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		Research High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans Arun K Ramani, Andrew C Nelson, Philipp Kapranov, Ian Bell, Thomas R Gingeras, Andrew G Fraser Genome Biology 2009, 10:R101 (24 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high-resolution transcriptome of wild-type and nonsense-mediated decay (NMD) defective C. elegans during development reveals insights into the NMD pathway and it’s role in development.
		Research Many LINE1 elements contribute to the transcriptome of human somatic cells Sanjida H Rangwala, Lili Zhang, Haig H Kazazian Genome Biology 2009, 10:R100 (22 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome.
		Research A cell surface interaction network of neural leucine-rich repeat receptors Christian Söllner, Gavin J Wright Genome Biology 2009, 10:R99 (18 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A network of Zebrafish extracellular neuroreceptor interactions are revealed using AVEXIS, a highly stringent interaction assay.
		Software Simultaneous alignment of short reads against multiple genomes Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel Genome Biology 2009, 10:R98 (17 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New software for the alignment of short-read sequence data to multiple genomes allows identification of polymorphisms that cannot be identified by alignment to a single reference genome.
		Research Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.
		Research Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Santiago F Elena Genome Biology 2009, 10:R96 (15 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Arabidopsis thaliana transcriptional network reveals regulatory mechanisms for the control of genes related to stress adaptation.
		Research Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae Sandra Merz, Benedikt Westermann Genome Biology 2009, 10:R95 (14 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide deletion mutant analysis in budding yeast reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis.
		Method De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones Genome Biology 2009, 10:R94 (11 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data
		Research Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection Nicoletta Bivi, Milena Romanello, Richard Harrison, Ian Clarke, David C Hoyle, Luigi Moro, Fulvia Ortolani, Antonella Bonetti, Franco Quadrifoglio, Gianluca Tell, Daniela Delneri Genome Biology 2009, 10:R93 (10 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Growth competition assays using barcoded yeast deletion-mutants reveal the molecular targets of nitrogen containing bisphosphonates used for the treatment of bone cancers and osteoporosis.
		Research A global survey identifies novel upstream components of the Ath5 neurogenic network Marcel Souren, Juan Martinez-Morales, Panagiota Makri, Beate Wittbrodt, Joachim Wittbrodt Genome Biology 2009, 10:R92 (7 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Regulators of vertebrate Ath5 expression were identified by high-throughput screening; extending the current gene regulatory model network controlling retinal neurogenesis.
		Method Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network Bolan Linghu, Evan S Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi Genome Biology 2009, 10:R91 (3 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes
		Minireview Predicting drug side-effects by chemical systems biology Nicholas P Tatonetti, Tianyun Liu, Russ B Altman Genome Biology 2009, 10:238 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chemical systems biology approaches can explain unexpected observations of drug inefficacy or side-effects.
		Minireview The promise and reality of personal genomics Bryndis Yngvadottir, Daniel G MacArthur, Hanjun Jin, Chris Tyler-Smith Genome Biology 2009, 10:237 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The second personal genome sequence of a Korean tells something about genetic ancestry but still little of medical relevance.
		Research mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer Chao Cheng, Xuping Fu, Pedro Alves, Mark Gerstein Genome Biology 2009, 10:R90 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers
		Research Nucleosome deposition and DNA methylation at coding region boundaries Jung Choi, Jae-Bum Bae, Jaemyun Lyu, Tae-Yoon Kim, Young-Joon Kim Genome Biology 2009, 10:R89 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nucleosomes and methylation have been observed to peak at both ends of protein coding units in a genome-wide survey.
		Meeting report New tricks for an old-favorite model Charalampos Rallis Genome Biology 2009, 10:315 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 24th International Conference on Yeast Genetics and Molecular Biology, Manchester, UK, 19-24 July 2009.
		Comment Nation of twits Gregory A Petsko Genome Biology 2009, 10:110 (28 August 2009) Abstract \| Full text \| PDF \| Editor’s summary Gregory Petsko bemoans the rise of the Twittering classes.
