Genome Biology | Volume 13 Issue 11

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	Volume 13 Issue 11
	Comment
	Comment Computational thinking in the era of big data biology Michael C Schatz Genome Biology 2012, 13:177 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary by Mike Schatz
	Research highlight Why rodent pseudogenes refuse to retire Manyuan Long, Li Zhang Genome Biology 2012, 13:178 (20 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional entities or curmudgeonly junk? The ceRNA hypothesis may explain why many rodent pseudogenes resist evolutionary erosion
	Research highlight Dicer partners expand the repertoire of miRNA targets Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks
	Report
	Meeting report Strategies towards sequencing complex crop genomes James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Strategies for de novo assemblies of complex crop genomes workshop held at The Genome Analysis Centre, Norwich, UK, 8-10 October 2012.
	Meeting report International plant molecular biology: a bright future for green science Sibum Sung, Enamul Huq, Z Jeffrey Chen Genome Biology 2012, 13:323 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
	Research
	Research Microbiome dynamics of human epidermis following skin barrier disruption Patrick LJM Zeeuwen, Jos Boekhorst, Ellen H van den Bogaard, Heleen D de Koning, Peter MC van de Kerkhof, Delphine M Saulnier, Iris I van Swam, Sacha AFT van Hijum, Michiel Kleerebezem, Joost Schalkwijk, Harro M Timmerman Genome Biology 2012, 13:R101 (15 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of the microbiota of the surface and deeper layers of skin, and how it changes following skin barrier disruption
	Research Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs Ana C Marques, Jennifer Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P Ponting Genome Biology 2012, 13:R102 (15 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of pseudogenes in the mouse genome shows that some transcripts have a regulatory role separate from their protein coding potential
	Research The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success Kelly L Wyres, Lotte M Lambertsen, Nicholas J Croucher, Lesley McGee, Anne von Gottberg, Josefina Liñares, Michael R Jacobs, Karl G Kristinsson, Bernard W Beall, Keith P Klugman, Julian Parkhill, Regine Hakenbeck, Stephen D Bentley, Angela B Brueggemann Genome Biology 2012, 13:R103 (16 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of a collection of isolates of Streptococcus pneumoniae reveals extensive gene transfer between the virulent strain PMEN1 and other strains
	Research Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling Mariona Nadal-Ribelles, Núria Conde, Oscar Flores, Juan González-Vallinas, Eduardo Eyras, Modesto Orozco, Eulàlia de Nadal, Francesc Posas Genome Biology 2012, 13:R106 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hog1 bypasses gene expression regulation by targeting RNA polymerase II machinery and inducing chromatin remodeling at stress-responsive loci
	Research Transposable elements reveal a stem cell-specific class of long noncoding RNAs David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
	Research Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss Genome Biology 2012, 13:R108 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
	Research Human genes with CpG island promoters have a distinct transcription-associated chromatin organization Tanya Vavouri, Ben Lehner Genome Biology 2012, 13:R110 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
	Method A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis Simon E Alfred, Anuradha Surendra, Chris Le, Ken Lin, Alexander Mok, Iain M Wallace, Michael Proctor, Malene L Urbanus, Guri Giaever, Corey Nislow Genome Biology 2012, 13:R105 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An automated small molecule screening method for Chlamydomonas reinhardtii, and its application to identify bioactive compounds for agriculture, biofuels and therapeutics
	Method Computational discovery of regulatory elements in a continuous expression space Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Bréhélin Genome Biology 2012, 13:R109 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method that identifies regulatory elements by estimating motif densities around each gene, using overlapping neighborhoods in expression space
	Method MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks Edward Vitkin, Tomer Shlomi Genome Biology 2012, 13:R111 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
	Software InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Y Weiss Solís Genome Biology 2012, 13:R104 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A web-based data storage hub that connects genomics datasets to GUI and command line data analysis tools

	Volume 13 Issue 11
	Comment
	Comment Computational thinking in the era of big data biology Michael C Schatz Genome Biology 2012, 13:177 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary by Mike Schatz
	Research highlight Why rodent pseudogenes refuse to retire Manyuan Long, Li Zhang Genome Biology 2012, 13:178 (20 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional entities or curmudgeonly junk? The ceRNA hypothesis may explain why many rodent pseudogenes resist evolutionary erosion
	Research highlight Dicer partners expand the repertoire of miRNA targets Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks
	Report
	Meeting report Strategies towards sequencing complex crop genomes James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Strategies for de novo assemblies of complex crop genomes workshop held at The Genome Analysis Centre, Norwich, UK, 8-10 October 2012.
	Meeting report International plant molecular biology: a bright future for green science Sibum Sung, Enamul Huq, Z Jeffrey Chen Genome Biology 2012, 13:323 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
	Research
	Research Microbiome dynamics of human epidermis following skin barrier disruption Patrick LJM Zeeuwen, Jos Boekhorst, Ellen H van den Bogaard, Heleen D de Koning, Peter MC van de Kerkhof, Delphine M Saulnier, Iris I van Swam, Sacha AFT van Hijum, Michiel Kleerebezem, Joost Schalkwijk, Harro M Timmerman Genome Biology 2012, 13:R101 (15 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of the microbiota of the surface and deeper layers of skin, and how it changes following skin barrier disruption
	Research Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs Ana C Marques, Jennifer Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P Ponting Genome Biology 2012, 13:R102 (15 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of pseudogenes in the mouse genome shows that some transcripts have a regulatory role separate from their protein coding potential
	Research The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success Kelly L Wyres, Lotte M Lambertsen, Nicholas J Croucher, Lesley McGee, Anne von Gottberg, Josefina Liñares, Michael R Jacobs, Karl G Kristinsson, Bernard W Beall, Keith P Klugman, Julian Parkhill, Regine Hakenbeck, Stephen D Bentley, Angela B Brueggemann Genome Biology 2012, 13:R103 (16 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of a collection of isolates of Streptococcus pneumoniae reveals extensive gene transfer between the virulent strain PMEN1 and other strains
	Research Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling Mariona Nadal-Ribelles, Núria Conde, Oscar Flores, Juan González-Vallinas, Eduardo Eyras, Modesto Orozco, Eulàlia de Nadal, Francesc Posas Genome Biology 2012, 13:R106 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hog1 bypasses gene expression regulation by targeting RNA polymerase II machinery and inducing chromatin remodeling at stress-responsive loci
	Research Transposable elements reveal a stem cell-specific class of long noncoding RNAs David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
	Research Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss Genome Biology 2012, 13:R108 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
	Research Human genes with CpG island promoters have a distinct transcription-associated chromatin organization Tanya Vavouri, Ben Lehner Genome Biology 2012, 13:R110 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
	Method A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis Simon E Alfred, Anuradha Surendra, Chris Le, Ken Lin, Alexander Mok, Iain M Wallace, Michael Proctor, Malene L Urbanus, Guri Giaever, Corey Nislow Genome Biology 2012, 13:R105 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An automated small molecule screening method for Chlamydomonas reinhardtii, and its application to identify bioactive compounds for agriculture, biofuels and therapeutics
	Method Computational discovery of regulatory elements in a continuous expression space Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Bréhélin Genome Biology 2012, 13:R109 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method that identifies regulatory elements by estimating motif densities around each gene, using overlapping neighborhoods in expression space
	Method MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks Edward Vitkin, Tomer Shlomi Genome Biology 2012, 13:R111 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
	Software InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Y Weiss Solís Genome Biology 2012, 13:R104 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A web-based data storage hub that connects genomics datasets to GUI and command line data analysis tools

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Volume 13 Issue 11

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