Genome Biology | Volume 13 Issue 3

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	Volume 13 Issue 3
	Comment
	Comment Apocalypse now? Gregory A Petsko Genome Biology 2012, 13:151 (30 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko identifies some signs of the coming end of the world and, in that context, urges readers to pay close attention to the coming US presidential election
	Research highlight Toward a complete Drosophila deficiency kit John Roote, Steven Russell Genome Biology 2012, 13:149 (23 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Roote and Russell discuss our Research article describing the development of a second-generation Drosophila deficiency kit
	Research highlight Modifier genetics in neuropsychiatric disease: challenges and opportunities Elizabeth K Ruzzo, Andrea L Pappas, David B Goldstein Genome Biology 2012, 13:150 (28 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary David Goldstein and colleagues highlight a recent study that focuses attention on multigenic interactions influencing the risk of autism spectrum disorders
	Review
	Review Life at the extreme: lessons from the genome Dong-Ha Oh, Maheshi Dassanayake, Hans J Bohnert, John M Cheeseman Genome Biology 2012, 13:241 (6 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput studies are providing insights into how extremophile plants adapt to life in places where most plant species cannot survive
	Protein family review The R-spondin protein family Wim BM de Lau, Berend Snel, Hans C Clevers Genome Biology 2012, 13:242 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Hans Clevers and colleagues review R-spondins, a protein family of potent stem cell proliferation stimulators with potential utility in regenerative medicine
	Opinion Women in Science Genome Biology Genome Biology 2012, 13:148 (8 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Four leading scientists answer our questions on how being female can impact upon a scientific career
	Opinion Q & A: the Snyderome Michael Snyder Genome Biology 2012, 13:147 (16 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Snyder answers Genome Biology's questions on the human and professional stories underlying his Snyderome integrative omics project
	Report
	Meeting report Faster sequencers, larger datasets, new challenges Christopher E Mason, Olivier Elemento Genome Biology 2012, 13:314 (27 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Advances in Genome Biology and Technology (AGBT) meeting included announcements of some major advances in sequencing technology
	Research
	Research The fine-scale architecture of structural variants in 17 mouse genomes Binnaz Yalcin, Kim Wong, Amarjit Bhomra, Martin Goodson, Thomas M Keane, David J Adams, Jonathan Flint Genome Biology 2012, 13:R18 (20 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extensive characterization of structural variations in the genomes of seventeen inbred mouse strains
	Research The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes Minna-Liisa Änkö, Michaela Müller-McNicoll, Holger Brandl, Tomaz Curk, Crtomir Gorup, Ian Henry, Jernej Ule, Karla M Neugebauer Genome Biology 2012, 13:R17 (21 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA-binding protein SRSF3 is the master regulator of a splicing network, and - together with SRSF4 - mysteriously regulates unsplicable histone transcripts
	Research Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach Jordi Solana, Damian Kao, Yuliana Mihaylova, Farah Jaber-Hijazi, Sunir Malla, Ray Wilson, Aziz Aboobaker Genome Biology 2012, 13:R19 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Planarian stem cells are ablated by RNAi against histone 2B and the neoblast-specific transcriptome is determined
	Research Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function Xiaoming Zhang, Jing Xia, Yifan E Lii, Blanca E Barrera-Figueroa, Xuefeng Zhou, Shang Gao, Lu Lu, Dongdong Niu, Zheng Chen, Christy Leung, Timothy Wong, Huiming Zhang, Jianhua Guo, Yi Li, Renyi Liu, Wanqi Liang, Jian-Kang Zhu, Weixiong Zhang, Hailing Jin Genome Biology 2012, 13:R20 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In Arabidopsis and rice, natural antisense transcripts are processed into siRNAs by DCL1 and DCL3
	Research The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome R Kimberley Cook, Stacey J Christensen, Jennifer A Deal, Rachel A Coburn, Megan E Deal, Jill M Gresens, Thomas C Kaufman, Kevin R Cook Genome Biology 2012, 13:R21 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new, large-scale collection of Drosophila deficiency strains from the BDSC, providing increased coverage of the genome
	Method MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets Zhen Shao, Yijing Zhang, Guo-Cheng Yuan, Stuart H Orkin, David J Waxman Genome Biology 2012, 13:R16 (16 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MAnorm is a method for quantitative comparison of ChIP-seq datasets
	Method An integrative probabilistic model for identification of structural variation in sequencing data Suzanne S Sindi, Selim Önal, Luke C Peng, Hsin-Ta Wu, Benjamin J Raphael Genome Biology 2012, 13:R22 (27 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GASVpro is a method for structural variant detection that takes in to account both paired read and read depth signals
	Method Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas, Jacques Izard, Joshua Z Levin, Jonathan Livny, Ashlee M Earl, Dirk Gevers, Doyle V Ward, Chad Nusbaum, Bruce W Birren, Andreas Gnirke Genome Biology 2012, 13:r23 (28 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented for transcriptome sequencing of complex bacterial mixtures or communities
	Software The Transcription Factor Encyclopedia Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao Cindy Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Bérénice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al. Genome Biology 2012, 13:R24 (29 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system

