Genome Biology | Volume 5 Issue 5

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	Volume 5 Issue 5
	Comment
	Comment The Ascent of Man? Gregory A Petsko Genome Biology 2004, 5:106 (26 April 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Anyone who cares about the moral and social implications of genomics, genetic engineering and biotechnology should read Michael J. Sandel's article, 'The Case Against Perfection', in the April 2004 issue of The Atlantic Monthly.
	Review
	Protein family review Sirtuins: Sir2-related NAD-dependent protein deacetylases Brian J North, Eric Verdin Genome Biology 2004, 5:224 (28 April 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and regulate transcriptional repression, recombination, the cell-division cycle, microtubule organization, and cellular responses to DNA-damaging agents.
	Minireview Maize DNA-sequencing strategies and genome organization Ron J Okagaki, Ronald L Phillips Genome Biology 2004, 5:223 (16 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Genome-filtration techniques, which enrich gene sequences in genomic libraries, provide a low-cost alternative to whole-genome sequencing for maize and other complex genomes.
	Minireview The mechanism of prion strain propagation Glenn C Telling Genome Biology 2004, 5:222 (22 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Two recent studies of yeast prions have now formally demonstrated that multiple stable protein conformations are the basis of strain variation.
	Minireview Insights from the rat genome sequence Linda J Mullins, John J Mullins Genome Biology 2004, 5:221 (30 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Detailed three-way comparison of the rat, mouse and human genomes, is revealing a great deal about mammalian genome evolution and together with recent developments in cloning technologies, this heralds an important phase in rat research.
	Opinion Progress towards mapping the universe of protein folds Alastair Grant, David Lee, Christine Orengo Genome Biology 2004, 5:107 (29 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary How well can the current set of known protein families and folds be used to estimate the total number of folds in nature, and will structural genomics initiatives yield representatives for all the major protein families within a reasonable time scale?
	Report
	Paper report Articles selected by Faculty of 1000: microarrays to study antibiotic resistance; identifying SUMO substrate proteins; parallel SNP genotyping; intron origin and evolution; variation in CpG-island methylation in humans Genome Biology 2004, 5:325 (20 April 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering microarrays to study antibiotic resistance, identifying SUMO substrate proteins, parallel SNP genotyping, intron origin and evolution and variation in CpG-island methylation in humans.
	Paper report Articles selected by Faculty of 1000: chromosomal rearrangements and mental retardation; peptide-MHC microarrays; antimicrobial drug discovery; core set of Arabidopsis accessions; comparing mouse development and human tumorigenesis Genome Biology 2004, 5:326 (27 April 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering chromosomal rearrangements and mental retardation, peptide-MHC microarrays, antimicrobial drug discovery, a core set of Arabidopsis accessions and comparing mouse development and human tumorigenesis.
	Meeting report A European focus on proteomics Christian MT Spahn, Hans Lehrach, Peter R Jungblut Genome Biology 2004, 5:322 (16 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the First International Symposium of the Austrian Proteomics Platform, Seefeld, Austria, 26-29 January 2004.
	Meeting report Discovering the seeds of diversity in plant genomes James A Birchler, Kathleen J Newton Genome Biology 2004, 5:323 (26 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Keystone Symposium 'Comparative Genomics of Plants', Taos, USA, 4-9 March 2004.
	Meeting report The changing face of genomics Manolis Kellis Genome Biology 2004, 5:324 (30 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the 5th annual Advances in Genome Biology and Technology (AGBT) and Automation in DNA Mapping and Sequencing (AMS) meeting, Marco Island, USA, 4-7 February 2004.
	Deposited research article A new estimate of the proportion unchanged genes in a microarray experiment Per Broberg Genome Biology 2004, 5:P10 (1 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A new approach for estimating the proportion of genes changed in microarray experiments is presented.
