Genome Biology | Volume 10 Issue 10

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	Volume 10 Issue 10
	Comment
	Comment The dog days of autumn Gregory A Petsko Genome Biology 2009, 10:112 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg's two dogs are impressed that only a few genes control the different lengths, growth patterns and curl of their coats.
	Review
	Protein family review The SR protein family Peter J Shepard, Klemens J Hertel Genome Biology 2009, 10:242 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The SR proteins are not only involved in pre-mRNA splicing but in mRNA export and the initiation of translation.
	Minireview Runaway repeats force expansion of the Phytophthora infestans genome Mark Gijzen Genome Biology 2009, 10:241 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of the potato late blight pathogen Phytophthora infestans provides insight into the structure and evolution of its genome.
	Minireview Comparing cellular proteomes by mass spectrometry Florian Fröhlich, Tobias C Walther Genome Biology 2009, 10:240 (28 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mass spectrometry and cryo-electron tomography together can enable absolute protein abundance to be determined.
	Report
	Meeting report Watching proteins in motion Mary Munson, Daniel N Bolon Genome Biology 2009, 10:316 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 23rd Protein Symposium 'Proteins in Motion', Boston, USA, 23-27 July 2009.
	Research
	Research Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, Gordon K Smyth, Seong-Seng Tan, Tim Thomas, Hamish S Scott Genome Biology 2009, 10:R104 (2 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SAGE analysis reveals spatiotemporally regulated transcripts and overlapping sense and antisense transcripts that are important for mouse cerebral cortex development
	Research Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions Nicolas Corradi, Karen L Haag, Jean-François Pombert, Dieter Ebert, Patrick J Keeling Genome Biology 2009, 10:R106 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The draft genome sequence of Octosporea bayeri, a microsporidian pathogen of Daphnia, provides insights into the content and evolution of a large microsporidian genome
	Research Defining the chromatin signature of inducible genes in T cells Pek S Lim, Kristine Hardy, Karen L Bunting, Lina Ma, Kaiman Peng, Xinxin Chen, Mary F Shannon Genome Biology 2009, 10:R107 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Inducible genes in T cells show the chromatin characteristics of active genes, suggesting they are primed for transcription.
	Research Genomic DNA k-mer spectra: models and modalities Benny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham Genome Biology 2009, 10:R108 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes
	Research NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis Christophe Rusniok, David Vallenet, Stéphanie Floquet, Helen Ewles, Coralie Mouzé-Soulama, Daniel Brown, Aurélie Lajus, Carmen Buchrieser, Claudine Médigue, Philippe Glaser, Vladimir Pelicic Genome Biology 2009, 10:R110 (9 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of a clinical isolate of Neisseria meningitidis is described. This and other reannotated Neisseria genomes are compiled in a database.
	Research Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Young-Joo Seol, Mina Jin, Jin-A Kim, Myung-Ho Lim, Jung Sun Kim, Seunghoon Baek, Beom-Soon Choi, Hee-Ju Yu, Dae-Soo Kim, Namshin Kim, Ki-Byung Lim, Soo-In Lee, Jang-Ho Hahn, Yong Pyo Lim, Ian Bancroft, Beom-Seok Park Genome Biology 2009, 10:R111 (12 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Euchromatic regions of the Brassica rapa genome were sequenced and mapped onto the corresponding regions in the Arabidopsis thaliana genome.
	Research Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia Xiaobo Xia, Andrew L Kung Genome Biology 2009, 10:R113 (14 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ChIP-chip and microarray expression studies show that, in response to hypoxia, HIF-1 preferentially binds to and up-regulates already active genes.
	Research Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell Peter von Dassow, Hiroyuki Ogata, Ian Probert, Patrick Wincker, Corinne Da Silva, Stéphane Audic, Jean-Michel Claverie, Colomban de Vargas Genome Biology 2009, 10:R114 (15 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An EST analysis of the phytoplankton Emiliania huxleyi reveals genes involved in haploid- and diploid-specific processes and provides insights into environmental adaptation.
	Research Simultaneous transcription of duplicated var2csa gene copies in individual Plasmodium falciparum parasites Kim JM Brolin, Ulf Ribacke, Sandra Nilsson, Johan Ankarklev, Kirsten Moll, Mats Wahlgren, Qijun Chen Genome Biology 2009, 10:R117 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Duplicated var2csa genes in one strain of Plasmodium falciparum are simultaneously transcribed, challenging the dogma of mutual exclusive var gene transcription
	Research Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations Tom M Conrad, Andrew R Joyce, M Kenyon Applebee, Christian L Barrett, Bin Xie, Yuan Gao, Bernhard Ø Palsson Genome Biology 2009, 10:R118 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Escherichia coli strains that have evolved in the laboratory in response to lactate minimal media show a wide range of different genetic adaptations.
