Genome Biology | Volume 8 Issue 11

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	Volume 8 Issue 11
	Comment
	Comment What if Watson had said "Apes evolved from man"? Gregory A Petsko Genome Biology 2007, 8:113 (30 November 2007) Abstract \| Full text \| PDF \| PubMed \| 3 comments \| Editor’s summary Our status as genome biologists gives us both ammunition and a powerful line of attack when we are confronted with ignorance, prejudice, and bigotry.
	Review
	Review Chromatin, gene silencing and HIV latency Hoi-Ping Mok, Andrew ML Lever Genome Biology 2007, 8:228 (23 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cellular defence mechanisms against HIV contribute to its persistence.
	Minireview Termites in the woodwork Samuel Chaffron, Christian von Mering Genome Biology 2007, 8:229 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metagenomic analysis of termite gut flora reveals a diversity of wood-degrading enzymes.
	Minireview Nose thyself: individuality in the human olfactory genome Xiaohong Zhang, Stuart Firestein Genome Biology 2007, 8:230 (26 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A link between a genetic polymorphism in an odorant receptor and variability in perception of the smell of the steroid androstenone.
	Report
	Meeting report Chromatin meets RNA polymerase II Bryan J Venters, B Franklin Pugh Genome Biology 2007, 8:319 (13 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Mechanisms of eukaryotic transcription', Cold Spring Harbor, USA, 2 August-2 September 2007.
	Meeting report Shaken not stirred: a global research cocktail served in Hinxton Samuel Marguerat, Brian T Wilhelm, Jürg Bähler Genome Biology 2007, 8:320 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 2007 Cold Spring Harbor Laboratory/Wellcome Trust Conference on Functional Genomics and Systems Biology, Hinxton, UK, 10-13 October 2007.
	Research
	Research The determinants of gene order conservation in yeasts Juan F Poyatos, Laurence D Hurst Genome Biology 2007, 8:R233 (5 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Current intergene distance is shown to be consistently the strongest predictor of synteny conservation as expected under a simple null model, and other variables are of lesser importance.
	Research Gene expression atlas of the mouse central nervous system: impact and interactions of age, energy intake and gender Xiangru Xu, Ming Zhan, Wenzhen Duan, Vinayakumar Prabhu, Randall Brenneman, William Wood, Jeff Firman, Huai Li, Peisu Zhang, Carol Ibe, Alan B Zonderman, Dan L Longo, Suresh Poosala, Kevin G Becker, Mark P Mattson Genome Biology 2007, 8:R234 (7 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptional profiles of five regions of the central nervous system (CNS) of mice varying in age, gender and dietary intake were measured by microarray. The resulting data provide insights into the mechanisms of age-, diet- and gender-related CNS plasticity and vulnerability in mammals.
	Research Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution Filipe G Vieira, Alejandro Sánchez-Gracia, Julio Rozas Genome Biology 2007, 8:R235 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The comparative analysis of the odorant binding protein family in 12 Drosophila genomes allowed the identification of 595 putative family member genes and revealed insights into the evolution of this family in these species.
	Research Sequence and functional analyses of Haemophilus spp. genomic islands Mario Juhas, Peter M Power, Rosalind M Harding, David JP Ferguson, Ioanna D Dimopoulou, Abdel RE Elamin, Zaini Mohd-Zain, Derek W Hood, Richard Adegbola, Alice Erwin, Arnold Smith, Robert S Munson, Alistair Harrison, Lucielle Mansfield, Stephen Bentley, Derrick W Crook Genome Biology 2007, 8:R237 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Comparative analysis of genomic islands of Haemophilus species shows that they are co-evolving as semi-autonomous genomes within the host genome.
	Research The global landscape of sequence diversity José Peregrín-Álvarez, John Parkinson Genome Biology 2007, 8:R238 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of genomic and EST sequences reveals a greater genetic diversity within eukaryotes than prokaryotes and enables identification of taxon-specific sequences.
	Research The distributions, mechanisms, and structures of metabolite-binding riboswitches Jeffrey E Barrick, Ronald R Breaker Genome Biology 2007, 8:R239 (12 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic analyses revealed insights into the distribution of riboswitch classes in different microbial groups, and structural analyses led to updated aptamer structure models and insights into the mechanism of these non-coding RNA structures.
