Genome Biology | Volume 8 Issue 3

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	Volume 8 Issue 3
	Comment
	Comment A day in the life of a genome biologist in the not-too-distant future Gregory A Petsko Genome Biology 2007, 8:104 (29 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A look into the future of a biologist: daily activities governed by presidential mandates and acts.
	Review
	Protein family review The ring between ring fingers (RBR) protein family Birgit Eisenhaber, Nina Chumak, Frank Eisenhaber, Marie-Theres Hauser Genome Biology 2007, 8:209 (15 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An overview of the large and functionally diverse RBR protein family that mediates protein-protein interactions of various kinds in development and disease.
	Minireview Phagosome proteomes open the way to a better understanding of phagosome function Gareth Griffiths, Luis Mayorga Genome Biology 2007, 8:207 (15 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Determination of the global protein composition of phagosomes is a first step to understanding how these organelles carry out their function.
	Minireview Hox go omics: insights from Drosophila into Hox gene targets Anastasios Pavlopoulos, Michael Akam Genome Biology 2007, 8:208 (29 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Microarray analysis reveals hundreds of hitherto unsuspected Hox gene targets.
	Research
	Research Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics Claire Horlock, Farouk Shakib, Jafar Mahdavi, Nick S Jones, Herb F Sewell, Amir M Ghaemmaghami Genome Biology 2007, 8:R30 (1 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Important proteomic and functional differences between peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells (moDC) and KG-1 cells have been identified.
	Research Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimer's disease Erin L Heinzen, Woohyun Yoon, Michael E Weale, Arjune Sen, Nicholas W Wood, James R Burke, Kathleen A Welsh-Bohmer, Christine M Hulette, Sanjay M Sisodiya, David B Goldstein Genome Biology 2007, 8:R32 (7 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel microarray technology that permits the screening of alternative splice variants identifies disease-associated alternative splicing patterns in ion channel genes of patients with mesial temporal lobe epilepsy and Alzheimers disease.
	Research Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation Lichen Ren, Ge Gao, Dongxin Zhao, Mingxiao Ding, Jingchu Luo, Hongkui Deng Genome Biology 2007, 8:R35 (12 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Developmental-stage-related patterns of gene expression correlate with codon usage and genomic GC content in stem cell hierarchies.
	Research New genes in the evolution of the neural crest differentiation program Juan-Ramon Martinez-Morales, Thorsten Henrich, Mirana Ramialison, Joachim Wittbrodt Genome Biology 2007, 8:R36 (12 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The phylogenetic classification of genes that are ontologically associated with neural crest development reveals that neural crest evolution is associated with the emergence of new signalling peptides.
	Research Repetitive DNA is associated with centromeric domains in Trypanosoma brucei but not Trypanosoma cruzi Samson O Obado, Christopher Bot, Daniel Nilsson, Bjorn Andersson, John M Kelly Genome Biology 2007, 8:R37 (12 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Centromeres in Trypanosoma cruzi and Trypanosoma brucei can be localised to regions between directional gene clusters that contain degenerate retroelements, and in the case of T. brucei, repetitive DNA.
	Research Mobilization of pro-inflammatory lipids in obese Plscr3-deficient mice David M Mutch, Grace O'Maille, William R Wikoff, Therese Wiedmer, Peter J Sims, Gary Siuzdak Genome Biology 2007, 8:R38 (13 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metabolic profiling of mice deficient in phospholipid scramblase 3 reveals a possible molecular link between obesity and inflammation.
	Research Sense-antisense pairs in mammals: functional and evolutionary considerations Pedro AF Galante, Daniel O Vidal, Jorge E de Souza, Anamaria A Camargo, Sandro J de Souza Genome Biology 2007, 8:R40 (19 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a catalog of S-AS pairs in the human and mouse genomes revealed several putative roles for natural antisense transcripts and showed that some are artifacts of cDNA library construction.
	Research Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription Helder I Nakaya, Paulo P Amaral, Rodrigo Louro, André Lopes, Angela A Fachel, Yuri B Moreira, Tarik A El-Jundi, Aline M da Silva, Eduardo M Reis, Sergio Verjovski-Almeida Genome Biology 2007, 8:R43 (26 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the expression of 7,135 human totally intronic noncoding RNA transcripts plus the corresponding protein-coding genes using oligonucleotide arrays has identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles.
	Method Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database Chi-Hua Tung, Jhang-Wei Huang, Jinn-Moon Yang Genome Biology 2007, 8:R31 (3 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 3D BLAST, a novel protein structure database search tool, is a useful tool for analysing novel structures, capable of returning a list of aligned structures ordered according to E-values.
	Method A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome Kerrin S Small, Michael Brudno, Matthew M Hill, Arend Sidow Genome Biology 2007, 8:R41 (20 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high degree of polymorphism in the genome of the sea squirt Ciona savignyi complicated the assembly of sequence contigs, but a new alignment method results in a much improved sequence.
	Method CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts Shintaro Katayama, Mutsumi Kanamori-Katayama, Kazumi Yamaguchi, Piero Carninci, Yoshihide Hayashizaki Genome Biology 2007, 8:R42 (26 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel approach that combines CAGE expression analysis with oligonucleotide array technology allows for the accurate and sensitive detection of promoter-based transcriptional activity.
	Method Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships Alan R Dabney, John D Storey Genome Biology 2007, 8:R44 (28 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary eCADS is a new method for multiple array normalization of two-channel microarrays that takes into account general experimental designs and intensity-dependent relationships and allows for a more efficient dye-swap design that requires only one array per sample pair.
	Software GOTax: investigating biological processes and biochemical activities along the taxonomic tree Andreas Schlicker, Jörg Rahnenführer, Mario Albrecht, Thomas Lengauer, Francisco S Domingues Genome Biology 2007, 8:R33 (8 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GOTax, a novel web-based platform that integrates protein annotation with protein family classification and taxonomy, allows for an extensive assessment of functional similarity between proteins and for comparing and analyzing the distribution of protein families and protein functions over different taxonomic groups.
	Software Hawkeye: an interactive visual analytics tool for genome assemblies Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg Genome Biology 2007, 8:R34 (9 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Hawkeye is a new, freely available visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors.
	Software Reactome: a knowledge base of biologic pathways and processes Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein Genome Biology 2007, 8:R39 (16 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the interpretation of microarrays and other high-throughput data sets.
	Correspondence
	Correspondence The genome of Apis mellifera: dialog between linkage mapping and sequence assembly Michel Solignac, Lan Zhang, Florence Mougel, Bingshan Li, Dominique Vautrin, Monique Monnerot, Jean-Marie Cornuet, Kim C Worley, George M Weinstock, Richard A Gibbs Genome Biology 2007, 8:403 (19 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two independent genome projects for the honey bee, a microsatellite linkage map and a genome sequence assembly, have interactively produced an almost complete organization of the euchromatic genome.

