Genome Biology | Volume 7 Issue 3

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	Volume 7 Issue 3
	Comment
	Comment The system is broken Gregory A Petsko Genome Biology 2006, 7:105 (30 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary When a scientist doing work in genomics, or cell biology, or biochemistry, or immunology submits a grant proposal to the US National Institutes of Health (NIH), the largest supporter of life science research in the world, his or her chance of it being funded are at historic lows.
	Review
	Protein family review The semaphorins Umar Yazdani, Jonathan R Terman Genome Biology 2006, 7:211 (30 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Semaphorins are secreted, transmembrane, and GPI-linked proteins found in mammals, Drosophila, nematodes, and crustaceans. They alter the cytoskeleton and the organization of actin filaments and the microtubule network, and are important in a wide range of functions, including neural connectivity, angiogenesis, immunoregulation, and cancer.
	Minireview The dynamic proteome of Lyme disease Borrelia Steven J Norris Genome Biology 2006, 7:209 (17 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The proteome of the spirochete bacterium Borrelia burgdorferi, the tick-borne agent of Lyme disease, has been characterized by two different approaches using mass spectrometry, providing a launching point for future studies.
	Minireview Genetic control of hippocampal neurogenesis Christine D Pozniak, Samuel J Pleasure Genome Biology 2006, 7:207 (30 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Quantitative trait locus analysis of two inbred mouse strains has revealed that cell survival is most highly correlated with neurogenesis.
	Minireview Distinct yet linked: chaperone networks in the eukaryotic cytosol Sabine Rospert, Agnieszka Chacinska Genome Biology 2006, 7:208 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Although one subset of chaperones is induced by heat stress, a distinct group fails to respond in the same manner. Recent work reveals that this latter group is linked to the translational apparatus and functions in co-translational processes.
	Minireview Partners in dicing René F Ketting Genome Biology 2006, 7:210 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies of the protein Dicer, a key enzyme in the RNA interference process, have started to reveal how this single enzyme is targeted to different RNA-silencing pathways.
	Report
	Meeting report Small genomes and big science Jeremy Edwards Genome Biology 2006, 7:308 (13 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 13th Annual International Conference on Microbial Genomes, Madison, USA, 11-15 September 2005.
	Meeting report Mining the genome and regulatory networks Anatolij P Potapov, Edgar Wingender Genome Biology 2006, 7:309 (22 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Conference on Genome Informatics (GIW 2005), Yokohama, Japan, 19-21 December 2005.
	Meeting report Mining the HapMap to dissect complex traits Sung K Kim, Justin Borevitz Genome Biology 2006, 7:310 (28 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Keystone Symposium 'Genome Sequence Variation and the Inherited Basis of Common Disease and Complex Traits', Big Sky, USA, 8-13 January 2006.
	Meeting report A cornucopia of genomes Andrew H Paterson Genome Biology 2006, 7:311 (28 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Plant and Animal Genome XIV Conference, San Diego, USA, 14-18 January 2006.
	Research
	Research Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level Tatiana Subkhankulova, Frederick J Livesey Genome Biology 2006, 7:R18 (7 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the performance of three methods for amplifying single-cell amounts of RNA for use in expression profiling shows that PCT amplification is more reliable than linear amplification.
	Research Modulation of the transcription regulatory program in yeast cells committed to sporulation Gilgi Friedlander, Daphna Joseph-Strauss, Miri Carmi, Drora Zenvirth, Giora Simchen, Naama Barkai Genome Biology 2006, 7:R20 (8 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the gene expression program in yeast cells suggests that commitment to sporulation involves an active modulation of the gene expression program.
	Research Comparative profiling of the sense and antisense transcriptome of maize lines Jiong Ma, Darren J Morrow, John Fernandes, Virginia Walbot Genome Biology 2006, 7:R22 (13 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative transcriptome profiling of inbred maize lines demonstrates remarkable similarities and a large number of antisense transcripts.
	Research Deciphering cellular states of innate tumor drug responses Esther Graudens, Virginie Boulanger, Cindy Mollard, Régine Mariage-Samson, Xavier Barlet, Guilaine Grémy, Christine Couillault, Malika Lajémi, Dominique Piatier-Tonneau, Patrick Zaborski, Eric Eveno, Charles Auffray, Sandrine Imbeaud Genome Biology 2006, 7:R19 (15 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nearly 700 genes were identified that are differently expressed between tumors of patients with colorectal cancer who subsequently responded well to combined chemotherapy and those of patients who were resistant to the therapy.
	Research Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins Patrick Meraldi, Andrew D McAinsh, Esther Rheinbay, Peter K Sorger Genome Biology 2006, 7:R23 (22 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of centromeric DNA and kinetochore proteins suggests that critical structural features of kinetochores have been well conserved from yeast to man.
	Research Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms Jun Li, Michelle M Riehle, Yan Zhang, Jiannong Xu, Frederick Oduol, Shawn M Gomez, Karin Eiglmeier, Beatrix M Ueberheide, Jeffrey Shabanowitz, Donald F Hunt, José MC Ribeiro, Kenneth D Vernick Genome Biology 2006, 7:R24 (27 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive reannotation of the Anopheles gambiae genome using a combination of comparative and ab initio gene prediction algorithms has identified novel coding sequences.
	Research The contributions of normal variation and genetic background to mammalian gene expression Colin Pritchard, David Coil, Sarah Hawley, Li Hsu, Peter S Nelson Genome Biology 2006, 7:R26 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Analysis of microarray-based transcript levels within and between five different mouse strains show that 23-44% of all genes exhibit differences in expression levels between genetically identical individuals.
	Method Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera) Beatriz Sabater-Muñoz, Fabrice Legeai, Claude Rispe, Joël Bonhomme, Peter Dearden, Carole Dossat, Aymeric Duclert, Jean-Pierre Gauthier, Danièle Ducray, Wayne Hunter, Phat Dang, Srini Kambhampati, David Martinez-Torres, Teresa Cortes, Andrès Moya, Atsushi Nakabachi, Cathy Philippe, Nathalie Prunier-Leterme, Yvan Rahbé, Jean-Christophe Simon, David L Stern, Patrick Wincker, Denis Tagu Genome Biology 2006, 7:R21 (10 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale sequencing analysis of the Hemiptera Acyrthosiphon pisumexpressed sequence tags corresponding to about 12,000 unique transcripts is described, along with an in silico profiling analysis that identifies 135 aphid tissue-specific transcripts.
	Method Ranked prediction of p53 targets using hidden variable dynamic modeling Martino Barenco, Daniela Tomescu, Daniel Brewer, Robin Callard, Jaroslav Stark, Michael Hubank Genome Biology 2006, 7:R25 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Hidden Variable Dynamic Modelling is a new approach to microarray analysis that quantitatively predicts the regulation of gene activity.
	Correspondence
	Correspondence A reanalysis of a published Affymetrix GeneChip control dataset Alan R Dabney, John D Storey Genome Biology 2006, 7:401 (22 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16