	Research GeneChip analysis of human embryonic stem cell differentiation into hemangioblasts: an in silico dissection of mixed phenotypes Shi-Jiang Lu, Jennifer A Hipp, Qiang Feng, Jason D Hipp, Robert Lanza, Anthony Atala Genome Biology 2007, 8:R240 (13 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of human embryonic stem cells differentiating into blast cells reveals that erythroblasts are the predominant cell type in the blast cell population. In silico comparisons with publicly available data sets revealed the presence of endothelia, cardiomyocytes and hematopoietic lineages.
	Research Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks Daphna Joseph-Strauss, Drora Zenvirth, Giora Simchen, Naama Barkai Genome Biology 2007, 8:R241 (14 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide expression profiling of spore germination in Saccharomyces cerevisiae reveals two major stages and identifies germination-specific regulation of cell cycle machinery.
	Research Quantification of ortholog losses in insects and vertebrates Stefan Wyder, Evgenia V Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M Zdobnov Genome Biology 2007, 8:R242 (16 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene repertoires of 5 vertebrates and 5 insects showed that the rate of losses correlates well with the species' rates of molecular evolution and radiation times and suggests that the Urbilateria genome contained more than 7,000 genes.
	Research The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z Willem Rens, Patricia CM O'Brien, Frank Grützner, Oliver Clarke, Daria Graphodatskaya, Enkhjargal Tsend-Ayush, Vladimir A Trifonov, Helen Skelton, Mary C Wallis, Steve Johnston, Frederic Veyrunes, Jennifer AM Graves, Malcolm A Ferguson-Smith Genome Biology 2007, 8:R243 (16 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative study of the karyotype of the short-beaked echidna shows that monotremes appear to have a unique XY sex chromosome system that shares some homology with the avian Z.
	Research Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain Jing Li, Zijing J Liu, Yuchun C Pan, Qi Liu, Xing Fu, Nigel GF Cooper, Yixue Li, Mengsheng Qiu, Tieliu Shi Genome Biology 2007, 8:R244 (19 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive regulatory module network of 15 bHLH transcription factors over 150 target genes in mouse brain has been constructed.
	Research Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia Gui-Sheng Wu, Yong-Gang Yao, Kai-Xing Qu, Zhao-Li Ding, Hui Li, Malliya G Palanichamy, Zi-Yuan Duan, Ning Li, Yao-Sheng Chen, Ya-Ping Zhang Genome Biology 2007, 8:R245 (19 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A fine-grained mitochondrial DNA phylogenomic analysis was conducted in domestic pigs and wild boars, revealing that pig domestication in East Asia occurred in the Mekong and the middle and downstream regions of the Yangtze river.
	Research Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex Shuzhang Yang, Kai Wang, Otto Valladares, Sridhar Hannenhalli, Maja Bucan Genome Biology 2007, 8:R247 (20 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Microarray analysis shows that approximately 10% of transcripts in the mouse prefrontal cortex have diurnally regulated expression patterns.
	Research Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa Carol J Loscher, Karsten Hokamp, Paul F Kenna, Alasdair C Ivens, Peter Humphries, Arpad Palfi, G Jane Farrar Genome Biology 2007, 8:R248 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MicroRNA expression profiling showed that the retina of mice carrying a rhodopsin mutation that leads to retinitis pigmentosa have notably different microRNA profiles from wildtype mice; further in silico analyses identified potential retinal targets for differentially regulated microRNAs.
	Research MADS-complexes regulate transcriptome dynamics during pollen maturation Wim Verelst, David Twell, Stefan de Folter, Richard Immink, Heinz Saedler, Thomas Münster Genome Biology 2007, 8:R249 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pollen transcript profiling of mutants defective in MADS-domain MIKC* protein complexes suggests they control a transcriptional network directing cellular differentiation during pollen maturation.
	Research Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish Cornelia Stein, Mario Caccamo, Gavin Laird, Maria Leptin Genome Biology 2007, 8:R251 (27 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of several fish genomes reveals components of the innate immune system and identifies orthologous relationships between gene families of fish and mammals.
