Genome Biology | Volume 6 Issue 3

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	Volume 6 Issue 3
	Comment
	Comment Feet in mouth disease Gregory A Petsko Genome Biology 2005, 6:105 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We can, and should, use the financial resources of our institutions to redress the serious inequities and problems that bright, ambitious women face in the scientific workplace.
	Review
	Protein family review The opsins Akihisa Terakita Genome Biology 2005, 6:213 (1 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Opsins, G-protein-coupled receptors including rhodopsin, are found in animals, and more than a thousand have been identified so far. Most opsins act as pigments that activate G proteins in a light-dependent manner in both visual and non-visual systems.
	Minireview Connecting the dots in Huntington's disease with protein interaction networks Flaviano Giorgini, Paul J Muchowski Genome Biology 2005, 6:210 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of protein-protein interaction networks has identified new proteins and interactions that might be involved in the pathogenesis of the neurodegenerative disorder Huntington's disease.
	Minireview Tumor microenvironments, the immune system and cancer survival Robert L Strausberg Genome Biology 2005, 6:211 (1 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent microarray analyses of lymphomas suggest that the prognosis of cancer patients is related to an interplay between cancer cells and their microenvironment, including the immune response.
	Minireview New evolutionary frontiers from unusual virus genomes Christopher Desjardins, Jonathan A Eisen, Vishvanath Nene Genome Biology 2005, 6:212 (2 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sequences of two giant viral genomes, Mimivirus and a polydnavirus, have revealed unusual features that challenge the way we view the evolution and definition of viruses.
	Opinion Flexible peptides and cytoplasmic gels Dennis Bray Genome Biology 2005, 6:106 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent progress in predicting protein structures has revealed a surprising abundance of proteins that are significantly unfolded under physiological conditions. Unstructured, flexible polypeptides are likely to be functionally important and may cause local cytoplasmic regions to become gel-like.
	Report
	Paper report Articles selected by Faculty of 1000: sorghum genome sequencing; carbohydrate microarrays; metabolite profiling in fungi; in silico fate mapping; investigating cri du chat syndrome using array CGH Genome Biology 2005, 6:313 (9 February 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering sorghum genome sequencing, carbohydrate microarrays, metabolite profiling in fungi, in silico fate mapping and investigating cri du chat syndrome using array CGH.
	Paper report Articles selected by Faculty of 1000: microRNA-target interactions; hominid gene control regions; pre-mRNA splicing; gene silencing during pathogenesis; multiple use of microarrays Genome Biology 2005, 6:314 (24 February 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering microRNA-target interactions; hominid gene control regions; pre-mRNA splicing; gene silencing during pathogenesis; multiple use of microarrays.
	Meeting report Ways to get from plant genomes to phenomes: via yeast Pablo D Rabinowicz, Willem Rensink Genome Biology 2005, 6:310 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Plant Genomes: From Sequence to Phenome', Cold Spring Harbor, USA, 9-12 December 2004.
	Meeting report A full menu for stem-cell research Francesca M Spagnoli, Ali H Brivanlou Genome Biology 2005, 6:311 (25 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Stem Cell EuroConference, Paris, France, 9-10 December 2004.
	Meeting report Large-scale discovery and validation of functional elements in the human genome Bradley E Bernstein, Manolis Kellis Genome Biology 2005, 6:312 (1 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004.