	Volume 7 Issue 3
	Comment
	Comment The system is broken Gregory A Petsko Genome Biology 2006, 7:105 (30 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary When a scientist doing work in genomics, or cell biology, or biochemistry, or immunology submits a grant proposal to the US National Institutes of Health (NIH), the largest supporter of life science research in the world, his or her chance of it being funded are at historic lows.
	Review
	Protein family review The semaphorins Umar Yazdani, Jonathan R Terman Genome Biology 2006, 7:211 (30 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Semaphorins are secreted, transmembrane, and GPI-linked proteins found in mammals, Drosophila, nematodes, and crustaceans. They alter the cytoskeleton and the organization of actin filaments and the microtubule network, and are important in a wide range of functions, including neural connectivity, angiogenesis, immunoregulation, and cancer.
	Minireview The dynamic proteome of Lyme disease Borrelia Steven J Norris Genome Biology 2006, 7:209 (17 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The proteome of the spirochete bacterium Borrelia burgdorferi, the tick-borne agent of Lyme disease, has been characterized by two different approaches using mass spectrometry, providing a launching point for future studies.
	Minireview Genetic control of hippocampal neurogenesis Christine D Pozniak, Samuel J Pleasure Genome Biology 2006, 7:207 (30 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Quantitative trait locus analysis of two inbred mouse strains has revealed that cell survival is most highly correlated with neurogenesis.
	Minireview Distinct yet linked: chaperone networks in the eukaryotic cytosol Sabine Rospert, Agnieszka Chacinska Genome Biology 2006, 7:208 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Although one subset of chaperones is induced by heat stress, a distinct group fails to respond in the same manner. Recent work reveals that this latter group is linked to the translational apparatus and functions in co-translational processes.
	Minireview Partners in dicing René F Ketting Genome Biology 2006, 7:210 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies of the protein Dicer, a key enzyme in the RNA interference process, have started to reveal how this single enzyme is targeted to different RNA-silencing pathways.
	Report
	Meeting report Small genomes and big science Jeremy Edwards Genome Biology 2006, 7:308 (13 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 13th Annual International Conference on Microbial Genomes, Madison, USA, 11-15 September 2005.
	Meeting report Mining the genome and regulatory networks Anatolij P Potapov, Edgar Wingender Genome Biology 2006, 7:309 (22 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Conference on Genome Informatics (GIW 2005), Yokohama, Japan, 19-21 December 2005.
	Meeting report Mining the HapMap to dissect complex traits Sung K Kim, Justin Borevitz Genome Biology 2006, 7:310 (28 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Keystone Symposium 'Genome Sequence Variation and the Inherited Basis of Common Disease and Complex Traits', Big Sky, USA, 8-13 January 2006.
	Meeting report A cornucopia of genomes Andrew H Paterson Genome Biology 2006, 7:311 (28 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Plant and Animal Genome XIV Conference, San Diego, USA, 14-18 January 2006.
	Research
	Research Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level Tatiana Subkhankulova, Frederick J Livesey Genome Biology 2006, 7:R18 (7 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the performance of three methods for amplifying single-cell amounts of RNA for use in expression profiling shows that PCT amplification is more reliable than linear amplification.
	Research Modulation of the transcription regulatory program in yeast cells committed to sporulation Gilgi Friedlander, Daphna Joseph-Strauss, Miri Carmi, Drora Zenvirth, Giora Simchen, Naama Barkai Genome Biology 2006, 7:R20 (8 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the gene expression program in yeast cells suggests that commitment to sporulation involves an active modulation of the gene expression program.