	Research Using protein complexes to predict phenotypic effects of gene mutation Hunter B Fraser, Joshua B Plotkin Genome Biology 2007, 8:R252 (27 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The best predictor of a protein's knockout phenotype is shown to be the knockout phenotype of other proteins that are present in a protein complex with it.
	Research Integrative analysis for finding genes and networks involved in diabetes and other complex diseases Regine Bergholdt, Zenia M Størling, Kasper Lage, E Olof Karlberg, Páll Í Ólason, Mogens Aalund, Jørn Nerup, Søren Brunak, Christopher T Workman, Flemming Pociot Genome Biology 2007, 8:R253 (28 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An integrative analysis combining genetic interactions and protein interactions can be used to identify candidate genes/proteins for type 1 diabetes and other complex diseases.
	Research Identification of candidate predictive and surrogate molecular markers for dasatinib in prostate cancer: rationale for patient selection and efficacy monitoring Xi-De Wang, Karen Reeves, Feng R Luo, Li-An Xu, Francis Lee, Edwin Clark, Fei Huang Genome Biology 2007, 8:R255 (29 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression profiling was used to identify genes associated with sensitivity to the tyrosine kinase drug Dasatinib in prostate cancer cell lines, revealing a possible Dasatinib efficacy signature in prostate cancer.
	Method Determinants of protein function revealed by combinatorial entropy optimization Boris Reva, Yevgeniy Antipin, Chris Sander Genome Biology 2007, 8:R232 (1 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new algorithm is presented allows protein specificity residues to be assigned from multiple sequence alignments alone. This information can be used, amongst other things, to infer protein functions.
	Method Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study Arjun Bhutkar, William M Gelbart, Temple F Smith Genome Biology 2007, 8:R236 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A simple, fast, and biologically-inspired computational approach to infer genome-scale rearrangement phylogeny and ancestral gene order has been developed and applied to eight Drosophila genomes, providing insights into evolutionary chromosomal dynamics.
	Method Analysis of molecular inversion probe performance for allele copy number determination Yuker Wang, Martin Moorhead, George Karlin-Neumann, Nicholas J Wang, James Ireland, Steven Lin, Chunnuan Chen, Laura M Heiser, Koei Chin, Laura Esserman, Joe W Gray, Paul T Spellman, Malek Faham Genome Biology 2007, 8:R246 (20 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new protocol for using molecular inversion probes to specifically and accurately measure allele copy numbers.
	Method Application of phage display to high throughput antibody generation and characterization Darren J Schofield, Anthony R Pope, Veronica Clementel, Jenny Buckell, Susan DJ Chapple, Kay F Clarke, Jennie S Conquer, Anna M Crofts, Sandra RE Crowther, Michael R Dyson, Gillian Flack, Gareth J Griffin, Yvette Hooks, William J Howat, Anja Kolb-Kokocinski, Susan Kunze, Cecile D Martin, Gareth L Maslen, Joanne N Mitchell, Maureen O'Sullivan, Rajika L Perera, Wendy Roake, S Paul Shadbolt, Karen J Vincent, Anthony Warford, Wendy E Wilson, Jane Xie, Joyce L Young, John McCafferty Genome Biology 2007, 8:R254 (29 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A phage display library has been constructed containing over 1010 human antibodies, allowing the large-scale generation of antibodies. Over 38,000 recombinant antibodies against 292 antigens were selected, screened and sequenced, and 4,400 resultant unique clones characterized further.
	Software PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites Florian Gnad, Shubin Ren, Juergen Cox, Jesper V Olsen, Boris Macek, Mario Oroshi, Matthias Mann Genome Biology 2007, 8:R250 (26 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PHOSIDA, a phosphorylation site database, integrates thousands of phosphosites identified by proteomics in various species.
	Correspondence
	Correspondence An idea whose time has come Lucia Banci, Wolfgang Baumeister, Udo Heinemann, Gunter Schneider, Israel Silman, David I Stuart, Joel L Sussman Genome Biology 2007, 8:408 (9 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to An idea whose time has gone by Gregory A Petsko, Genome Biology 2007, 8:107.

