Genome Biology | Volume 12 Issue 1

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	Volume 12 Issue 1
	Comment
	Comment Preserving some sanity Gregory A Petsko Genome Biology 2011, 12:102 (31 January 2011) Full text \| PDF \| PubMed \| Editor’s summary Supply versus demand: can the focus on translational medicine deliver?
	Research highlight The similarity of gene expression between human and mouse tissues Robin D Dowell Genome Biology 2011, 12:101 (17 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Meta-analysis of human and mouse microarray data reveals conservation of patterns of gene expression.
	Review
	Review Silencing signals in plants: a long journey for small RNAs Attila Molnar, Charles Melnyk, David C Baulcombe Genome Biology 2011, 12:215 (11 January 2011) Abstract \| Full text \| PDF \| PubMed
	Report
	Meeting report Exploiting the complexity of the genome and transcriptome using pharmacogenomics towards personalized medicine Reiner Hoppe, Hiltrud Brauch, Deanna L Kroetz, Manel Esteller Genome Biology 2011, 12:301 (17 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 8th annual Pharmacogenomics and Personalized Therapy meeting, Cold Spring Harbor Laboratory, USA, 17-21 November 2010.
	Meeting report Integrating systems biology data to yield functional genomics insights Polly Fordyce, Nicholas Ingolia Genome Biology 2011, 12:302 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010.
	Research
	Research Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis Shaun Mahony, Esteban O Mazzoni, Scott McCuine, Richard A Young, Hynek Wichterle, David K Gifford Genome Biology 2011, 12:R2 (13 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-seq for retinoic acid receptor binding during early neuronal differentiation reveals a complex landscape of transcriptional control.
	Research Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins Tanja Scherrer, Christian Femmer, Ralph Schiess, Ruedi Aebersold, André P Gerber Genome Biology 2011, 12:R3 (13 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The RNA targets of the yeast zinc-finger RNA binding protein, Gis2p, are conserved in the human homolog, ZNF9.
	Research Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires Christian M Zmasek, Adam Godzik Genome Biology 2011, 12:R4 (17 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Reconstruction of protein domain repertoires of ancestral species suggests the last common eukaryotic ancestor had a surprisingly complex proteome
	Research Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility David A Quigley, Minh D To, Il Jin Kim, Kevin K Lin, Donna G Albertson, Jonas Sjolund, Jesús Pérez-Losada, Allan Balmain Genome Biology 2011, 12:R5 (18 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary eQTL analysis of a mouse model of skin cancer finds changes as tumours progress from normal skin to malignant tumour
	Research Identification of fusion genes in breast cancer by paired-end RNA-sequencing Henrik Edgren, Astrid Murumagi, Sara Kangaspeska, Daniel Nicorici, Vesa Hongisto, Kristine Kleivi, Inga H Rye, Sandra Nyberg, Maija Wolf, Anne-Lise Borresen-Dale, Olli Kallioniemi Genome Biology 2011, 12:R6 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq has been used to identify transcribed fusion genes in breast cancer cell lines
	Research Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi Anke Burmester, Ekaterina Shelest, Gernot Glöckner, Christoph Heddergott, Susann Schindler, Peter Staib, Andrew Heidel, Marius Felder, Andreas Petzold, Karol Szafranski, Marc Feuermann, Ivo Pedruzzi, Steffen Priebe, Marco Groth, Robert Winkler, Wenjun Li, Olaf Kniemeyer, Volker Schroeckh, Christian Hertweck, Bernhard Hube, Theodore C White, Matthias Platzer, Reinhard Guthke, Joseph Heitman, Johannes Wöstemeyer, Peter F Zipfel, Michel Monod, Axel A Brakhage Genome Biology 2011, 12:R7 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome sequences from two dermatophytic fungi shed light on the biology and pathogenesis of these skin disease-causing organisms
	Research Coding potential of the products of alternative splicing in human Guido Leoni, Loredana Le Pera, Fabrizio Ferrè, Domenico Raimondo, Anna Tramontano Genome Biology 2011, 12:R9 (20 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of proteomic datasets with transcription libraries allows exploration of to what extent alternatively spliced variants are translated into variant proteins
	Research DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard Genome Biology 2011, 12:R10 (20 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Profiling lymphoblastoid cell lines from HapMap individuals reveals a significant genetic component for inter-individual DNA methylation and gene expression
	Method A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries Sheila Fisher, Andrew Barry, Justin Abreu, Brian Minie, Jillian Nolan, Toni M Delorey, Geneva Young, Timothy J Fennell, Alexander Allen, Lauren Ambrogio, Aaron M Berlin, Brendan Blumenstiel, Kristian Cibulskis, Dennis Friedrich, Ryan Johnson, Frank Juhn, Brian Reilly, Ramy Shammas, John Stalker, Sean M Sykes, Jon Thompson, John Walsh, Andrew Zimmer, Zac Zwirko, Stacey Gabriel, Robert Nicol, Chad Nusbaum Genome Biology 2011, 12:R1 (4 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An automated and highly-scalable method for the construction of exome-capture libraries for sequencing.
	Method A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language Ronny Herzog, Dominik Schwudke, Kai Schuhmann, Julio L Sampaio, Stefan R Bornstein, Michael Schroeder, Andrej Shevchenko Genome Biology 2011, 12:R8 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method for lipid identification from all mass spectrometry platforms is presented within the software LipidXplorer