	Deposited research article AutoPrime: selecting primers for expressed sequences Gunnar Wrobel, Felix Kokocinski, Peter Lichter Genome Biology 2004, 5:P11 (15 April 2004) Abstract \| Full text \| PDF \| Editor’s summary The software AutoPrime automates the task of generating primers for RT-PCR experiments by combining the information from sequence databases with primer design software.
	Research news A 500,000-person study? Maria W Anderson Genome Biology 2004, 5:spotlight-20040527-01 (27 May 2004) Abstract \| Full text \| Editor’s summary Gene-environment interactions would be focus of NIH-led effort
	Research news Chimps are not like humans Cathy Holding Genome Biology 2004, 5:spotlight-20040528-01 (28 May 2004) Abstract \| Full text \| Editor’s summary Whole-chromosome comparison reveals much greater genetic differences than expected
	Research
	Research A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain L Aravind, Lakshminarayan M Iyer, Detlef D Leipe, Eugene V Koonin Genome Biology 2004, 5:R30 (16 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study characterizes the KAP protein family - a newly identified sub-group of the P-loop NTPases, which have transmembrane helices inserted into the P-loop NTPase domain. Their unusual phyletic distribution suggests KAP proteins were transferred from bacteria to animals by horizontal gene transfer.
	Research Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns Galina V Glazko, Arcady R Mushegian Genome Biology 2004, 5:R32 (27 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A hierarchy of 3,688 phyletic patterns was characterized encompassing more than 5,000 known protein-coding genes from 66 complete microbial genomes. The results indicate that gene loss and displacement has occurred in the evolution of most pathways.
	Research Multi-tissue gene-expression analysis in a mouse model of thyroid hormone resistance Lance D Miller, Peter McPhie, Hideyo Suzuki, Yasuhito Kato, Edison T Liu, Sheue-yann Cheng Genome Biology 2004, 5:R31 (29 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Gene-expression analysis in cerebellum, heart and white adipose tissue from a knock-in mouse that harbors a human mutation and faithfully reproduces human resistance to thyroid hormone, uncovered complex multiple signaling pathways that mediate the molecular actions of TRβ mutants in vivo.
	Research Transcriptional regulation of protein complexes in yeast Nicolas Simonis, Jacques van Helden, George N Cohen, Shoshana J Wodak Genome Biology 2004, 5:R33 (30 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study shows that only a small fraction of yeast protein complexes are coregulated at the transcriptional level.
	Method Orthologous gene-expression profiling in multi-species models: search for candidate genes Dmitry N Grigoryev, Shwu-Fan Ma, Rafael A Irizarry, Shui Ye, John Quackenbush, Joe GN Garcia Genome Biology 2004, 5:R34 (27 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary An analytical approach that simultaneously evaluates multi-species experimental models is presented. This approach may be a useful tool in the selection of process-related candidate genes.
	Software Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data Richard JS Baerends, Wiep Smits, Anne de Jong, Leendert W Hamoen, Jan Kok, Oscar P Kuipers Genome Biology 2004, 5:R37 (5 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Genome2D is a software tool that enables bacterial transcriptome data to be visualized on chromosome maps.
	Software Prolinks: a database of protein functional linkages derived from coevolution Peter M Bowers, Matteo Pellegrini, Mike J Thompson, Joe Fierro, Todd O Yeates, David Eisenberg Genome Biology 2004, 5:R35 (16 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Four methods that infer protein function and linkages have been combined in a single database, Prolinks, which spans 83 organisms and includes 10 million high-confidence links.
	Software ELXR: a resource for rapid exon-directed sequence analysis Jeoffrey J Schageman, Christopher J Horton, Sijing Niu, Harold R Garner, Alexander Pertsemlidis Genome Biology 2004, 5:R36 (28 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary ELXR is a web-based tool for designing exon-specific PCR/sequencing primers. A database, ELXRdb, containing precomputed primer pairs has been developed.