	Research Comparative profiling of the sense and antisense transcriptome of maize lines Jiong Ma, Darren J Morrow, John Fernandes, Virginia Walbot Genome Biology 2006, 7:R22 (13 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative transcriptome profiling of inbred maize lines demonstrates remarkable similarities and a large number of antisense transcripts.
	Research Deciphering cellular states of innate tumor drug responses Esther Graudens, Virginie Boulanger, Cindy Mollard, Régine Mariage-Samson, Xavier Barlet, Guilaine Grémy, Christine Couillault, Malika Lajémi, Dominique Piatier-Tonneau, Patrick Zaborski, Eric Eveno, Charles Auffray, Sandrine Imbeaud Genome Biology 2006, 7:R19 (15 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nearly 700 genes were identified that are differently expressed between tumors of patients with colorectal cancer who subsequently responded well to combined chemotherapy and those of patients who were resistant to the therapy.
	Research Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins Patrick Meraldi, Andrew D McAinsh, Esther Rheinbay, Peter K Sorger Genome Biology 2006, 7:R23 (22 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of centromeric DNA and kinetochore proteins suggests that critical structural features of kinetochores have been well conserved from yeast to man.
	Research Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms Jun Li, Michelle M Riehle, Yan Zhang, Jiannong Xu, Frederick Oduol, Shawn M Gomez, Karin Eiglmeier, Beatrix M Ueberheide, Jeffrey Shabanowitz, Donald F Hunt, José MC Ribeiro, Kenneth D Vernick Genome Biology 2006, 7:R24 (27 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive reannotation of the Anopheles gambiae genome using a combination of comparative and ab initio gene prediction algorithms has identified novel coding sequences.
	Research The contributions of normal variation and genetic background to mammalian gene expression Colin Pritchard, David Coil, Sarah Hawley, Li Hsu, Peter S Nelson Genome Biology 2006, 7:R26 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Analysis of microarray-based transcript levels within and between five different mouse strains show that 23-44% of all genes exhibit differences in expression levels between genetically identical individuals.
	Method Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera) Beatriz Sabater-Muñoz, Fabrice Legeai, Claude Rispe, Joël Bonhomme, Peter Dearden, Carole Dossat, Aymeric Duclert, Jean-Pierre Gauthier, Danièle Ducray, Wayne Hunter, Phat Dang, Srini Kambhampati, David Martinez-Torres, Teresa Cortes, Andrès Moya, Atsushi Nakabachi, Cathy Philippe, Nathalie Prunier-Leterme, Yvan Rahbé, Jean-Christophe Simon, David L Stern, Patrick Wincker, Denis Tagu Genome Biology 2006, 7:R21 (10 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale sequencing analysis of the Hemiptera Acyrthosiphon pisumexpressed sequence tags corresponding to about 12,000 unique transcripts is described, along with an in silico profiling analysis that identifies 135 aphid tissue-specific transcripts.
	Method Ranked prediction of p53 targets using hidden variable dynamic modeling Martino Barenco, Daniela Tomescu, Daniel Brewer, Robin Callard, Jaroslav Stark, Michael Hubank Genome Biology 2006, 7:R25 (31 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Hidden Variable Dynamic Modelling is a new approach to microarray analysis that quantitatively predicts the regulation of gene activity.
	Correspondence
	Correspondence A reanalysis of a published Affymetrix GeneChip control dataset Alan R Dabney, John D Storey Genome Biology 2006, 7:401 (22 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16

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Volume 7 Issue 3

Comment

Review

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Research

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