		Method Assisted assembly: how to improve a de novo genome assembly by using related species Sante Gnerre, Eric S Lander, Kerstin Lindblad-Toh, David B Jaffe Genome Biology 2009, 10:R88 (27 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is described for improving low sequence coverage genome assemblies
		Research Depletion of T-cell intracellular antigen proteins promotes cell proliferation Raquel Reyes, José Alcalde, José M Izquierdo Genome Biology 2009, 10:R87 (26 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptome of TIA-1/TIAR-depleted cells indicates roles in inflammation, cell-cell signaling, immune suppression, angiogenesis, metabolism and cell proliferation.
		Protein family review The claudins Madhu Lal-Nag, Patrice J Morin Genome Biology 2009, 10:235 (26 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Claudins are crucial components of tight junctions and are important in regulating permeability and maintaining cell polarity in cell sheets.
		Minireview Reprogramming the epigenome during germline and seed development Mark A Johnson, Judith Bender Genome Biology 2009, 10:232 (24 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene silencing by DNA methylation and small RNAs is globally reconfigured during gametogenesis in Arabidopsis.
		Software Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes Xianjun Dong, David Fredman, Boris Lenhard Genome Biology 2009, 10:R86 (21 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Synorth is a web resource for exploring and categorizing the syntenic relationships in gene regulatory blocks across multiple genomes.
		Research Community-wide analysis of microbial genome sequence signatures Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members.
		Software MouseCyc: a curated biochemical pathways database for the laboratory mouse Alexei V Evsikov, Mary E Dolan, Michael P Genrich, Emily Patek, Carol J Bult Genome Biology 2009, 10:R84 (14 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MouseCyc is a database of curated metabolic pathways for the laboratory mouse.
		Software Improved base calling for the Illumina Genome Analyzer using machine learning strategies Martin Kircher, Udo Stenzel, Janet Kelso Genome Biology 2009, 10:R83 (14 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ibis is an accurate, fast and easy-to-use base caller for the Illumina Genome Analyzer that reduces error rates and increases output of usable reads.
		Meeting report Malaria genomics meets drug-resistance phenotyping in the field Paul Hunt, Bronwyn MacInnis, Cally Roper Genome Biology 2009, 10:314 (11 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the 2nd Wellcome Trust Conference on Genomic Epidemiology of Malaria, Hinxton, UK, 14-17 June 2009.
		Minireview Virus-mediated mRNA decay by hyperadenylation Kevin J Sokoloski, Emily L Chaskey, Jeffrey Wilusz Genome Biology 2009, 10:234 (11 August 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Degradation of cellular mRNAs in Kaposi's sarcoma-associated herpesvirus infection is associated with hyperadenylation of transcripts.
		Research Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery Sebastian H Eck, Anna Benet-Pagès, Krzysztof Flisikowski, Thomas Meitinger, Ruedi Fries, Tim M Strom Genome Biology 2009, 10:R82 (6 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The next generation sequencing of a single cow genome with low-to-medium coverage has revealed 2.44 million new SNPs.
		Meeting report Phenotypic variation meets systems biology Teresa M Przytycka Genome Biology 2009, 10:313 (3 August 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 18th Annual Growth Factor and Signal Transduction Symposium, Ames, USA, 11-14 June 2009.
		Minireview New levels of sophistication in the transcriptional landscape of bacteria Arnoud HM van Vliet, Brendan W Wren Genome Biology 2009, 10:233 (3 August 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Previously unanticipated roles of noncoding and antisense RNAs give the regulation of gene expression in bacteria an extra layer of complexity.
		Research Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine Katharine J Webb, William HJ Norton, Dietrich Trümbach, Annemarie H Meijer, Jovica Ninkovic, Stefanie Topp, Daniel Heck, Carsten Marr, Wolfgang Wurst, Fabian J Theis, Herman P Spaink, Laure Bally-Cuif Genome Biology 2009, 10:R81 (31 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome analysis of a zebrafish mutant that does not respond to amphetamine identifies a network of coordinated gene regulation that may underlie the susceptibility to addiction.