	Volume 5 Issue 5
	Comment
	Comment The Ascent of Man? Gregory A Petsko Genome Biology 2004, 5:106 (26 April 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Anyone who cares about the moral and social implications of genomics, genetic engineering and biotechnology should read Michael J. Sandel's article, 'The Case Against Perfection', in the April 2004 issue of The Atlantic Monthly.
	Review
	Protein family review Sirtuins: Sir2-related NAD-dependent protein deacetylases Brian J North, Eric Verdin Genome Biology 2004, 5:224 (28 April 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and regulate transcriptional repression, recombination, the cell-division cycle, microtubule organization, and cellular responses to DNA-damaging agents.
	Minireview Maize DNA-sequencing strategies and genome organization Ron J Okagaki, Ronald L Phillips Genome Biology 2004, 5:223 (16 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Genome-filtration techniques, which enrich gene sequences in genomic libraries, provide a low-cost alternative to whole-genome sequencing for maize and other complex genomes.
	Minireview The mechanism of prion strain propagation Glenn C Telling Genome Biology 2004, 5:222 (22 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Two recent studies of yeast prions have now formally demonstrated that multiple stable protein conformations are the basis of strain variation.
	Minireview Insights from the rat genome sequence Linda J Mullins, John J Mullins Genome Biology 2004, 5:221 (30 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Detailed three-way comparison of the rat, mouse and human genomes, is revealing a great deal about mammalian genome evolution and together with recent developments in cloning technologies, this heralds an important phase in rat research.
	Opinion Progress towards mapping the universe of protein folds Alastair Grant, David Lee, Christine Orengo Genome Biology 2004, 5:107 (29 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary How well can the current set of known protein families and folds be used to estimate the total number of folds in nature, and will structural genomics initiatives yield representatives for all the major protein families within a reasonable time scale?
	Report
	Paper report Articles selected by Faculty of 1000: microarrays to study antibiotic resistance; identifying SUMO substrate proteins; parallel SNP genotyping; intron origin and evolution; variation in CpG-island methylation in humans Genome Biology 2004, 5:325 (20 April 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering microarrays to study antibiotic resistance, identifying SUMO substrate proteins, parallel SNP genotyping, intron origin and evolution and variation in CpG-island methylation in humans.
	Paper report Articles selected by Faculty of 1000: chromosomal rearrangements and mental retardation; peptide-MHC microarrays; antimicrobial drug discovery; core set of Arabidopsis accessions; comparing mouse development and human tumorigenesis Genome Biology 2004, 5:326 (27 April 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering chromosomal rearrangements and mental retardation, peptide-MHC microarrays, antimicrobial drug discovery, a core set of Arabidopsis accessions and comparing mouse development and human tumorigenesis.
	Meeting report A European focus on proteomics Christian MT Spahn, Hans Lehrach, Peter R Jungblut Genome Biology 2004, 5:322 (16 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the First International Symposium of the Austrian Proteomics Platform, Seefeld, Austria, 26-29 January 2004.
	Meeting report Discovering the seeds of diversity in plant genomes James A Birchler, Kathleen J Newton Genome Biology 2004, 5:323 (26 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Keystone Symposium 'Comparative Genomics of Plants', Taos, USA, 4-9 March 2004.
	Meeting report The changing face of genomics Manolis Kellis Genome Biology 2004, 5:324 (30 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the 5th annual Advances in Genome Biology and Technology (AGBT) and Automation in DNA Mapping and Sequencing (AMS) meeting, Marco Island, USA, 4-7 February 2004.
	Deposited research article A new estimate of the proportion unchanged genes in a microarray experiment Per Broberg Genome Biology 2004, 5:P10 (1 April 2004) Abstract \| Full text \| PDF \| Editor’s summary A new approach for estimating the proportion of genes changed in microarray experiments is presented.
