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		Research Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation Claudia C Weber, Laurence D Hurst Genome Biology 2011, 12:R23 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The conservation of syntenic gene order previously described in yeast is not apparent in D. melanogaster
		Method Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extension to Cufflinks corrects bias in RNA-seq datasets
		Method hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets Todd A Johnson, Yoshihito Niimura, Hiroshi Tanaka, Yusuke Nakamura, Tatsuhiko Tsunoda Genome Biology 2011, 12:R21 (11 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel methods are presented for the detection and analysis of homozygous tracts from genotype data
		Research Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang, Alan Kuo, Xiangjun Tian, William Salerno, Anup Parikh, Christa L Feasley, Eileen Dalin, Hank Tu, Eryong Huang, Kerrie Barry, Erika Lindquist, Harris Shapiro, David Bruce, Jeremy Schmutz, Asaf Salamov, Petra Fey, Pascale Gaudet, Christophe Anjard, M Madan Babu, Siddhartha Basu, Yulia Bushmanova, Hanke van der Wel, Mariko Katoh-Kurasawa, Christopher Dinh, Pedro M Coutinho, Tamao Saito, Marek Elias, Pauline Schaap, Robert R Kay, Bernard Henrissat, Ludwig Eichinger, Francisco Rivero, Nicholas H Putnam, Christopher M West, William F Loomis, Rex L Chisholm, Gad Shaulsky, Joan E Strassmann, David C Queller, Adam Kuspa, Igor V Grigoriev et al. Genome Biology 2011, 12:R20 (28 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Dictyostelium purpureum is reported and compared with that of D. discoideum
		Method Dating the age of admixture via wavelet transform analysis of genome-wide data Irina Pugach, Rostislav Matveyev, Andreas Wollstein, Manfred Kayser, Mark Stoneking Genome Biology 2011, 12:R19 (25 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combination of PCA and wavelet transform analysis defines admixture structure and dates its history
		Comment There is a sanity clause Gregory A Petsko Genome Biology 2011, 12:105 (25 February 2011) Full text \| PDF \| PubMed \| Editor’s summary Supply versus demand part II: will funding basic research lead to medical advances?
		Review The properties and applications of single-molecule DNA sequencing John F Thompson, Patrice M Milos Genome Biology 2011, 12:217 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Single-molecule sequencing works directly from biological samples and generates very long reads, making it well suited for diagnostic and clinical applications.
		Research highlight Piecing together the FTO jigsaw Timothy M Frayling, Ken Ong Genome Biology 2011, 12:104 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two recent studies of the FTO gene provide more information on how it affects body mass index
		Review The domestic dog: man's best friend in the genomic era Adam R Boyko Genome Biology 2011, 12:216 (22 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The tremendous phenotypic diversity of domestic dog breeds, coupled with the availability of dog genome sequences, point to the dog as as an important model organism for complex-trait analysis
		Method Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias
		Correspondence Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses Albert J Vilella, Ewan Birney, Paul Flicek, Javier Herrero Genome Biology 2011, 12:401 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16.
		Research Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli Maarten Vercruysse, Maarten Fauvart, Ann Jans, Serge Beullens, Kristien Braeken, Lore Cloots, Kristof Engelen, Kathleen Marchal, Jan Michiels Genome Biology 2011, 12:R17 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The stress response of Rhizobium etli is dissected through transcriptomics of a mutant that does not synthesize the alarmone molecule ppGpp
		Research Genomewide characterization of non-polyadenylated RNAs Li Yang, Michael O Duff, Brenton R Graveley, Gordon G Carmichael, Ling-Ling Chen Genome Biology 2011, 12:R16 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An RNA-seq study of two cell types finds that a significant proportion of mRNAs are not polyadenylated.
		Method A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets Chao Cheng, Koon-Kiu Yan, Kevin Y Yip, Joel Rozowsky, Roger Alexander, Chong Shou, Mark Gerstein Genome Biology 2011, 12:R15 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for analyzing matched RNA-seq and ChIP datasets reveals that expression correlates to histone modifications but not a histone code
		Research Bringing order to protein disorder through comparative genomics and genetic interactions Jeremy Bellay, Sangjo Han, Magali Michaut, TaeHyung Kim, Michael Costanzo, Brenda J Andrews, Charles Boone, Gary D Bader, Chad L Myers, Philip M Kim Genome Biology 2011, 12:R14 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics combined with genetic interaction analyses reveals three distinct functional classes of protein disorder
		Research highlight A Drosophila model for the role of epigenetics in brain function and development Roman M Stilling, André Fischer Genome Biology 2011, 12:103 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic studies in Drosophila give insights into the possible role of epigenetic regulation of gene expression in a human mental retardation syndrome.