	Volume 8 Issue 11
	Comment
	Comment What if Watson had said "Apes evolved from man"? Gregory A Petsko Genome Biology 2007, 8:113 (30 November 2007) Abstract \| Full text \| PDF \| PubMed \| 3 comments \| Editor’s summary Our status as genome biologists gives us both ammunition and a powerful line of attack when we are confronted with ignorance, prejudice, and bigotry.
	Review
	Review Chromatin, gene silencing and HIV latency Hoi-Ping Mok, Andrew ML Lever Genome Biology 2007, 8:228 (23 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cellular defence mechanisms against HIV contribute to its persistence.
	Minireview Termites in the woodwork Samuel Chaffron, Christian von Mering Genome Biology 2007, 8:229 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metagenomic analysis of termite gut flora reveals a diversity of wood-degrading enzymes.
	Minireview Nose thyself: individuality in the human olfactory genome Xiaohong Zhang, Stuart Firestein Genome Biology 2007, 8:230 (26 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A link between a genetic polymorphism in an odorant receptor and variability in perception of the smell of the steroid androstenone.
	Report
	Meeting report Chromatin meets RNA polymerase II Bryan J Venters, B Franklin Pugh Genome Biology 2007, 8:319 (13 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Mechanisms of eukaryotic transcription', Cold Spring Harbor, USA, 2 August-2 September 2007.
	Meeting report Shaken not stirred: a global research cocktail served in Hinxton Samuel Marguerat, Brian T Wilhelm, Jürg Bähler Genome Biology 2007, 8:320 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 2007 Cold Spring Harbor Laboratory/Wellcome Trust Conference on Functional Genomics and Systems Biology, Hinxton, UK, 10-13 October 2007.
	Research
	Research The determinants of gene order conservation in yeasts Juan F Poyatos, Laurence D Hurst Genome Biology 2007, 8:R233 (5 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Current intergene distance is shown to be consistently the strongest predictor of synteny conservation as expected under a simple null model, and other variables are of lesser importance.
	Research Gene expression atlas of the mouse central nervous system: impact and interactions of age, energy intake and gender Xiangru Xu, Ming Zhan, Wenzhen Duan, Vinayakumar Prabhu, Randall Brenneman, William Wood, Jeff Firman, Huai Li, Peisu Zhang, Carol Ibe, Alan B Zonderman, Dan L Longo, Suresh Poosala, Kevin G Becker, Mark P Mattson Genome Biology 2007, 8:R234 (7 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptional profiles of five regions of the central nervous system (CNS) of mice varying in age, gender and dietary intake were measured by microarray. The resulting data provide insights into the mechanisms of age-, diet- and gender-related CNS plasticity and vulnerability in mammals.
	Research Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution Filipe G Vieira, Alejandro Sánchez-Gracia, Julio Rozas Genome Biology 2007, 8:R235 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The comparative analysis of the odorant binding protein family in 12 Drosophila genomes allowed the identification of 595 putative family member genes and revealed insights into the evolution of this family in these species.
	Research Sequence and functional analyses of Haemophilus spp. genomic islands Mario Juhas, Peter M Power, Rosalind M Harding, David JP Ferguson, Ioanna D Dimopoulou, Abdel RE Elamin, Zaini Mohd-Zain, Derek W Hood, Richard Adegbola, Alice Erwin, Arnold Smith, Robert S Munson, Alistair Harrison, Lucielle Mansfield, Stephen Bentley, Derrick W Crook Genome Biology 2007, 8:R237 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Comparative analysis of genomic islands of Haemophilus species shows that they are co-evolving as semi-autonomous genomes within the host genome.
	Research The global landscape of sequence diversity José Peregrín-Álvarez, John Parkinson Genome Biology 2007, 8:R238 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of genomic and EST sequences reveals a greater genetic diversity within eukaryotes than prokaryotes and enables identification of taxon-specific sequences.
	Research The distributions, mechanisms, and structures of metabolite-binding riboswitches Jeffrey E Barrick, Ronald R Breaker Genome Biology 2007, 8:R239 (12 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic analyses revealed insights into the distribution of riboswitch classes in different microbial groups, and structural analyses led to updated aptamer structure models and insights into the mechanism of these non-coding RNA structures.