	Method ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe Genome Biology 2009, 10:R103 (1 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Allpaths2, a method for accurately assembling small genomes with high continuity using short paired reads.
	Method Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels Ian Sudbery, Jim Stalker, Jared T Simpson, Thomas Keane, Alistair G Rust, Matthew E Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve D Brown, Heng Li, Zemin Ning, Joseph H Nadeau, Colleen M Croniger, Richard Durbin, David J Adams Genome Biology 2009, 10:R112 (13 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for accurate identification of nucleotide and structural variation using de novo short read sequencing of mouse chromosomes are described.
	Method Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A Garraway, Andreas Gnirke Genome Biology 2009, 10:R115 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Combining next-generation sequencing with capture of sequences from a relevant subset of a transcriptome produces an enhanced view of this subset
	Method Enrichment of sequencing targets from the human genome by solution hybridization Ryan Tewhey, Masakazu Nakano, Xiaoyun Wang, Carlos Pabón-Peña, Barbara Novak, Angelica Giuffre, Eric Lin, Scott Happe, Doug N Roberts, Emily M LeProust, Eric J Topol, Olivier Harismendy, Kelly A Frazer Genome Biology 2009, 10:R116 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for target sequence enrichment from the human genome is described. This hybridization-based approach using oligonucleotide probes in solution has excellent sensitivity and accuracy for calling SNPs
	Method An optimization framework for unsupervised identification of rare copy number variation from SNP array data Gökhan Yavaş, Mehmet Koyutürk, Meral Özsoyoğlu, Meetha P Gould, Thomas LaFramboise Genome Biology 2009, 10:R119 (23 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A highly sensitive and configurable method for calling copy number variants from SNP array data is presented that can identify even rare CNVs
	Software MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock Genome Biology 2009, 10:R105 (5 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A software workflow to translate known differentially methylated regions into clinical biomarkers
	Software A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome Cizhong Jiang, B Franklin Pugh Genome Biology 2009, 10:R109 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Different genome-wide reference maps of Saccharomyces cerevisiae nucleosome positions are compiled and can be visualized on a browser.

	Volume 10 Issue 10
	Comment
	Comment The dog days of autumn Gregory A Petsko Genome Biology 2009, 10:112 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg's two dogs are impressed that only a few genes control the different lengths, growth patterns and curl of their coats.
	Review
	Protein family review The SR protein family Peter J Shepard, Klemens J Hertel Genome Biology 2009, 10:242 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The SR proteins are not only involved in pre-mRNA splicing but in mRNA export and the initiation of translation.
	Minireview Runaway repeats force expansion of the Phytophthora infestans genome Mark Gijzen Genome Biology 2009, 10:241 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of the potato late blight pathogen Phytophthora infestans provides insight into the structure and evolution of its genome.
	Minireview Comparing cellular proteomes by mass spectrometry Florian Fröhlich, Tobias C Walther Genome Biology 2009, 10:240 (28 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mass spectrometry and cryo-electron tomography together can enable absolute protein abundance to be determined.
	Report
	Meeting report Watching proteins in motion Mary Munson, Daniel N Bolon Genome Biology 2009, 10:316 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 23rd Protein Symposium 'Proteins in Motion', Boston, USA, 23-27 July 2009.
	Research
	Research Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, Gordon K Smyth, Seong-Seng Tan, Tim Thomas, Hamish S Scott Genome Biology 2009, 10:R104 (2 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SAGE analysis reveals spatiotemporally regulated transcripts and overlapping sense and antisense transcripts that are important for mouse cerebral cortex development
	Research Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions Nicolas Corradi, Karen L Haag, Jean-François Pombert, Dieter Ebert, Patrick J Keeling Genome Biology 2009, 10:R106 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The draft genome sequence of Octosporea bayeri, a microsporidian pathogen of Daphnia, provides insights into the content and evolution of a large microsporidian genome
	Research Defining the chromatin signature of inducible genes in T cells Pek S Lim, Kristine Hardy, Karen L Bunting, Lina Ma, Kaiman Peng, Xinxin Chen, Mary F Shannon Genome Biology 2009, 10:R107 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Inducible genes in T cells show the chromatin characteristics of active genes, suggesting they are primed for transcription.
