Genome Biology | Volume 10 Issue 3

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	Volume 10 Issue 3
	Comment
	Comment Too big to succeed? Gregory A Petsko Genome Biology 2009, 10:103 (30 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Bigger is not necessarily more beautiful when big pharma mergers are at issue.
	Review
	Protein family review The origin recognition complex protein family Bernard P Duncker, Igor N Chesnokov, Brendan J McConkey Genome Biology 2009, 10:214 (17 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The proteins of the origin recognition complex are found throughout all eukaryotes and have roles beyond that of DNA replication.
	Minireview Rac and Rho driving tumor invasion: who's at the wheel? Marc Symons, Jeffrey E Segall Genome Biology 2009, 10:213 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Interplay between Rho and Rac controls the invasive behavior of melanoma cells.
	Minireview The need for speed Paul Flicek Genome Biology 2009, 10:212 (27 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new sequence-alignment algorithm that uses advanced data structures to help data analysis keep pace with data generation.
	Report
	Meeting report Yeasts as models in evolutionary biology Zhenglong Gu, Stephen Oliver Genome Biology 2009, 10:304 (2 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the workshop 'Evolutionary and Environmental Genomics of Yeasts', Heidelberg, Germany, 1-5 October 2008.
	Meeting report Building bridges from 'omics' to cell biology Brian Cox Genome Biology 2009, 10:305 (10 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the Keystone Symposium on Molecular and Cellular Biology, 'Omics Meets Cell Biology', Breckenridge, Colorado, 25-30 January, 2009.
	Research
	Research Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology Tao Liu, David Sims, Buzz Baum Genome Biology 2009, 10:R26 (5 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Parallel RNA interference screens and gene expression arrays in six Drosophila cell lines identified regulators of cell morphology, including a neuronal function for the kinase minibrain/DYRK1A in the regulation of protrusion morphology.
	Research Integrated analysis of breast cancer cell lines reveals unique signaling pathways Laura M Heiser, Nicholas J Wang, Carolyn L Talcott, Keith R Laderoute, Merrill Knapp, Yinghui Guan, Zhi Hu, Safiyyah Ziyad, Barbara L Weber, Sylvie Laquerre, Jeffrey R Jackson, Richard F Wooster, Wen Kuo, Joe W Gray, Paul T Spellman Genome Biology 2009, 10:R31 (25 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mapping of sub-networks in the EGFR-MAPK pathway in different breast cancer cell lines reveals that PAK1 may be a marker for sensitivity to MEK inhibitors.
	Research Evaluation of next generation sequencing platforms for population targeted sequencing studies Olivier Harismendy, Pauline C Ng, Robert L Strausberg, Xiaoyun Wang, Timothy B Stockwell, Karen Y Beeson, Nicholas J Schork, Sarah S Murray, Eric J Topol, Samuel Levy, Kelly A Frazer Genome Biology 2009, 10:R32 (27 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics.
	Research Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions Thiago M Venancio, S Balaji, Lakshminarayan M Iyer, L Aravind Genome Biology 2009, 10:R33 (30 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational model of the yeast Ubiquitin system highlights interesting biological features including functional interactions between components and interplay with other regulatory mechanisms.
	Method DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli Karen Lemmens, Tijl De Bie, Thomas Dhollander, Sigrid C De Keersmaecker, Inge M Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal Genome Biology 2009, 10:R27 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DISTILLER, a data integration framework for the inference of transcriptional module networks, is presented and used to investigate the condition dependency and modularity in Escherichia coli networks.
	Method Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes Gabi Kastenmüller, Maria Schenk, Johann Gasteiger, Hans-Werner Mewes Genome Biology 2009, 10:R28 (10 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new machine learning-based method is presented here for the identification of metabolic pathways related to specific phenotypes in multiple microbial genomes.
	Method A computational approach for genome-wide mapping of splicing factor binding sites Martin Akerman, Hilda David-Eden, Ron Y Pinter, Yael Mandel-Gutfreund Genome Biology 2009, 10:R30 (18 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational method is presented for genome-wide mapping of splicing factor binding sites that considers both the genomic environment and evolutionary conservation.
	Software Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R25 (4 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
	Software TFCat: the curated catalog of mouse and human transcription factors Debra L Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R Hughes, Wyeth W Wasserman, Jared C Roach, Rob Sladek Genome Biology 2009, 10:R29 (12 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TFCat is a catalog of mouse and human transcription factors based on a reliable core collection of annotations obtained by expert review of the scientific literature

