacking pathogens through their hosts Paul Kellam Genome Biology 2006, 7:201 (30 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions.
	Minireview Functional genomics of early cortex patterning David Chambers, Gord Fishell Genome Biology 2006, 7:202 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study has sought to unravel the underlying genetic control of pattern formation in the cortex by elucidating the transcriptional profile of discrete neocortical regions.
	Minireview Where is the difference between the genomes of humans and annelids? Alexei Fedorov, Larisa Fedorova Genome Biology 2006, 7:203 (1 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The first systematic investigation of an annelid genome has revealed that the genes of the marine worm Platynereis dumerilii are more closely related to those of vertebrates than to those of insects or nematodes.
	Opinion On the evolution of the standard amino-acid alphabet Yi Lu, Stephen Freeland Genome Biology 2006, 7:102 (1 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fresh insights into the origin of the amino-acid alphabet are now emerging from disciplines as diverse as astrobiology, biochemical engineering and bioinformatics.
	Report
	Meeting report Interactome networks: the state of the science Guy J Warner, Yeyejide A Adeleye, Trey Ideker Genome Biology 2006, 7:301 (23 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the joint Cold Spring Harbor/Wellcome Trust Meeting 'Interactome Networks', Hinxton, UK, 31 August-4 September 2005.
	Meeting report Epigenetic regulation: DNA confers identity but is not enough to maintain it Raymond A Poot, Richard Festenstein Genome Biology 2006, 7:302 (27 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the conference 'Epigenetics and the dynamic genome', 30 June-2 July 2005, Babraham, Cambridge, UK.
	Meeting report Bioinformatics meets systems biology Carlos Salazar, Jana Schütze, Oliver Ebenhöh Genome Biology 2006, 7:303 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Fifth International Workshop on Bioinformatics and Systems Biology, Berlin, Germany, 22-25 August 2005.
	Meeting report Towards the visualization of genome activity at nanoscale dimensions Joan Politz Genome Biology 2006, 7:304 (1 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Fifth Annual Nanostructural Genomics meeting, Bar Harbor, USA, 7-10 September 2005.
	Research
	Research A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones Clare Gooding, Francis Clark, Matthew C Wollerton, Sushma-Nagaraja Grellscheid, Harriet Groom, Christopher WJ Smith Genome Biology 2006, 7:R1 (13 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exons with predicted branch points were identified from a large dataset of human exons and the importance of these branch points for splicing was verified.
	Research Variable window binding for mutually exclusive alternative splicing Dimitris Anastassiou, Hairuo Liu, Vinay Varadan Genome Biology 2006, 7:R2 (13 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A mechanism called Variable Window Binding for mutually exclusive alternative splicing is described for exon 6 of the Drosophila Dscam gene, which represents an extreme case of alternative splicing.
	Research Challenging the spliceosome machine Michael Weir, Matthew Eaton, Michael Rice Genome Biology 2006, 7:R3 (17 January 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of a set of almost 25,000 donor and acceptor splice sites in Drosophila shows that information content increases near splice sites flanking very long of very short introns and exons.
	Research Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference Ben Lehner, Andrea Calixto, Catriona Crombie, Julia Tischler, Angelo Fortunato, Martin Chalfie, Andrew G Fraser Genome Biology 2006, 7:R4 (20 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mutations in lin-35, the worm ortholog of a mammalian tumor suppressor gene, and other synMuv B genes result in an increased sensitivity to RNAi and enhanced somatic transgene silencing.
	Research Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases Alistair RR Forrest, Darrin F Taylor, Mark L Crowe, Alistair M Chalk, Nic J Waddell, Gabriel Kolle, Geoffrey J Faulkner, Rimantas Kodzius, Shintaro Katayama, Christine Wells, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Sean M Grimmond Genome Biology 2006, 7:R5 (26 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic study of the transcript variants of all protein kinase- and phosphatase-like loci in mouse shows that at least 75% of them generate alternative transcripts, many of which encode different domain structures.
	Method Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes Rammohan Narayanaswamy, Wei Niu, Alexander D Scouras, G Traver Hart, Jonathan Davies, Andrew D Ellington, Vishwanath R Iyer, Edward M Marcotte Genome Biology 2006, 7:R6 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Spotted cell microarrays were developed for measuring cellular phenotypes on a large scale and used to identify genes involved in the response of yeast to mating pheromone.
	Method Identifying repeat domains in large genomes Degui Zhi, Benjamin J Raphael, Alkes L Price, Haixu Tang, Pavel A Pevzner Genome Biology 2006, 7:R7 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A graph-based method for the analysis of repeat families in a repeat library is presented that helps elucidating the evolutionary history of repeats.
	Method A gold standard set of mechanistically diverse enzyme superfamilies Shoshana D Brown, John A Gerlt, Jennifer L Seffernick, Patricia C Babbitt Genome Biology 2006, 7:R8 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A gold standard set of enzyme superfamilies, clustered according to sequence, structure and functional criteria, is presented.

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Volume 7 Issue 1

Comment

Review

Report

Research