	Research Genomic DNA k-mer spectra: models and modalities Benny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham Genome Biology 2009, 10:R108 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes
	Research NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis Christophe Rusniok, David Vallenet, Stéphanie Floquet, Helen Ewles, Coralie Mouzé-Soulama, Daniel Brown, Aurélie Lajus, Carmen Buchrieser, Claudine Médigue, Philippe Glaser, Vladimir Pelicic Genome Biology 2009, 10:R110 (9 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of a clinical isolate of Neisseria meningitidis is described. This and other reannotated Neisseria genomes are compiled in a database.
	Research Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Young-Joo Seol, Mina Jin, Jin-A Kim, Myung-Ho Lim, Jung Sun Kim, Seunghoon Baek, Beom-Soon Choi, Hee-Ju Yu, Dae-Soo Kim, Namshin Kim, Ki-Byung Lim, Soo-In Lee, Jang-Ho Hahn, Yong Pyo Lim, Ian Bancroft, Beom-Seok Park Genome Biology 2009, 10:R111 (12 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Euchromatic regions of the Brassica rapa genome were sequenced and mapped onto the corresponding regions in the Arabidopsis thaliana genome.
	Research Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia Xiaobo Xia, Andrew L Kung Genome Biology 2009, 10:R113 (14 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ChIP-chip and microarray expression studies show that, in response to hypoxia, HIF-1 preferentially binds to and up-regulates already active genes.
	Research Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell Peter von Dassow, Hiroyuki Ogata, Ian Probert, Patrick Wincker, Corinne Da Silva, Stéphane Audic, Jean-Michel Claverie, Colomban de Vargas Genome Biology 2009, 10:R114 (15 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An EST analysis of the phytoplankton Emiliania huxleyi reveals genes involved in haploid- and diploid-specific processes and provides insights into environmental adaptation.
	Research Simultaneous transcription of duplicated var2csa gene copies in individual Plasmodium falciparum parasites Kim JM Brolin, Ulf Ribacke, Sandra Nilsson, Johan Ankarklev, Kirsten Moll, Mats Wahlgren, Qijun Chen Genome Biology 2009, 10:R117 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Duplicated var2csa genes in one strain of Plasmodium falciparum are simultaneously transcribed, challenging the dogma of mutual exclusive var gene transcription
	Research Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations Tom M Conrad, Andrew R Joyce, M Kenyon Applebee, Christian L Barrett, Bin Xie, Yuan Gao, Bernhard Ø Palsson Genome Biology 2009, 10:R118 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Escherichia coli strains that have evolved in the laboratory in response to lactate minimal media show a wide range of different genetic adaptations.
	Method ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe Genome Biology 2009, 10:R103 (1 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Allpaths2, a method for accurately assembling small genomes with high continuity using short paired reads.
	Method Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels Ian Sudbery, Jim Stalker, Jared T Simpson, Thomas Keane, Alistair G Rust, Matthew E Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve D Brown, Heng Li, Zemin Ning, Joseph H Nadeau, Colleen M Croniger, Richard Durbin, David J Adams Genome Biology 2009, 10:R112 (13 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for accurate identification of nucleotide and structural variation using de novo short read sequencing of mouse chromosomes are described.
	Method Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A Garraway, Andreas Gnirke Genome Biology 2009, 10:R115 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Combining next-generation sequencing with capture of sequences from a relevant subset of a transcriptome produces an enhanced view of this subset
	Method Enrichment of sequencing targets from the human genome by solution hybridization Ryan Tewhey, Masakazu Nakano, Xiaoyun Wang, Carlos Pabón-Peña, Barbara Novak, Angelica Giuffre, Eric Lin, Scott Happe, Doug N Roberts, Emily M LeProust, Eric J Topol, Olivier Harismendy, Kelly A Frazer Genome Biology 2009, 10:R116 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for target sequence enrichment from the human genome is described. This hybridization-based approach using oligonucleotide probes in solution has excellent sensitivity and accuracy for calling SNPs
	Method An optimization framework for unsupervised identification of rare copy number variation from SNP array data Gökhan Yavaş, Mehmet Koyutürk, Meral Özsoyoğlu, Meetha P Gould, Thomas LaFramboise Genome Biology 2009, 10:R119 (23 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A highly sensitive and configurable method for calling copy number variants from SNP array data is presented that can identify even rare CNVs
	Software MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock Genome Biology 2009, 10:R105 (5 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A software workflow to translate known differentially methylated regions into clinical biomarkers
	Software A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome Cizhong Jiang, B Franklin Pugh Genome Biology 2009, 10:R109 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Different genome-wide reference maps of Saccharomyces cerevisiae nucleosome positions are compiled and can be visualized on a browser.

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