	Volume 10 Issue 3
	Comment
	Comment Too big to succeed? Gregory A Petsko Genome Biology 2009, 10:103 (30 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Bigger is not necessarily more beautiful when big pharma mergers are at issue.
	Review
	Protein family review The origin recognition complex protein family Bernard P Duncker, Igor N Chesnokov, Brendan J McConkey Genome Biology 2009, 10:214 (17 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The proteins of the origin recognition complex are found throughout all eukaryotes and have roles beyond that of DNA replication.
	Minireview Rac and Rho driving tumor invasion: who's at the wheel? Marc Symons, Jeffrey E Segall Genome Biology 2009, 10:213 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Interplay between Rho and Rac controls the invasive behavior of melanoma cells.
	Minireview The need for speed Paul Flicek Genome Biology 2009, 10:212 (27 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new sequence-alignment algorithm that uses advanced data structures to help data analysis keep pace with data generation.
	Report
	Meeting report Yeasts as models in evolutionary biology Zhenglong Gu, Stephen Oliver Genome Biology 2009, 10:304 (2 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the workshop 'Evolutionary and Environmental Genomics of Yeasts', Heidelberg, Germany, 1-5 October 2008.
	Meeting report Building bridges from 'omics' to cell biology Brian Cox Genome Biology 2009, 10:305 (10 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the Keystone Symposium on Molecular and Cellular Biology, 'Omics Meets Cell Biology', Breckenridge, Colorado, 25-30 January, 2009.
	Research
	Research Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology Tao Liu, David Sims, Buzz Baum Genome Biology 2009, 10:R26 (5 March 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Parallel RNA interference screens and gene expression arrays in six Drosophila cell lines identified regulators of cell morphology, including a neuronal function for the kinase minibrain/DYRK1A in the regulation of protrusion morphology.
	Research Integrated analysis of breast cancer cell lines reveals unique signaling pathways Laura M Heiser, Nicholas J Wang, Carolyn L Talcott, Keith R Laderoute, Merrill Knapp, Yinghui Guan, Zhi Hu, Safiyyah Ziyad, Barbara L Weber, Sylvie Laquerre, Jeffrey R Jackson, Richard F Wooster, Wen Kuo, Joe W Gray, Paul T Spellman Genome Biology 2009, 10:R31 (25 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mapping of sub-networks in the EGFR-MAPK pathway in different breast cancer cell lines reveals that PAK1 may be a marker for sensitivity to MEK inhibitors.
	Research Evaluation of next generation sequencing platforms for population targeted sequencing studies Olivier Harismendy, Pauline C Ng, Robert L Strausberg, Xiaoyun Wang, Timothy B Stockwell, Karen Y Beeson, Nicholas J Schork, Sarah S Murray, Eric J Topol, Samuel Levy, Kelly A Frazer Genome Biology 2009, 10:R32 (27 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics.
	Research Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions Thiago M Venancio, S Balaji, Lakshminarayan M Iyer, L Aravind Genome Biology 2009, 10:R33 (30 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational model of the yeast Ubiquitin system highlights interesting biological features including functional interactions between components and interplay with other regulatory mechanisms.
	Method DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli Karen Lemmens, Tijl De Bie, Thomas Dhollander, Sigrid C De Keersmaecker, Inge M Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal Genome Biology 2009, 10:R27 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DISTILLER, a data integration framework for the inference of transcriptional module networks, is presented and used to investigate the condition dependency and modularity in Escherichia coli networks.
	Method Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes Gabi Kastenmüller, Maria Schenk, Johann Gasteiger, Hans-Werner Mewes Genome Biology 2009, 10:R28 (10 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new machine learning-based method is presented here for the identification of metabolic pathways related to specific phenotypes in multiple microbial genomes.
	Method A computational approach for genome-wide mapping of splicing factor binding sites Martin Akerman, Hilda David-Eden, Ron Y Pinter, Yael Mandel-Gutfreund Genome Biology 2009, 10:R30 (18 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computational method is presented for genome-wide mapping of splicing factor binding sites that considers both the genomic environment and evolutionary conservation.
	Software Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R25 (4 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
	Software TFCat: the curated catalog of mouse and human transcription factors Debra L Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R Hughes, Wyeth W Wasserman, Jared C Roach, Rob Sladek Genome Biology 2009, 10:R29 (12 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TFCat is a catalog of mouse and human transcription factors based on a reliable core collection of annotations obtained by expert review of the scientific literature

Explore Genome Biology

Articles

Volume 10 Issue 3

Comment

Review

Report

Research