	Research news Males can grow egg cells, too Laura M Hrastar Genome Biology 2005, 6:spotlight-20050302-01 (2 March 2005) Abstract \| Full text \| Editor’s summary Female cells become eggs despite surrounding signals for male development
	Research news Evidence for organelle origin Charles Q Choi Genome Biology 2005, 6:spotlight-20050303-01 (3 March 2005) Abstract \| Full text \| Editor’s summary Genetic clues point to 'missing links' between hydrogenosomes and mitochondria
	Research news No microcephaly for Hobbit Tabitha M Powledge Genome Biology 2005, 6:spotlight-20050307-01 (7 March 2005) Abstract \| Full text \| Editor’s summary Endocast studies suggest that overall brain shape of Homo floresiensis resembles Homo erectus
	Research news Fast track to longevity Graciela Flores Genome Biology 2005, 6:spotlight-20050308-01 (8 March 2005) Abstract \| Full text \| Editor’s summary A mouse study shows molecular connections between caloric restriction and lifespan extension
	Research news Sperm fusion protein identified Graciela Flores Genome Biology 2005, 6:spotlight-20050314-01 (14 March 2005) Abstract \| Full text \| Editor’s summary Japanese research opens the door to better understanding of how egg and sperm fuse
	Research news X sequence published Stephen Pincock Genome Biology 2005, 6:spotlight-20050317-01 (17 March 2005) Abstract \| Full text \| Editor’s summary Report in Nature details disease density of the sex chromosome and surprises about X inactivation
	Research news Epithelial pathway revealed Charles Q Choi Genome Biology 2005, 6:spotlight-20050318-01 (18 March 2005) Abstract \| Full text \| Editor’s summary Two reports show how, in Drosophila, DPP controls epithelial cell shape and organization
	Research news Mammals feed off yeast pathway Melissa Phillips Genome Biology 2005, 6:spotlight-20050321-01 (21 March 2005) Abstract \| Full text \| Editor’s summary Conserved amino acid-sensing mechanism affects eating behavior in rats
	Research news HIF-1α hinders mismatch repair Clementine Wallace Genome Biology 2005, 6:spotlight-20050322-01 (22 March 2005) Abstract \| Full text \| Editor’s summary The infamous hypoxia-induced factor enhances risk of genetic instability, study shows
	Research news Is RNA inheritance possible? Laura M Hrastar Genome Biology 2005, 6:spotlight-20050324-01 (24 March 2005) Abstract \| Full text \| Editor’s summary Researchers find plant clues to a non-DNA pathway for genetic transmission
	Research news Eda controls stickleback armor Sarah Lovinger Genome Biology 2005, 6:spotlight-20050329-01 (29 March 2005) Abstract \| Full text \| Editor’s summary Finding reinforces idea that small genetic changes control widespread and major evolution
	Research news Quality control in the nucleus Graciela Flores Genome Biology 2005, 6:spotlight-20050329-02 (29 March 2005) Abstract \| Full text \| Editor’s summary Yeast system involving ubiquitin-protein ligase is first described in non-protein synthesis compartment
	Research
	Research A DNA microarray survey of gene expression in normal human tissues Radha Shyamsundar, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, Jonathan R Pollack Genome Biology 2005, 6:R22 (14 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic survey of gene expression in 115 human tissue samples using cDNA microarrays provides a dataset that can be used as a baseline for comparison with expression in diseased tissue.
	Research Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression Pavel V Baranov, Andrew W Hammer, Jiadong Zhou, Raymond F Gesteland, John F Atkins Genome Biology 2005, 6:R25 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To find a length of slippage-prone sequences at which selection against transcriptional slippage is evident, the transcription of repetitive runs of A and T of different lengths in 108 bacterial genomes was analyzed. IS element genes were found to exploit transcriptional slippage for regulation of gene expression.
	Research Serendipitous discovery of Wolbachia genomes in multiple Drosophila species Steven L Salzberg, Julie Hotopp, Arthur L Delcher, Mihai Pop, Douglas R Smith, Michael B Eisen, William C Nelson Genome Biology 2005, 6:R23 (22 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis.
	Research Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea Resham D Kulkarni, Michael R Thon, Huaqin Pan, Ralph A Dean Genome Biology 2005, 6:R24 (2 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the Magnaporthe grisea genome and comparison with other fungi identified homologs of known G protein-coupled receptor-like proteins and a novel class of GPCR-like receptors in M. grisea that are specific to filamentous ascomycete fungi.
	Research The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum Rowena E Martin, Roselani I Henry, Janice L Abbey, John D Clements, Kiaran Kirk Genome Biology 2005, 6:R26 (2 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bioinformatic and expression analyses attribute putative functions to transporters and channels encoded by the Plasmodium falciparum genome. The malaria parasite has substantially more membrane transport proteins than previously thought.
	Method Comparative context analysis of codon pairs on an ORFeome scale Gabriela Moura, Miguel Pinheiro, Raquel Silva, Isabel Miranda, Vera Afreixo, Gaspar Dias, Adelaide Freitas, José L Oliveira, Manuel AS Santos Genome Biology 2005, 6:R28 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We have developed a system for comparative codon context analysis of open reading frames in whole genomes, providing insights into the rules that govern the evolution of codon-pair context.
	Method Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expression Kenneth F Manly, Jintao Wang, Robert W Williams Genome Biology 2005, 6:R27 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The use of recombinant inbred lines allows an estimate of the heritability of expression measured by individual probes. By testing heritability-weighted averages to define expression of a transcript, more QTLs can be detected than with previously described methods.
	Software The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data Terry F Hayamizu, Mary Mangan, John P Corradi, James A Kadin, Martin Ringwald Genome Biology 2005, 6:R29 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary The Adult Mouse Anatomical Dictionary was developed to provide an ontology for standardized nomenclature for anatomical terms in the postnatal mouse. The ontology will be used to annotate and integrate different types of data pertinent to anatomy.