	Volume 12 Issue 1
	Comment
	Comment Preserving some sanity Gregory A Petsko Genome Biology 2011, 12:102 (31 January 2011) Full text \| PDF \| PubMed \| Editor’s summary Supply versus demand: can the focus on translational medicine deliver?
	Research highlight The similarity of gene expression between human and mouse tissues Robin D Dowell Genome Biology 2011, 12:101 (17 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Meta-analysis of human and mouse microarray data reveals conservation of patterns of gene expression.
	Review
	Review Silencing signals in plants: a long journey for small RNAs Attila Molnar, Charles Melnyk, David C Baulcombe Genome Biology 2011, 12:215 (11 January 2011) Abstract \| Full text \| PDF \| PubMed
	Report
	Meeting report Exploiting the complexity of the genome and transcriptome using pharmacogenomics towards personalized medicine Reiner Hoppe, Hiltrud Brauch, Deanna L Kroetz, Manel Esteller Genome Biology 2011, 12:301 (17 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 8th annual Pharmacogenomics and Personalized Therapy meeting, Cold Spring Harbor Laboratory, USA, 17-21 November 2010.
	Meeting report Integrating systems biology data to yield functional genomics insights Polly Fordyce, Nicholas Ingolia Genome Biology 2011, 12:302 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010.
	Research
	Research Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis Shaun Mahony, Esteban O Mazzoni, Scott McCuine, Richard A Young, Hynek Wichterle, David K Gifford Genome Biology 2011, 12:R2 (13 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-seq for retinoic acid receptor binding during early neuronal differentiation reveals a complex landscape of transcriptional control.
	Research Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins Tanja Scherrer, Christian Femmer, Ralph Schiess, Ruedi Aebersold, André P Gerber Genome Biology 2011, 12:R3 (13 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The RNA targets of the yeast zinc-finger RNA binding protein, Gis2p, are conserved in the human homolog, ZNF9.
	Research Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires Christian M Zmasek, Adam Godzik Genome Biology 2011, 12:R4 (17 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Reconstruction of protein domain repertoires of ancestral species suggests the last common eukaryotic ancestor had a surprisingly complex proteome
	Research Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility David A Quigley, Minh D To, Il Jin Kim, Kevin K Lin, Donna G Albertson, Jonas Sjolund, Jesús Pérez-Losada, Allan Balmain Genome Biology 2011, 12:R5 (18 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary eQTL analysis of a mouse model of skin cancer finds changes as tumours progress from normal skin to malignant tumour
	Research Identification of fusion genes in breast cancer by paired-end RNA-sequencing Henrik Edgren, Astrid Murumagi, Sara Kangaspeska, Daniel Nicorici, Vesa Hongisto, Kristine Kleivi, Inga H Rye, Sandra Nyberg, Maija Wolf, Anne-Lise Borresen-Dale, Olli Kallioniemi Genome Biology 2011, 12:R6 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq has been used to identify transcribed fusion genes in breast cancer cell lines
	Research Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi Anke Burmester, Ekaterina Shelest, Gernot Glöckner, Christoph Heddergott, Susann Schindler, Peter Staib, Andrew Heidel, Marius Felder, Andreas Petzold, Karol Szafranski, Marc Feuermann, Ivo Pedruzzi, Steffen Priebe, Marco Groth, Robert Winkler, Wenjun Li, Olaf Kniemeyer, Volker Schroeckh, Christian Hertweck, Bernhard Hube, Theodore C White, Matthias Platzer, Reinhard Guthke, Joseph Heitman, Johannes Wöstemeyer, Peter F Zipfel, Michel Monod, Axel A Brakhage Genome Biology 2011, 12:R7 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome sequences from two dermatophytic fungi shed light on the biology and pathogenesis of these skin disease-causing organisms
	Research Coding potential of the products of alternative splicing in human Guido Leoni, Loredana Le Pera, Fabrizio Ferrè, Domenico Raimondo, Anna Tramontano Genome Biology 2011, 12:R9 (20 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of proteomic datasets with transcription libraries allows exploration of to what extent alternatively spliced variants are translated into variant proteins
	Research DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard Genome Biology 2011, 12:R10 (20 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Profiling lymphoblastoid cell lines from HapMap individuals reveals a significant genetic component for inter-individual DNA methylation and gene expression
	Method A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries Sheila Fisher, Andrew Barry, Justin Abreu, Brian Minie, Jillian Nolan, Toni M Delorey, Geneva Young, Timothy J Fennell, Alexander Allen, Lauren Ambrogio, Aaron M Berlin, Brendan Blumenstiel, Kristian Cibulskis, Dennis Friedrich, Ryan Johnson, Frank Juhn, Brian Reilly, Ramy Shammas, John Stalker, Sean M Sykes, Jon Thompson, John Walsh, Andrew Zimmer, Zac Zwirko, Stacey Gabriel, Robert Nicol, Chad Nusbaum Genome Biology 2011, 12:R1 (4 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An automated and highly-scalable method for the construction of exome-capture libraries for sequencing.
	Method A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language Ronny Herzog, Dominik Schwudke, Kai Schuhmann, Julio L Sampaio, Stefan R Bornstein, Michael Schroeder, Andrej Shevchenko Genome Biology 2011, 12:R8 (19 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method for lipid identification from all mass spectrometry platforms is presented within the software LipidXplorer

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Volume 12 Issue 1

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