	Research GeneChip analysis of human embryonic stem cell differentiation into hemangioblasts: an in silico dissection of mixed phenotypes Shi-Jiang Lu, Jennifer A Hipp, Qiang Feng, Jason D Hipp, Robert Lanza, Anthony Atala Genome Biology 2007, 8:R240 (13 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of human embryonic stem cells differentiating into blast cells reveals that erythroblasts are the predominant cell type in the blast cell population. In silico comparisons with publicly available data sets revealed the presence of endothelia, cardiomyocytes and hematopoietic lineages.
	Research Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks Daphna Joseph-Strauss, Drora Zenvirth, Giora Simchen, Naama Barkai Genome Biology 2007, 8:R241 (14 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide expression profiling of spore germination in Saccharomyces cerevisiae reveals two major stages and identifies germination-specific regulation of cell cycle machinery.
	Research Quantification of ortholog losses in insects and vertebrates Stefan Wyder, Evgenia V Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M Zdobnov Genome Biology 2007, 8:R242 (16 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene repertoires of 5 vertebrates and 5 insects showed that the rate of losses correlates well with the species' rates of molecular evolution and radiation times and suggests that the Urbilateria genome contained more than 7,000 genes.
	Research The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z Willem Rens, Patricia CM O'Brien, Frank Grützner, Oliver Clarke, Daria Graphodatskaya, Enkhjargal Tsend-Ayush, Vladimir A Trifonov, Helen Skelton, Mary C Wallis, Steve Johnston, Frederic Veyrunes, Jennifer AM Graves, Malcolm A Ferguson-Smith Genome Biology 2007, 8:R243 (16 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative study of the karyotype of the short-beaked echidna shows that monotremes appear to have a unique XY sex chromosome system that shares some homology with the avian Z.
	Research Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain Jing Li, Zijing J Liu, Yuchun C Pan, Qi Liu, Xing Fu, Nigel GF Cooper, Yixue Li, Mengsheng Qiu, Tieliu Shi Genome Biology 2007, 8:R244 (19 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive regulatory module network of 15 bHLH transcription factors over 150 target genes in mouse brain has been constructed.
	Research Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia Gui-Sheng Wu, Yong-Gang Yao, Kai-Xing Qu, Zhao-Li Ding, Hui Li, Malliya G Palanichamy, Zi-Yuan Duan, Ning Li, Yao-Sheng Chen, Ya-Ping Zhang Genome Biology 2007, 8:R245 (19 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A fine-grained mitochondrial DNA phylogenomic analysis was conducted in domestic pigs and wild boars, revealing that pig domestication in East Asia occurred in the Mekong and the middle and downstream regions of the Yangtze river.
	Research Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex Shuzhang Yang, Kai Wang, Otto Valladares, Sridhar Hannenhalli, Maja Bucan Genome Biology 2007, 8:R247 (20 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Microarray analysis shows that approximately 10% of transcripts in the mouse prefrontal cortex have diurnally regulated expression patterns.
	Research Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa Carol J Loscher, Karsten Hokamp, Paul F Kenna, Alasdair C Ivens, Peter Humphries, Arpad Palfi, G Jane Farrar Genome Biology 2007, 8:R248 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MicroRNA expression profiling showed that the retina of mice carrying a rhodopsin mutation that leads to retinitis pigmentosa have notably different microRNA profiles from wildtype mice; further in silico analyses identified potential retinal targets for differentially regulated microRNAs.
	Research MADS-complexes regulate transcriptome dynamics during pollen maturation Wim Verelst, David Twell, Stefan de Folter, Richard Immink, Heinz Saedler, Thomas Münster Genome Biology 2007, 8:R249 (22 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pollen transcript profiling of mutants defective in MADS-domain MIKC* protein complexes suggests they control a transcriptional network directing cellular differentiation during pollen maturation.
	Research Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish Cornelia Stein, Mario Caccamo, Gavin Laird, Maria Leptin Genome Biology 2007, 8:R251 (27 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of several fish genomes reveals components of the innate immune system and identifies orthologous relationships between gene families of fish and mammals.