	Volume 6 Issue 3
	Comment
	Comment Feet in mouth disease Gregory A Petsko Genome Biology 2005, 6:105 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We can, and should, use the financial resources of our institutions to redress the serious inequities and problems that bright, ambitious women face in the scientific workplace.
	Review
	Protein family review The opsins Akihisa Terakita Genome Biology 2005, 6:213 (1 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Opsins, G-protein-coupled receptors including rhodopsin, are found in animals, and more than a thousand have been identified so far. Most opsins act as pigments that activate G proteins in a light-dependent manner in both visual and non-visual systems.
	Minireview Connecting the dots in Huntington's disease with protein interaction networks Flaviano Giorgini, Paul J Muchowski Genome Biology 2005, 6:210 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of protein-protein interaction networks has identified new proteins and interactions that might be involved in the pathogenesis of the neurodegenerative disorder Huntington's disease.
	Minireview Tumor microenvironments, the immune system and cancer survival Robert L Strausberg Genome Biology 2005, 6:211 (1 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent microarray analyses of lymphomas suggest that the prognosis of cancer patients is related to an interplay between cancer cells and their microenvironment, including the immune response.
	Minireview New evolutionary frontiers from unusual virus genomes Christopher Desjardins, Jonathan A Eisen, Vishvanath Nene Genome Biology 2005, 6:212 (2 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The sequences of two giant viral genomes, Mimivirus and a polydnavirus, have revealed unusual features that challenge the way we view the evolution and definition of viruses.
	Opinion Flexible peptides and cytoplasmic gels Dennis Bray Genome Biology 2005, 6:106 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent progress in predicting protein structures has revealed a surprising abundance of proteins that are significantly unfolded under physiological conditions. Unstructured, flexible polypeptides are likely to be functionally important and may cause local cytoplasmic regions to become gel-like.
	Report
	Paper report Articles selected by Faculty of 1000: sorghum genome sequencing; carbohydrate microarrays; metabolite profiling in fungi; in silico fate mapping; investigating cri du chat syndrome using array CGH Genome Biology 2005, 6:313 (9 February 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering sorghum genome sequencing, carbohydrate microarrays, metabolite profiling in fungi, in silico fate mapping and investigating cri du chat syndrome using array CGH.
	Paper report Articles selected by Faculty of 1000: microRNA-target interactions; hominid gene control regions; pre-mRNA splicing; gene silencing during pathogenesis; multiple use of microarrays Genome Biology 2005, 6:314 (24 February 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering microRNA-target interactions; hominid gene control regions; pre-mRNA splicing; gene silencing during pathogenesis; multiple use of microarrays.
	Meeting report Ways to get from plant genomes to phenomes: via yeast Pablo D Rabinowicz, Willem Rensink Genome Biology 2005, 6:310 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Plant Genomes: From Sequence to Phenome', Cold Spring Harbor, USA, 9-12 December 2004.
	Meeting report A full menu for stem-cell research Francesca M Spagnoli, Ali H Brivanlou Genome Biology 2005, 6:311 (25 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Stem Cell EuroConference, Paris, France, 9-10 December 2004.
	Meeting report Large-scale discovery and validation of functional elements in the human genome Bradley E Bernstein, Manolis Kellis Genome Biology 2005, 6:312 (1 March 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004.