	Volume 13 Issue 3
	Comment
	Comment Apocalypse now? Gregory A Petsko Genome Biology 2012, 13:151 (30 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko identifies some signs of the coming end of the world and, in that context, urges readers to pay close attention to the coming US presidential election
	Research highlight Toward a complete Drosophila deficiency kit John Roote, Steven Russell Genome Biology 2012, 13:149 (23 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Roote and Russell discuss our Research article describing the development of a second-generation Drosophila deficiency kit
	Research highlight Modifier genetics in neuropsychiatric disease: challenges and opportunities Elizabeth K Ruzzo, Andrea L Pappas, David B Goldstein Genome Biology 2012, 13:150 (28 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary David Goldstein and colleagues highlight a recent study that focuses attention on multigenic interactions influencing the risk of autism spectrum disorders
	Review
	Review Life at the extreme: lessons from the genome Dong-Ha Oh, Maheshi Dassanayake, Hans J Bohnert, John M Cheeseman Genome Biology 2012, 13:241 (6 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput studies are providing insights into how extremophile plants adapt to life in places where most plant species cannot survive
	Protein family review The R-spondin protein family Wim BM de Lau, Berend Snel, Hans C Clevers Genome Biology 2012, 13:242 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Hans Clevers and colleagues review R-spondins, a protein family of potent stem cell proliferation stimulators with potential utility in regenerative medicine
	Opinion Women in Science Genome Biology Genome Biology 2012, 13:148 (8 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Four leading scientists answer our questions on how being female can impact upon a scientific career
	Opinion Q & A: the Snyderome Michael Snyder Genome Biology 2012, 13:147 (16 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Snyder answers Genome Biology's questions on the human and professional stories underlying his Snyderome integrative omics project
	Report
	Meeting report Faster sequencers, larger datasets, new challenges Christopher E Mason, Olivier Elemento Genome Biology 2012, 13:314 (27 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Advances in Genome Biology and Technology (AGBT) meeting included announcements of some major advances in sequencing technology
	Research
	Research The fine-scale architecture of structural variants in 17 mouse genomes Binnaz Yalcin, Kim Wong, Amarjit Bhomra, Martin Goodson, Thomas M Keane, David J Adams, Jonathan Flint Genome Biology 2012, 13:R18 (20 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extensive characterization of structural variations in the genomes of seventeen inbred mouse strains
	Research The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes Minna-Liisa Änkö, Michaela Müller-McNicoll, Holger Brandl, Tomaz Curk, Crtomir Gorup, Ian Henry, Jernej Ule, Karla M Neugebauer Genome Biology 2012, 13:R17 (21 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA-binding protein SRSF3 is the master regulator of a splicing network, and - together with SRSF4 - mysteriously regulates unsplicable histone transcripts
	Research Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach Jordi Solana, Damian Kao, Yuliana Mihaylova, Farah Jaber-Hijazi, Sunir Malla, Ray Wilson, Aziz Aboobaker Genome Biology 2012, 13:R19 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Planarian stem cells are ablated by RNAi against histone 2B and the neoblast-specific transcriptome is determined
	Research Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function Xiaoming Zhang, Jing Xia, Yifan E Lii, Blanca E Barrera-Figueroa, Xuefeng Zhou, Shang Gao, Lu Lu, Dongdong Niu, Zheng Chen, Christy Leung, Timothy Wong, Huiming Zhang, Jianhua Guo, Yi Li, Renyi Liu, Wanqi Liang, Jian-Kang Zhu, Weixiong Zhang, Hailing Jin Genome Biology 2012, 13:R20 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In Arabidopsis and rice, natural antisense transcripts are processed into siRNAs by DCL1 and DCL3
	Research The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome R Kimberley Cook, Stacey J Christensen, Jennifer A Deal, Rachel A Coburn, Megan E Deal, Jill M Gresens, Thomas C Kaufman, Kevin R Cook Genome Biology 2012, 13:R21 (22 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new, large-scale collection of Drosophila deficiency strains from the BDSC, providing increased coverage of the genome
	Method MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets Zhen Shao, Yijing Zhang, Guo-Cheng Yuan, Stuart H Orkin, David J Waxman Genome Biology 2012, 13:R16 (16 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MAnorm is a method for quantitative comparison of ChIP-seq datasets
	Method An integrative probabilistic model for identification of structural variation in sequencing data Suzanne S Sindi, Selim Önal, Luke C Peng, Hsin-Ta Wu, Benjamin J Raphael Genome Biology 2012, 13:R22 (27 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GASVpro is a method for structural variant detection that takes in to account both paired read and read depth signals
	Method Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas, Jacques Izard, Joshua Z Levin, Jonathan Livny, Ashlee M Earl, Dirk Gevers, Doyle V Ward, Chad Nusbaum, Bruce W Birren, Andreas Gnirke Genome Biology 2012, 13:r23 (28 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented for transcriptome sequencing of complex bacterial mixtures or communities
	Software The Transcription Factor Encyclopedia Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao Cindy Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Bérénice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al. Genome Biology 2012, 13:R24 (29 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system

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Volume 13 Issue 3

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