Genome Biology | Volume 14 Issue 2

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	Volume 14 Issue 2
	Comment
	Comment Science: it's a role model thing Chris Gunter Genome Biology 2013, 14:105 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science
	Research highlight What is it about 'eye of newt'? Yuliana Mihaylova, A Aziz Aboobaker Genome Biology 2013, 14:106 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Aziz Aboobaker and Yuliana Mihaylova muse on the peculiar powers that led 'eye of newt' to find favor with Macbeth's witches
	Research highlight A CRISPR way to engineer the human genome Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system
	Review
	Review Studying the microbiology of the indoor environment Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study
	Report
	Meeting report Food for thought from plant and animal genomes Emily Abrash Genome Biology 2013, 14:302 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
	Research
	Research Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang et al. Genome Biology 2013, 14:R11 (1 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
	Research Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae Mallory A Freeberg, Ting Han, James J Moresco, Andy Kong, Yu-Cheng Yang, Zhi Lu, John R Yates, John K Kim Genome Biology 2013, 14:R13 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the global binding of RNA binding proteins in yeast in response to stress
	Research Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
	Research Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King Genome Biology 2013, 14:R15 (18 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity
	Research A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Höffner, Marcus Krüger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
	Research Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies Masayuki Sugawara, Brendan Epstein, Brian D Badgley, Tatsuya Unno, Lei Xu, Jennifer Reese, Prasad Gyaneshwar, Roxanne Denny, Joann Mudge, Arvind K Bharti, Andrew D Farmer, Gregory D May, Jimmy E Woodward, Claudine Médigue, David Vallenet, Aurélie Lajus, Zoé Rouy, Betsy Martinez-Vaz, Peter Tiffin, Nevin D Young, Michael J Sadowsky Genome Biology 2013, 14:R17 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family
	Research The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression
	Research Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes Cecilia Alsmark, Peter G Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T Martin Embley, Robert P Hirt Genome Biology 2013, 14:R19 (25 February 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes
	Research Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes Pedro G Ferreira, Solenn Patalano, Ritika Chauhan, Richard Ffrench-Constant, Toni Gabaldón, Roderic Guigó, Seirian Sumner Genome Biology 2013, 14:R20 (26 February 2013) Abstract \| Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary An RNA-seq analysis of the genetic mechanisms controlling alternative phenotypes in the primitive eusocial wasp Polistes canadensis
	Method SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu, Shaoliang Peng, Yingrui Li, Jun Wang, Guangwu Guo Genome Biology 2013, 14:R12 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements

	Volume 14 Issue 2
	Comment
	Comment Science: it's a role model thing Chris Gunter Genome Biology 2013, 14:105 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science
	Research highlight What is it about 'eye of newt'? Yuliana Mihaylova, A Aziz Aboobaker Genome Biology 2013, 14:106 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Aziz Aboobaker and Yuliana Mihaylova muse on the peculiar powers that led 'eye of newt' to find favor with Macbeth's witches
	Research highlight A CRISPR way to engineer the human genome Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system
	Review
	Review Studying the microbiology of the indoor environment Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study
	Report
	Meeting report Food for thought from plant and animal genomes Emily Abrash Genome Biology 2013, 14:302 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
	Research
	Research Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang et al. Genome Biology 2013, 14:R11 (1 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
	Research Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae Mallory A Freeberg, Ting Han, James J Moresco, Andy Kong, Yu-Cheng Yang, Zhi Lu, John R Yates, John K Kim Genome Biology 2013, 14:R13 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the global binding of RNA binding proteins in yeast in response to stress
	Research Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
	Research Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King Genome Biology 2013, 14:R15 (18 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity
	Research A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Höffner, Marcus Krüger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
	Research Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies Masayuki Sugawara, Brendan Epstein, Brian D Badgley, Tatsuya Unno, Lei Xu, Jennifer Reese, Prasad Gyaneshwar, Roxanne Denny, Joann Mudge, Arvind K Bharti, Andrew D Farmer, Gregory D May, Jimmy E Woodward, Claudine Médigue, David Vallenet, Aurélie Lajus, Zoé Rouy, Betsy Martinez-Vaz, Peter Tiffin, Nevin D Young, Michael J Sadowsky Genome Biology 2013, 14:R17 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family
	Research The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression
	Research Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes Cecilia Alsmark, Peter G Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T Martin Embley, Robert P Hirt Genome Biology 2013, 14:R19 (25 February 2013) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes
	Research Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes Pedro G Ferreira, Solenn Patalano, Ritika Chauhan, Richard Ffrench-Constant, Toni Gabaldón, Roderic Guigó, Seirian Sumner Genome Biology 2013, 14:R20 (26 February 2013) Abstract \| Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary An RNA-seq analysis of the genetic mechanisms controlling alternative phenotypes in the primitive eusocial wasp Polistes canadensis
	Method SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu, Shaoliang Peng, Yingrui Li, Jun Wang, Guangwu Guo Genome Biology 2013, 14:R12 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements

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Volume 14 Issue 2

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