		Method Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads Ernest Turro, Shu-Yi Su, Ângela Gonçalves, Lachlan JM Coin, Sylvia Richardson, Alex Lewin Genome Biology 2011, 12:R13 (10 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for estimating isoform-specific expression and allelic imbalance in diploid organisms from RNA-seq data
		Research The role of codon selection in regulation of translation efficiency deduced from synthetic libraries Sivan Navon, Yitzhak Pilpel Genome Biology 2011, 12:R12 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 5’ proximal translation bottlenecks are correlated with high expression levels in an E. coli synthetic gene library
		Method MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data Yiwen Chen, Clifford A Meyer, Tao Liu, Wei Li, Jun S Liu, Xiaole Shirley Liu Genome Biology 2011, 12:R11 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MM-ChIP is a method for integrating cross-platform and between laboratory ChIP-seq or ChIP-chip datasets.
		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 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 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
		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 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
		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 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 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
		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.
		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.
		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 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.
		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
		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.
		Software Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly Kim Wong, Thomas M Keane, James Stalker, David J Adams Genome Biology 2010, 11:R128 (31 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SVMerge is a pipeline combining the outputs of several structural variation detection programs to improve structural variation detection
		Research Novel genes exhibit distinct patterns of function acquisition and network integration John A Capra, Katherine S Pollard, Mona Singh Genome Biology 2010, 11:R127 (27 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes arising de novo from non-coding sequence in yeast have different functions and network properties from those arising from duplication.
		Software ArchAlign: coordinate-free chromatin alignment reveals novel architectures William KM Lai, Michael J Buck Genome Biology 2010, 11:R126 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An algorithm for discovery of chromatin architectures
		Research Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners Peter L Chang, Brian P Dilkes, Michelle McMahon, Luca Comai, Sergey V Nuzhdin Genome Biology 2010, 11:R125 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Arabidopsis suecica homoeolog-specific gene expression has a parent of origin preference
		Research Large scale comparison of global gene expression patterns in human and mouse Xiangqun Zheng-Bradley, Johan Rung, Helen Parkinson, Alvis Brazma Genome Biology 2010, 11:R124 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of all human and mouse arrays deposited in ArrayExpress reveals broadly similar transcription of orthologous genes between species
		Research Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis E Shasha, Gloria M Coruzzi Genome Biology 2010, 11:R123 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene networks downstream of nitrate signaling are characterized with temporal resolution in a transcriptome analysis, including an early response SPL9 hub
		Research Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic Shafagh Al Nadaf, Paul D Waters, Edda Koina, Janine E Deakin, Kristen S Jordan, Jennifer AM Graves Genome Biology 2010, 11:R122 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Incomplete escape from X inactivation in marsupials is revealed by a map of gene expression from the tammar wallaby X chromosome.
		Software The Genomic HyperBrowser: inferential genomics at the sequence level Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi, Eivind Hovig Genome Biology 2010, 11:R121 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel platform for the statistical analysis of sequence-level genomic information.
		Research Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2 Kohta Ikegami, Thea A Egelhofer, Susan Strome, Jason D Lieb Genome Biology 2010, 11:R120 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A modENCODE survey of chromosome interactions with the inner nuclear membrane finds interacting regions are distal and gene sparse
		Comment The long and the short of it Gregory A Petsko Genome Biology 2010, 11:145 (23 December 2010) Full text \| PDF \| PubMed \| Editor’s summary An end of year assessment of potential scientific investments.
		Review From RNA-seq reads to differential expression results Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
		Research highlight Whole-exome sequencing for finding de novo mutations in sporadic mental retardation Peter N Robinson Genome Biology 2010, 11:144 (21 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work has used a family-based approach and whole-exome sequencing to identify de novo mutations in sporadic cases of mental retardation.
		Research highlight Creating a blood line from human skin Michael H Sieweke Genome Biology 2010, 11:143 (20 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Blood cell progenitors with therapeutic potential have been produced directly from human fibroblasts without intermediate pluripotent stem cells.
		Method Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition Andrew Adey, Hilary G Morrison, Asan, Xu Xun, Jacob O Kitzman, Emily H Turner, Bethany Stackhouse, Alexandra P MacKenzie, Nicholas C Caruccio, Xiuqing Zhang, Jay Shendure Genome Biology 2010, 11:R119 (8 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protocols for rapid, low-input sequencing library construction without clean up.
		Meeting report Beyond the Genome: genomics research ten years after the human genome sequence Amanda M Casto, Clara Amid Genome Biology 2010, 11:309 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Beyond the Genome', Boston, USA, 11-13 October 2010.
		Opinion Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology Noam Kaplan, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal Genome Biology 2010, 11:140 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary There is less controversy over whether the preferences of histones for particular sequences determine nucleosome position than has been thought.