	Deposited research article AutoPrime: selecting primers for expressed sequences Gunnar Wrobel, Felix Kokocinski, Peter Lichter Genome Biology 2004, 5:P11 (15 April 2004) Abstract \| Full text \| PDF \| Editor’s summary The software AutoPrime automates the task of generating primers for RT-PCR experiments by combining the information from sequence databases with primer design software.
	Research news A 500,000-person study? Maria W Anderson Genome Biology 2004, 5:spotlight-20040527-01 (27 May 2004) Abstract \| Full text \| Editor’s summary Gene-environment interactions would be focus of NIH-led effort
	Research news Chimps are not like humans Cathy Holding Genome Biology 2004, 5:spotlight-20040528-01 (28 May 2004) Abstract \| Full text \| Editor’s summary Whole-chromosome comparison reveals much greater genetic differences than expected
	Research
	Research A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain L Aravind, Lakshminarayan M Iyer, Detlef D Leipe, Eugene V Koonin Genome Biology 2004, 5:R30 (16 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study characterizes the KAP protein family - a newly identified sub-group of the P-loop NTPases, which have transmembrane helices inserted into the P-loop NTPase domain. Their unusual phyletic distribution suggests KAP proteins were transferred from bacteria to animals by horizontal gene transfer.
	Research Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns Galina V Glazko, Arcady R Mushegian Genome Biology 2004, 5:R32 (27 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A hierarchy of 3,688 phyletic patterns was characterized encompassing more than 5,000 known protein-coding genes from 66 complete microbial genomes. The results indicate that gene loss and displacement has occurred in the evolution of most pathways.
	Research Multi-tissue gene-expression analysis in a mouse model of thyroid hormone resistance Lance D Miller, Peter McPhie, Hideyo Suzuki, Yasuhito Kato, Edison T Liu, Sheue-yann Cheng Genome Biology 2004, 5:R31 (29 April 2004) Abstract \| Full text \| PDF \| Editor’s summary Gene-expression analysis in cerebellum, heart and white adipose tissue from a knock-in mouse that harbors a human mutation and faithfully reproduces human resistance to thyroid hormone, uncovered complex multiple signaling pathways that mediate the molecular actions of TRβ mutants in vivo.
	Research Transcriptional regulation of protein complexes in yeast Nicolas Simonis, Jacques van Helden, George N Cohen, Shoshana J Wodak Genome Biology 2004, 5:R33 (30 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This study shows that only a small fraction of yeast protein complexes are coregulated at the transcriptional level.
	Method Orthologous gene-expression profiling in multi-species models: search for candidate genes Dmitry N Grigoryev, Shwu-Fan Ma, Rafael A Irizarry, Shui Ye, John Quackenbush, Joe GN Garcia Genome Biology 2004, 5:R34 (27 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary An analytical approach that simultaneously evaluates multi-species experimental models is presented. This approach may be a useful tool in the selection of process-related candidate genes.
	Software Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data Richard JS Baerends, Wiep Smits, Anne de Jong, Leendert W Hamoen, Jan Kok, Oscar P Kuipers Genome Biology 2004, 5:R37 (5 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Genome2D is a software tool that enables bacterial transcriptome data to be visualized on chromosome maps.
	Software Prolinks: a database of protein functional linkages derived from coevolution Peter M Bowers, Matteo Pellegrini, Mike J Thompson, Joe Fierro, Todd O Yeates, David Eisenberg Genome Biology 2004, 5:R35 (16 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Four methods that infer protein function and linkages have been combined in a single database, Prolinks, which spans 83 organisms and includes 10 million high-confidence links.
	Software ELXR: a resource for rapid exon-directed sequence analysis Jeoffrey J Schageman, Christopher J Horton, Sijing Niu, Harold R Garner, Alexander Pertsemlidis Genome Biology 2004, 5:R36 (28 April 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary ELXR is a web-based tool for designing exon-specific PCR/sequencing primers. A database, ELXRdb, containing precomputed primer pairs has been developed.

Explore Genome Biology

Articles

Volume 5 Issue 5

Comment

Review

Report

Research