Genome Biology | All articles

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Supplements

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
		Research Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast Daniel H Lackner, Michael W Schmidt, Shuangding Wu, Dieter A Wolf, Jürg Bähler Genome Biology 2012, 13:R25 (18 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Changes in transcription and translation are measured in fission yeast exposed to different stresses to elucidate layers of gene expression control
		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
		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
		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
		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
		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
		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 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 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
		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 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
		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
		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 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
		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 \| Editor’s summary MAnorm is a method for quantitative comparison of ChIP-seq datasets
		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
		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
		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
		Research Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms James T Lu, Yi Wang, Richard A Gibbs, Fuli Yu Genome Biology 2012, 13:R15 (29 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of 1000 Genomes phase 3 data reveals that indels are in tight linkage disequilibrium with SNPs
		Research Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence Julie MJ Lepesant, Céline Cosseau, Jérome Boissier, Michael Freitag, Julien Portela, Déborah Climent, Cécile Perrin, Adhemar Zerlotini, Christoph Grunau Genome Biology 2012, 13:R14 (29 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sex chromosome-specific sequences are identified in the blood fluke genome, shedding light on sex chromosome evolution
		Method All Your Base: a fast and accurate probabilistic approach to base calling Tim Massingham, Nick Goldman Genome Biology 2012, 13:R13 (29 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fast and accurate base calling method enables improved genotyping and assembly compared to existing tools
		Meeting report Epigenomics and chromatin dynamics Veronika Akopian, Michelle M Chan, Kendell Clement, Christina Galonska, Casey A Gifford, Elizabeth Lehtola, Jing Liao, Payman Samavarchi-Tehrani, Camille Sindhu, Zachary D Smith, Alexander M Tsankov, Jamie Webster, Yingying Zhang, Michael J Ziller, Alexander Meissner Genome Biology 2012, 13:313 (24 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Joint Keystone Symposium on Epigenomics and Chromatin Dynamics, Keystone, Colorado, 17-22 January 2012
		Comment A case of the flu Gregory A Petsko Genome Biology 2012, 13:146 (24 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The public perception of science is a crucial factor in whether the availability of recent work on constructing a virulent strain of influenza should be restricted
		Research highlight Maternal-to-zygotic transition: soma versus germline Martine Simonelig Genome Biology 2012, 13:145 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Martine Simonelig highlights our Research article on differences between the Drosophila maternal-to-zygotic transition in primordial germ cells and soma
		Research highlight Old soldiers never die .... Jacobus J Boomsma, Sanne Nygaard Genome Biology 2012, 13:144 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Boomsma and Nygaard on the evolutionary persistence of "supersoldier" development pathway potential in supersoldier-less ant lineages

	All
		Research Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast Daniel H Lackner, Michael W Schmidt, Shuangding Wu, Dieter A Wolf, Jürg Bähler Genome Biology 2012, 13:R25 (18 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Changes in transcription and translation are measured in fission yeast exposed to different stresses to elucidate layers of gene expression control
		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
		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
		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
		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
		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
		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 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 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
		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 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
		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
		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 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
		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 \| Editor’s summary MAnorm is a method for quantitative comparison of ChIP-seq datasets
		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
		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
		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
		Research Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms James T Lu, Yi Wang, Richard A Gibbs, Fuli Yu Genome Biology 2012, 13:R15 (29 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of 1000 Genomes phase 3 data reveals that indels are in tight linkage disequilibrium with SNPs
		Research Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence Julie MJ Lepesant, Céline Cosseau, Jérome Boissier, Michael Freitag, Julien Portela, Déborah Climent, Cécile Perrin, Adhemar Zerlotini, Christoph Grunau Genome Biology 2012, 13:R14 (29 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sex chromosome-specific sequences are identified in the blood fluke genome, shedding light on sex chromosome evolution
		Method All Your Base: a fast and accurate probabilistic approach to base calling Tim Massingham, Nick Goldman Genome Biology 2012, 13:R13 (29 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fast and accurate base calling method enables improved genotyping and assembly compared to existing tools
		Meeting report Epigenomics and chromatin dynamics Veronika Akopian, Michelle M Chan, Kendell Clement, Christina Galonska, Casey A Gifford, Elizabeth Lehtola, Jing Liao, Payman Samavarchi-Tehrani, Camille Sindhu, Zachary D Smith, Alexander M Tsankov, Jamie Webster, Yingying Zhang, Michael J Ziller, Alexander Meissner Genome Biology 2012, 13:313 (24 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Joint Keystone Symposium on Epigenomics and Chromatin Dynamics, Keystone, Colorado, 17-22 January 2012
		Comment A case of the flu Gregory A Petsko Genome Biology 2012, 13:146 (24 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The public perception of science is a crucial factor in whether the availability of recent work on constructing a virulent strain of influenza should be restricted
		Research highlight Maternal-to-zygotic transition: soma versus germline Martine Simonelig Genome Biology 2012, 13:145 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Martine Simonelig highlights our Research article on differences between the Drosophila maternal-to-zygotic transition in primordial germ cells and soma
		Research highlight Old soldiers never die .... Jacobus J Boomsma, Sanne Nygaard Genome Biology 2012, 13:144 (22 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Boomsma and Nygaard on the evolutionary persistence of "supersoldier" development pathway potential in supersoldier-less ant lineages