	All
		Research Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation Claudia C Weber, Laurence D Hurst Genome Biology 2011, 12:R23 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The conservation of syntenic gene order previously described in yeast is not apparent in D. melanogaster
		Method Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extension to Cufflinks corrects bias in RNA-seq datasets
		Method hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets Todd A Johnson, Yoshihito Niimura, Hiroshi Tanaka, Yusuke Nakamura, Tatsuhiko Tsunoda Genome Biology 2011, 12:R21 (11 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel methods are presented for the detection and analysis of homozygous tracts from genotype data
		Research Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang, Alan Kuo, Xiangjun Tian, William Salerno, Anup Parikh, Christa L Feasley, Eileen Dalin, Hank Tu, Eryong Huang, Kerrie Barry, Erika Lindquist, Harris Shapiro, David Bruce, Jeremy Schmutz, Asaf Salamov, Petra Fey, Pascale Gaudet, Christophe Anjard, M Madan Babu, Siddhartha Basu, Yulia Bushmanova, Hanke van der Wel, Mariko Katoh-Kurasawa, Christopher Dinh, Pedro M Coutinho, Tamao Saito, Marek Elias, Pauline Schaap, Robert R Kay, Bernard Henrissat, Ludwig Eichinger, Francisco Rivero, Nicholas H Putnam, Christopher M West, William F Loomis, Rex L Chisholm, Gad Shaulsky, Joan E Strassmann, David C Queller, Adam Kuspa, Igor V Grigoriev et al. Genome Biology 2011, 12:R20 (28 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Dictyostelium purpureum is reported and compared with that of D. discoideum
		Method Dating the age of admixture via wavelet transform analysis of genome-wide data Irina Pugach, Rostislav Matveyev, Andreas Wollstein, Manfred Kayser, Mark Stoneking Genome Biology 2011, 12:R19 (25 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combination of PCA and wavelet transform analysis defines admixture structure and dates its history
		Comment There is a sanity clause Gregory A Petsko Genome Biology 2011, 12:105 (25 February 2011) Full text \| PDF \| PubMed \| Editor’s summary Supply versus demand part II: will funding basic research lead to medical advances?
		Review The properties and applications of single-molecule DNA sequencing John F Thompson, Patrice M Milos Genome Biology 2011, 12:217 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Single-molecule sequencing works directly from biological samples and generates very long reads, making it well suited for diagnostic and clinical applications.
		Research highlight Piecing together the FTO jigsaw Timothy M Frayling, Ken Ong Genome Biology 2011, 12:104 (24 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two recent studies of the FTO gene provide more information on how it affects body mass index
		Review The domestic dog: man's best friend in the genomic era Adam R Boyko Genome Biology 2011, 12:216 (22 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The tremendous phenotypic diversity of domestic dog breeds, coupled with the availability of dog genome sequences, point to the dog as as an important model organism for complex-trait analysis
		Method Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias
		Correspondence Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses Albert J Vilella, Ewan Birney, Paul Flicek, Javier Herrero Genome Biology 2011, 12:401 (21 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16.
		Research Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli Maarten Vercruysse, Maarten Fauvart, Ann Jans, Serge Beullens, Kristien Braeken, Lore Cloots, Kristof Engelen, Kathleen Marchal, Jan Michiels Genome Biology 2011, 12:R17 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The stress response of Rhizobium etli is dissected through transcriptomics of a mutant that does not synthesize the alarmone molecule ppGpp
		Research Genomewide characterization of non-polyadenylated RNAs Li Yang, Michael O Duff, Brenton R Graveley, Gordon G Carmichael, Ling-Ling Chen Genome Biology 2011, 12:R16 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An RNA-seq study of two cell types finds that a significant proportion of mRNAs are not polyadenylated.
		Method A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets Chao Cheng, Koon-Kiu Yan, Kevin Y Yip, Joel Rozowsky, Roger Alexander, Chong Shou, Mark Gerstein Genome Biology 2011, 12:R15 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for analyzing matched RNA-seq and ChIP datasets reveals that expression correlates to histone modifications but not a histone code
		Research Bringing order to protein disorder through comparative genomics and genetic interactions Jeremy Bellay, Sangjo Han, Magali Michaut, TaeHyung Kim, Michael Costanzo, Brenda J Andrews, Charles Boone, Gary D Bader, Chad L Myers, Philip M Kim Genome Biology 2011, 12:R14 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics combined with genetic interaction analyses reveals three distinct functional classes of protein disorder
		Research highlight A Drosophila model for the role of epigenetics in brain function and development Roman M Stilling, André Fischer Genome Biology 2011, 12:103 (16 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic studies in Drosophila give insights into the possible role of epigenetic regulation of gene expression in a human mental retardation syndrome.
