Genome Biology | Volume 12 Issue 12

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	Volume 12 Issue 12
	Comment
	Comment The Columnist Manifesto Gregory A Petsko Genome Biology 2011, 12:136 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scientists need to explain to the public what science is and why it needs funding, especially when the economic situation is bad
	Research highlight Games with a scientific purpose Benjamin M Good, Andrew I Su Genome Biology 2011, 12:135 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potent algorithms and solved "unsolvable" structures: are the 230,000 players of the protein folding game Foldit the scientists of the future?
	Research highlight Making enhancers from spare parts of the genome David Fredman, Xianjun Dong, Boris Lenhard Genome Biology 2011, 12:138 (29 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Boris Lenhard and colleagues on how developmental enhancers form in genomes by the recycling of existing functional elements
	Review
	Review Evolution of biological interaction networks: from models to real data Mark GF Sun, Philip M Kim Genome Biology 2011, 12:235 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sun and Kim review progress in the study of biological network evolution, with a focus on the protein-protein interaction network
	Review Alu elements: know the SINEs Prescott Deininger Genome Biology 2011, 12:236 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prescott Deininger reviews the contribution of Alu elements to genome evolution, gene regulation and disease
	Opinion Genomics in 2011: challenges and opportunities David J Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X Shirley Liu, Chad L Myers, Alicia Oshlack, John L Rinn, Albertha J M Walhout Genome Biology 2011, 12:137 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Several members of the Genome Biology Editorial Board give their views on the state of play in genomics
	Report
	Meeting report Opening sequence: computational genomics in the era of high-throughput sequencing Emily V Chambers, Alida S Kindt, Colin AM Semple Genome Biology 2011, 12:310 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011.
	Research
	Research RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.) Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse Genome Biology 2011, 12:R119 (2 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization
	Research The relationship between proteome size, structural disorder and organism complexity Eva Schad, Peter Tompa, Hedi Hegyi Genome Biology 2011, 12:R120 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Complexity is a multi-parametric trait, determined by interaction potential, alternative splicing capacity, protein disorder and, above all, proteome size
	Research Loss of the bloom syndrome helicase increases DNA ligase 4-independent genome rearrangements and tumorigenesis in aging Drosophila Ana Garcia, Robert N Salomon, Alice Witsell, Justine Liepkalns, R Brent Calder, Moonsook Lee, Martha Lundell, Jan Vijg, Mitch McVey Genome Biology 2011, 12:R121 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Drosophila blm mutants show an increase in genome rearrangements which, surprisingly, are independent of DNA ligase 4
	Research Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism Peter Meister, Sonia Schott, Cécile Bedet, Yu Xiao, Sabine Rohner, Selena Bodennec, Bruno Hudry, Laurent Molin, Florence Solari, Susan M Gasser, Francesca Palladino Genome Biology 2011, 12:R123 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary HPL-2, the C. elegans homolog of heterochromatin protein 1, helps regulate longevity, dauer diapause and lipid metabolism
	Research Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights Raluca Gordân, Kevin F Murphy, Rachel P McCord, Cong Zhu, Anastasia Vedenko, Martha L Bulyk Genome Biology 2011, 12:R125 (21 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive resource of DNA binding specificity data for all characterized Saccharomyces cerevisiae transcription factors
	Research MicroRNAs and their isomiRs function cooperatively to target common biological pathways Nicole Cloonan, Shivangi Wani, Qinying Xu, Jian Gu, Kristi Lea, Sheila Heater, Catalin Barbacioru, Anita L Steptoe, Hilary C Martin, Ehsan Nourbakhsh, Keerthana Krishnan, Brooke Gardiner, Xiaohui Wang, Katia Nones, Jason A Steen, Nicholas A Matigian, David L Wood, Karin S Kassahn, Nic Waddell, Jill Shepherd, Clarence Lee, Jeff Ichikawa, Kevin McKernan, Kelli Bramlett, Scott Kuersten, Sean M Grimmond Genome Biology 2011, 12:R126 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
	Research Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera Tom A Mendum, Jane Newcombe, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden Genome Biology 2011, 12:R127 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A global screen of mutant fitness in Neisseria meningitidis was used to construct a genome-scale metabolic network
	Method Accurate proteome-wide protein quantification from high-resolution ¹⁵N mass spectra Zia Khan, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, Saeed Tavazoie Genome Biology 2011, 12:R122 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fast, user-friendly bioinformatic tool for accurate quantification of proteins in 15N mass spectrometry data
	Method Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples
	Correspondence
	Correction SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:413 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: A method to detect condition-specific gene expression from microarray data
	Correction Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Y Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:414 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology

	Volume 12 Issue 12
	Comment
	Comment The Columnist Manifesto Gregory A Petsko Genome Biology 2011, 12:136 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scientists need to explain to the public what science is and why it needs funding, especially when the economic situation is bad
	Research highlight Games with a scientific purpose Benjamin M Good, Andrew I Su Genome Biology 2011, 12:135 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potent algorithms and solved "unsolvable" structures: are the 230,000 players of the protein folding game Foldit the scientists of the future?
	Research highlight Making enhancers from spare parts of the genome David Fredman, Xianjun Dong, Boris Lenhard Genome Biology 2011, 12:138 (29 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Boris Lenhard and colleagues on how developmental enhancers form in genomes by the recycling of existing functional elements
	Review
	Review Evolution of biological interaction networks: from models to real data Mark GF Sun, Philip M Kim Genome Biology 2011, 12:235 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sun and Kim review progress in the study of biological network evolution, with a focus on the protein-protein interaction network
	Review Alu elements: know the SINEs Prescott Deininger Genome Biology 2011, 12:236 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Prescott Deininger reviews the contribution of Alu elements to genome evolution, gene regulation and disease
	Opinion Genomics in 2011: challenges and opportunities David J Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X Shirley Liu, Chad L Myers, Alicia Oshlack, John L Rinn, Albertha J M Walhout Genome Biology 2011, 12:137 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Several members of the Genome Biology Editorial Board give their views on the state of play in genomics
	Report
	Meeting report Opening sequence: computational genomics in the era of high-throughput sequencing Emily V Chambers, Alida S Kindt, Colin AM Semple Genome Biology 2011, 12:310 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011.
	Research
	Research RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.) Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse Genome Biology 2011, 12:R119 (2 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization
	Research The relationship between proteome size, structural disorder and organism complexity Eva Schad, Peter Tompa, Hedi Hegyi Genome Biology 2011, 12:R120 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Complexity is a multi-parametric trait, determined by interaction potential, alternative splicing capacity, protein disorder and, above all, proteome size
	Research Loss of the bloom syndrome helicase increases DNA ligase 4-independent genome rearrangements and tumorigenesis in aging Drosophila Ana Garcia, Robert N Salomon, Alice Witsell, Justine Liepkalns, R Brent Calder, Moonsook Lee, Martha Lundell, Jan Vijg, Mitch McVey Genome Biology 2011, 12:R121 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Drosophila blm mutants show an increase in genome rearrangements which, surprisingly, are independent of DNA ligase 4
	Research Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism Peter Meister, Sonia Schott, Cécile Bedet, Yu Xiao, Sabine Rohner, Selena Bodennec, Bruno Hudry, Laurent Molin, Florence Solari, Susan M Gasser, Francesca Palladino Genome Biology 2011, 12:R123 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary HPL-2, the C. elegans homolog of heterochromatin protein 1, helps regulate longevity, dauer diapause and lipid metabolism
	Research Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights Raluca Gordân, Kevin F Murphy, Rachel P McCord, Cong Zhu, Anastasia Vedenko, Martha L Bulyk Genome Biology 2011, 12:R125 (21 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive resource of DNA binding specificity data for all characterized Saccharomyces cerevisiae transcription factors
	Research MicroRNAs and their isomiRs function cooperatively to target common biological pathways Nicole Cloonan, Shivangi Wani, Qinying Xu, Jian Gu, Kristi Lea, Sheila Heater, Catalin Barbacioru, Anita L Steptoe, Hilary C Martin, Ehsan Nourbakhsh, Keerthana Krishnan, Brooke Gardiner, Xiaohui Wang, Katia Nones, Jason A Steen, Nicholas A Matigian, David L Wood, Karin S Kassahn, Nic Waddell, Jill Shepherd, Clarence Lee, Jeff Ichikawa, Kevin McKernan, Kelli Bramlett, Scott Kuersten, Sean M Grimmond Genome Biology 2011, 12:R126 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
	Research Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera Tom A Mendum, Jane Newcombe, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden Genome Biology 2011, 12:R127 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A global screen of mutant fitness in Neisseria meningitidis was used to construct a genome-scale metabolic network
	Method Accurate proteome-wide protein quantification from high-resolution ¹⁵N mass spectra Zia Khan, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, Saeed Tavazoie Genome Biology 2011, 12:R122 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fast, user-friendly bioinformatic tool for accurate quantification of proteins in 15N mass spectrometry data
	Method Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples
	Correspondence
	Correction SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:413 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: A method to detect condition-specific gene expression from microarray data
	Correction Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Y Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:414 (30 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Correction: The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology

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Volume 12 Issue 12

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