	Volume 8 Issue 3
	Comment
	Comment A day in the life of a genome biologist in the not-too-distant future Gregory A Petsko Genome Biology 2007, 8:104 (29 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A look into the future of a biologist: daily activities governed by presidential mandates and acts.
	Review
	Protein family review The ring between ring fingers (RBR) protein family Birgit Eisenhaber, Nina Chumak, Frank Eisenhaber, Marie-Theres Hauser Genome Biology 2007, 8:209 (15 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An overview of the large and functionally diverse RBR protein family that mediates protein-protein interactions of various kinds in development and disease.
	Minireview Phagosome proteomes open the way to a better understanding of phagosome function Gareth Griffiths, Luis Mayorga Genome Biology 2007, 8:207 (15 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Determination of the global protein composition of phagosomes is a first step to understanding how these organelles carry out their function.
	Minireview Hox go omics: insights from Drosophila into Hox gene targets Anastasios Pavlopoulos, Michael Akam Genome Biology 2007, 8:208 (29 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Microarray analysis reveals hundreds of hitherto unsuspected Hox gene targets.
	Research
	Research Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics Claire Horlock, Farouk Shakib, Jafar Mahdavi, Nick S Jones, Herb F Sewell, Amir M Ghaemmaghami Genome Biology 2007, 8:R30 (1 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Important proteomic and functional differences between peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells (moDC) and KG-1 cells have been identified.
	Research Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimer's disease Erin L Heinzen, Woohyun Yoon, Michael E Weale, Arjune Sen, Nicholas W Wood, James R Burke, Kathleen A Welsh-Bohmer, Christine M Hulette, Sanjay M Sisodiya, David B Goldstein Genome Biology 2007, 8:R32 (7 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel microarray technology that permits the screening of alternative splice variants identifies disease-associated alternative splicing patterns in ion channel genes of patients with mesial temporal lobe epilepsy and Alzheimers disease.
	Research Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation Lichen Ren, Ge Gao, Dongxin Zhao, Mingxiao Ding, Jingchu Luo, Hongkui Deng Genome Biology 2007, 8:R35 (12 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Developmental-stage-related patterns of gene expression correlate with codon usage and genomic GC content in stem cell hierarchies.
	Research New genes in the evolution of the neural crest differentiation program Juan-Ramon Martinez-Morales, Thorsten Henrich, Mirana Ramialison, Joachim Wittbrodt Genome Biology 2007, 8:R36 (12 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The phylogenetic classification of genes that are ontologically associated with neural crest development reveals that neural crest evolution is associated with the emergence of new signalling peptides.
	Research Repetitive DNA is associated with centromeric domains in Trypanosoma brucei but not Trypanosoma cruzi Samson O Obado, Christopher Bot, Daniel Nilsson, Bjorn Andersson, John M Kelly Genome Biology 2007, 8:R37 (12 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Centromeres in Trypanosoma cruzi and Trypanosoma brucei can be localised to regions between directional gene clusters that contain degenerate retroelements, and in the case of T. brucei, repetitive DNA.
	Research Mobilization of pro-inflammatory lipids in obese Plscr3-deficient mice David M Mutch, Grace O'Maille, William R Wikoff, Therese Wiedmer, Peter J Sims, Gary Siuzdak Genome Biology 2007, 8:R38 (13 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metabolic profiling of mice deficient in phospholipid scramblase 3 reveals a possible molecular link between obesity and inflammation.
	Research Sense-antisense pairs in mammals: functional and evolutionary considerations Pedro AF Galante, Daniel O Vidal, Jorge E de Souza, Anamaria A Camargo, Sandro J de Souza Genome Biology 2007, 8:R40 (19 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a catalog of S-AS pairs in the human and mouse genomes revealed several putative roles for natural antisense transcripts and showed that some are artifacts of cDNA library construction.