		Method Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads Ernest Turro, Shu-Yi Su, Ângela Gonçalves, Lachlan JM Coin, Sylvia Richardson, Alex Lewin Genome Biology 2011, 12:R13 (10 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for estimating isoform-specific expression and allelic imbalance in diploid organisms from RNA-seq data
		Research The role of codon selection in regulation of translation efficiency deduced from synthetic libraries Sivan Navon, Yitzhak Pilpel Genome Biology 2011, 12:R12 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 5’ proximal translation bottlenecks are correlated with high expression levels in an E. coli synthetic gene library
		Method MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data Yiwen Chen, Clifford A Meyer, Tao Liu, Wei Li, Jun S Liu, Xiaole Shirley Liu Genome Biology 2011, 12:R11 (1 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MM-ChIP is a method for integrating cross-platform and between laboratory ChIP-seq or ChIP-chip datasets.
		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 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 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
		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 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
		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 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 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
		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.
		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.
		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 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.
		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
		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.
		Software Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly Kim Wong, Thomas M Keane, James Stalker, David J Adams Genome Biology 2010, 11:R128 (31 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SVMerge is a pipeline combining the outputs of several structural variation detection programs to improve structural variation detection
		Research Novel genes exhibit distinct patterns of function acquisition and network integration John A Capra, Katherine S Pollard, Mona Singh Genome Biology 2010, 11:R127 (27 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes arising de novo from non-coding sequence in yeast have different functions and network properties from those arising from duplication.
		Software ArchAlign: coordinate-free chromatin alignment reveals novel architectures William KM Lai, Michael J Buck Genome Biology 2010, 11:R126 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An algorithm for discovery of chromatin architectures
		Research Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners Peter L Chang, Brian P Dilkes, Michelle McMahon, Luca Comai, Sergey V Nuzhdin Genome Biology 2010, 11:R125 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Arabidopsis suecica homoeolog-specific gene expression has a parent of origin preference
		Research Large scale comparison of global gene expression patterns in human and mouse Xiangqun Zheng-Bradley, Johan Rung, Helen Parkinson, Alvis Brazma Genome Biology 2010, 11:R124 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of all human and mouse arrays deposited in ArrayExpress reveals broadly similar transcription of orthologous genes between species
		Research Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis E Shasha, Gloria M Coruzzi Genome Biology 2010, 11:R123 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene networks downstream of nitrate signaling are characterized with temporal resolution in a transcriptome analysis, including an early response SPL9 hub
		Research Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic Shafagh Al Nadaf, Paul D Waters, Edda Koina, Janine E Deakin, Kristen S Jordan, Jennifer AM Graves Genome Biology 2010, 11:R122 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Incomplete escape from X inactivation in marsupials is revealed by a map of gene expression from the tammar wallaby X chromosome.
		Software The Genomic HyperBrowser: inferential genomics at the sequence level Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi, Eivind Hovig Genome Biology 2010, 11:R121 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel platform for the statistical analysis of sequence-level genomic information.
		Research Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2 Kohta Ikegami, Thea A Egelhofer, Susan Strome, Jason D Lieb Genome Biology 2010, 11:R120 (23 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A modENCODE survey of chromosome interactions with the inner nuclear membrane finds interacting regions are distal and gene sparse
		Comment The long and the short of it Gregory A Petsko Genome Biology 2010, 11:145 (23 December 2010) Full text \| PDF \| PubMed \| Editor’s summary An end of year assessment of potential scientific investments.
		Review From RNA-seq reads to differential expression results Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
		Research highlight Whole-exome sequencing for finding de novo mutations in sporadic mental retardation Peter N Robinson Genome Biology 2010, 11:144 (21 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work has used a family-based approach and whole-exome sequencing to identify de novo mutations in sporadic cases of mental retardation.
		Research highlight Creating a blood line from human skin Michael H Sieweke Genome Biology 2010, 11:143 (20 December 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Blood cell progenitors with therapeutic potential have been produced directly from human fibroblasts without intermediate pluripotent stem cells.
		Method Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition Andrew Adey, Hilary G Morrison, Asan, Xu Xun, Jacob O Kitzman, Emily H Turner, Bethany Stackhouse, Alexandra P MacKenzie, Nicholas C Caruccio, Xiuqing Zhang, Jay Shendure Genome Biology 2010, 11:R119 (8 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protocols for rapid, low-input sequencing library construction without clean up.
		Meeting report Beyond the Genome: genomics research ten years after the human genome sequence Amanda M Casto, Clara Amid Genome Biology 2010, 11:309 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Beyond the Genome', Boston, USA, 11-13 October 2010.
		Opinion Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology Noam Kaplan, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal Genome Biology 2010, 11:140 (30 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary There is less controversy over whether the preferences of histones for particular sequences determine nucleosome position than has been thought.