	Research Using protein complexes to predict phenotypic effects of gene mutation Hunter B Fraser, Joshua B Plotkin Genome Biology 2007, 8:R252 (27 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The best predictor of a protein's knockout phenotype is shown to be the knockout phenotype of other proteins that are present in a protein complex with it.
	Research Integrative analysis for finding genes and networks involved in diabetes and other complex diseases Regine Bergholdt, Zenia M Størling, Kasper Lage, E Olof Karlberg, Páll Í Ólason, Mogens Aalund, Jørn Nerup, Søren Brunak, Christopher T Workman, Flemming Pociot Genome Biology 2007, 8:R253 (28 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An integrative analysis combining genetic interactions and protein interactions can be used to identify candidate genes/proteins for type 1 diabetes and other complex diseases.
	Research Identification of candidate predictive and surrogate molecular markers for dasatinib in prostate cancer: rationale for patient selection and efficacy monitoring Xi-De Wang, Karen Reeves, Feng R Luo, Li-An Xu, Francis Lee, Edwin Clark, Fei Huang Genome Biology 2007, 8:R255 (29 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene expression profiling was used to identify genes associated with sensitivity to the tyrosine kinase drug Dasatinib in prostate cancer cell lines, revealing a possible Dasatinib efficacy signature in prostate cancer.
	Method Determinants of protein function revealed by combinatorial entropy optimization Boris Reva, Yevgeniy Antipin, Chris Sander Genome Biology 2007, 8:R232 (1 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new algorithm is presented allows protein specificity residues to be assigned from multiple sequence alignments alone. This information can be used, amongst other things, to infer protein functions.
	Method Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study Arjun Bhutkar, William M Gelbart, Temple F Smith Genome Biology 2007, 8:R236 (8 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A simple, fast, and biologically-inspired computational approach to infer genome-scale rearrangement phylogeny and ancestral gene order has been developed and applied to eight Drosophila genomes, providing insights into evolutionary chromosomal dynamics.
	Method Analysis of molecular inversion probe performance for allele copy number determination Yuker Wang, Martin Moorhead, George Karlin-Neumann, Nicholas J Wang, James Ireland, Steven Lin, Chunnuan Chen, Laura M Heiser, Koei Chin, Laura Esserman, Joe W Gray, Paul T Spellman, Malek Faham Genome Biology 2007, 8:R246 (20 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new protocol for using molecular inversion probes to specifically and accurately measure allele copy numbers.
	Method Application of phage display to high throughput antibody generation and characterization Darren J Schofield, Anthony R Pope, Veronica Clementel, Jenny Buckell, Susan DJ Chapple, Kay F Clarke, Jennie S Conquer, Anna M Crofts, Sandra RE Crowther, Michael R Dyson, Gillian Flack, Gareth J Griffin, Yvette Hooks, William J Howat, Anja Kolb-Kokocinski, Susan Kunze, Cecile D Martin, Gareth L Maslen, Joanne N Mitchell, Maureen O'Sullivan, Rajika L Perera, Wendy Roake, S Paul Shadbolt, Karen J Vincent, Anthony Warford, Wendy E Wilson, Jane Xie, Joyce L Young, John McCafferty Genome Biology 2007, 8:R254 (29 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A phage display library has been constructed containing over 1010 human antibodies, allowing the large-scale generation of antibodies. Over 38,000 recombinant antibodies against 292 antigens were selected, screened and sequenced, and 4,400 resultant unique clones characterized further.
	Software PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites Florian Gnad, Shubin Ren, Juergen Cox, Jesper V Olsen, Boris Macek, Mario Oroshi, Matthias Mann Genome Biology 2007, 8:R250 (26 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary PHOSIDA, a phosphorylation site database, integrates thousands of phosphosites identified by proteomics in various species.
	Correspondence
	Correspondence An idea whose time has come Lucia Banci, Wolfgang Baumeister, Udo Heinemann, Gunter Schneider, Israel Silman, David I Stuart, Joel L Sussman Genome Biology 2007, 8:408 (9 November 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A response to An idea whose time has gone by Gregory A Petsko, Genome Biology 2007, 8:107.

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Volume 8 Issue 11

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