	Research news Males can grow egg cells, too Laura M Hrastar Genome Biology 2005, 6:spotlight-20050302-01 (2 March 2005) Abstract \| Full text \| Editor’s summary Female cells become eggs despite surrounding signals for male development
	Research news Evidence for organelle origin Charles Q Choi Genome Biology 2005, 6:spotlight-20050303-01 (3 March 2005) Abstract \| Full text \| Editor’s summary Genetic clues point to 'missing links' between hydrogenosomes and mitochondria
	Research news No microcephaly for Hobbit Tabitha M Powledge Genome Biology 2005, 6:spotlight-20050307-01 (7 March 2005) Abstract \| Full text \| Editor’s summary Endocast studies suggest that overall brain shape of Homo floresiensis resembles Homo erectus
	Research news Fast track to longevity Graciela Flores Genome Biology 2005, 6:spotlight-20050308-01 (8 March 2005) Abstract \| Full text \| Editor’s summary A mouse study shows molecular connections between caloric restriction and lifespan extension
	Research news Sperm fusion protein identified Graciela Flores Genome Biology 2005, 6:spotlight-20050314-01 (14 March 2005) Abstract \| Full text \| Editor’s summary Japanese research opens the door to better understanding of how egg and sperm fuse
	Research news X sequence published Stephen Pincock Genome Biology 2005, 6:spotlight-20050317-01 (17 March 2005) Abstract \| Full text \| Editor’s summary Report in Nature details disease density of the sex chromosome and surprises about X inactivation
	Research news Epithelial pathway revealed Charles Q Choi Genome Biology 2005, 6:spotlight-20050318-01 (18 March 2005) Abstract \| Full text \| Editor’s summary Two reports show how, in Drosophila, DPP controls epithelial cell shape and organization
	Research news Mammals feed off yeast pathway Melissa Phillips Genome Biology 2005, 6:spotlight-20050321-01 (21 March 2005) Abstract \| Full text \| Editor’s summary Conserved amino acid-sensing mechanism affects eating behavior in rats
	Research news HIF-1α hinders mismatch repair Clementine Wallace Genome Biology 2005, 6:spotlight-20050322-01 (22 March 2005) Abstract \| Full text \| Editor’s summary The infamous hypoxia-induced factor enhances risk of genetic instability, study shows
	Research news Is RNA inheritance possible? Laura M Hrastar Genome Biology 2005, 6:spotlight-20050324-01 (24 March 2005) Abstract \| Full text \| Editor’s summary Researchers find plant clues to a non-DNA pathway for genetic transmission
	Research news Eda controls stickleback armor Sarah Lovinger Genome Biology 2005, 6:spotlight-20050329-01 (29 March 2005) Abstract \| Full text \| Editor’s summary Finding reinforces idea that small genetic changes control widespread and major evolution
	Research news Quality control in the nucleus Graciela Flores Genome Biology 2005, 6:spotlight-20050329-02 (29 March 2005) Abstract \| Full text \| Editor’s summary Yeast system involving ubiquitin-protein ligase is first described in non-protein synthesis compartment
	Research
	Research A DNA microarray survey of gene expression in normal human tissues Radha Shyamsundar, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, Jonathan R Pollack Genome Biology 2005, 6:R22 (14 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic survey of gene expression in 115 human tissue samples using cDNA microarrays provides a dataset that can be used as a baseline for comparison with expression in diseased tissue.
	Research Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression Pavel V Baranov, Andrew W Hammer, Jiadong Zhou, Raymond F Gesteland, John F Atkins Genome Biology 2005, 6:R25 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To find a length of slippage-prone sequences at which selection against transcriptional slippage is evident, the transcription of repetitive runs of A and T of different lengths in 108 bacterial genomes was analyzed. IS element genes were found to exploit transcriptional slippage for regulation of gene expression.
	Research Serendipitous discovery of Wolbachia genomes in multiple Drosophila species Steven L Salzberg, Julie Hotopp, Arthur L Delcher, Mihai Pop, Douglas R Smith, Michael B Eisen, William C Nelson Genome Biology 2005, 6:R23 (22 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis.
	Research Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea Resham D Kulkarni, Michael R Thon, Huaqin Pan, Ralph A Dean Genome Biology 2005, 6:R24 (2 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the Magnaporthe grisea genome and comparison with other fungi identified homologs of known G protein-coupled receptor-like proteins and a novel class of GPCR-like receptors in M. grisea that are specific to filamentous ascomycete fungi.
	Research The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum Rowena E Martin, Roselani I Henry, Janice L Abbey, John D Clements, Kiaran Kirk Genome Biology 2005, 6:R26 (2 March 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bioinformatic and expression analyses attribute putative functions to transporters and channels encoded by the Plasmodium falciparum genome. The malaria parasite has substantially more membrane transport proteins than previously thought.
	Method Comparative context analysis of codon pairs on an ORFeome scale Gabriela Moura, Miguel Pinheiro, Raquel Silva, Isabel Miranda, Vera Afreixo, Gaspar Dias, Adelaide Freitas, José L Oliveira, Manuel AS Santos Genome Biology 2005, 6:R28 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary We have developed a system for comparative codon context analysis of open reading frames in whole genomes, providing insights into the rules that govern the evolution of codon-pair context.
	Method Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expression Kenneth F Manly, Jintao Wang, Robert W Williams Genome Biology 2005, 6:R27 (28 February 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The use of recombinant inbred lines allows an estimate of the heritability of expression measured by individual probes. By testing heritability-weighted averages to define expression of a transcript, more QTLs can be detected than with previously described methods.
	Software The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data Terry F Hayamizu, Mary Mangan, John P Corradi, James A Kadin, Martin Ringwald Genome Biology 2005, 6:R29 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary The Adult Mouse Anatomical Dictionary was developed to provide an ontology for standardized nomenclature for anatomical terms in the postnatal mouse. The ontology will be used to annotate and integrate different types of data pertinent to anatomy.

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Volume 6 Issue 3

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