	Research Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription Helder I Nakaya, Paulo P Amaral, Rodrigo Louro, André Lopes, Angela A Fachel, Yuri B Moreira, Tarik A El-Jundi, Aline M da Silva, Eduardo M Reis, Sergio Verjovski-Almeida Genome Biology 2007, 8:R43 (26 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the expression of 7,135 human totally intronic noncoding RNA transcripts plus the corresponding protein-coding genes using oligonucleotide arrays has identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles.
	Method Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database Chi-Hua Tung, Jhang-Wei Huang, Jinn-Moon Yang Genome Biology 2007, 8:R31 (3 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 3D BLAST, a novel protein structure database search tool, is a useful tool for analysing novel structures, capable of returning a list of aligned structures ordered according to E-values.
	Method A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome Kerrin S Small, Michael Brudno, Matthew M Hill, Arend Sidow Genome Biology 2007, 8:R41 (20 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high degree of polymorphism in the genome of the sea squirt Ciona savignyi complicated the assembly of sequence contigs, but a new alignment method results in a much improved sequence.
	Method CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts Shintaro Katayama, Mutsumi Kanamori-Katayama, Kazumi Yamaguchi, Piero Carninci, Yoshihide Hayashizaki Genome Biology 2007, 8:R42 (26 March 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel approach that combines CAGE expression analysis with oligonucleotide array technology allows for the accurate and sensitive detection of promoter-based transcriptional activity.
	Method Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships Alan R Dabney, John D Storey Genome Biology 2007, 8:R44 (28 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary eCADS is a new method for multiple array normalization of two-channel microarrays that takes into account general experimental designs and intensity-dependent relationships and allows for a more efficient dye-swap design that requires only one array per sample pair.
	Software GOTax: investigating biological processes and biochemical activities along the taxonomic tree Andreas Schlicker, Jörg Rahnenführer, Mario Albrecht, Thomas Lengauer, Francisco S Domingues Genome Biology 2007, 8:R33 (8 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GOTax, a novel web-based platform that integrates protein annotation with protein family classification and taxonomy, allows for an extensive assessment of functional similarity between proteins and for comparing and analyzing the distribution of protein families and protein functions over different taxonomic groups.
	Software Hawkeye: an interactive visual analytics tool for genome assemblies Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg Genome Biology 2007, 8:R34 (9 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Hawkeye is a new, freely available visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors.
	Software Reactome: a knowledge base of biologic pathways and processes Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Geeta Joshi-Tope, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein Genome Biology 2007, 8:R39 (16 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the interpretation of microarrays and other high-throughput data sets.
	Correspondence
	Correspondence The genome of Apis mellifera: dialog between linkage mapping and sequence assembly Michel Solignac, Lan Zhang, Florence Mougel, Bingshan Li, Dominique Vautrin, Monique Monnerot, Jean-Marie Cornuet, Kim C Worley, George M Weinstock, Richard A Gibbs Genome Biology 2007, 8:403 (19 March 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two independent genome projects for the honey bee, a microsatellite linkage map and a genome sequence assembly, have interactively produced an almost complete organization of the euchromatic genome.

Explore Genome Biology

Articles

Volume 8 Issue 3

Comment

Review

Research

Correspondence