		Minireview Amphetamine recapitulates developmental programs in the zebrafish Jean Lud Cadet Genome Biology 2009, 10:231 (31 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The zebrafish as a model for drug addiction.
		Comment Wimps? What wimps? Gregory A Petsko Genome Biology 2009, 10:109 (29 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Older scientists should give researchers starting out on their careers more support and encouragement.
		Meeting report Defining and targeting transcription factors in cancer Aisling M Redmond, Jason S Carroll Genome Biology 2009, 10:311 (24 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the Keystone Symposium on Molecular and Cellular Biology, 'Deregulation of transcription in cancer: controlling cell fate decisions', Killarney, Ireland, 21-26 July 2009.
		Research Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen Genome Biology 2009, 10:R80 (23 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.
		Method Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen Genome Biology 2009, 10:R79 (22 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.
		Meeting report microRNAs mature with help from cancer biology Zain Paroo, Alexander Pertsemlidis Genome Biology 2009, 10:310 (20 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium on Molecular and Cellular Biology, 'MicroRNA and Cancer', Keystone, Colorado, USA, 10-15 June 2009.
		Research Identification and characterization of novel amphioxus microRNAs by Solexa sequencing Xi Chen, Qibin Li, Jin Wang, Xing Guo, Xiangrui Jiang, Zhiji Ren, Chunyue Weng, Guoxun Sun, Xiuqiang Wang, Yaping Liu, Lijia Ma, Jun-Yuan Chen, Jun Wang, Ke Zen, Junfeng Zhang, Chen-Yu Zhang Genome Biology 2009, 10:R78 (17 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of amphioxus miRNAs suggests an expansion of miRNAs played a key role in the evolution of chordates to vertebrates
		Method Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies Essi Laajala, Tero Aittokallio, Riitta Lahesmaa, Laura L Elo Genome Biology 2009, 10:R77 (16 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel statistical procedure is presented that uses probe-level information on Affymetrix exon arrays to detect differential splicing.
		Research A transcriptional network associated with natural variation in Drosophila aggressive behavior Alexis C Edwards, Julien F Ayroles, Eric A Stone, Mary Carbone, Richard F Lyman, Trudy FC Mackay Genome Biology 2009, 10:R76 (16 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide screen of inbred Drosophila lines together with transcriptional network modeling reveals insights into the genetic bases of heritable aggression.
		Review How to build a paraspeckle Yasnory TF Sasaki, Tetsuro Hirose Genome Biology 2009, 10:227 (16 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Noncoding RNAs have recently been identified as essential components of the enigmatic nuclear suborganelles called paraspeckles.
		Research Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans Vaishali Katju, James C Farslow, Ulfar Bergthorsson Genome Biology 2009, 10:R75 (13 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differences between yeast and worm duplicates result from differences in mechanisms of duplication and effective population size.
		Research Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals Shanye Yin, Ping Wang, Wenjun Deng, Hancheng Zheng, Landian Hu, Laurence D Hurst, Xiangyin Kong Genome Biology 2009, 10:R74 (13 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of gene expression variation in autosomal and X-linked genes reveals that high transcriptional noise is not a necessary consequence of haploid expression.
		Minireview A Candida-based view of fungal sex and pathogenesis Richard J Bennett Genome Biology 2009, 10:230 (10 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparisons of the genomes of multiple Candida species reveals several shared traits associated with pathogenesis, but striking differences in sexual reproduction.
		Research Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler Genome Biology 2009, 10:R73 (9 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions.
		Minireview Floral induction and monocarpic versus polycarpic life histories Richard Amasino Genome Biology 2009, 10:228 (2 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Subtle differences in control of flowering-induction genes might contribute to the annual versus perennial growth habits of related plant species.
		Research Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons Rui Liu, Sridhar Hannenhalli, Maja Bucan Genome Biology 2009, 10:R72 (1 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative strategy of comparative genomics, experimental and computational approaches reveals aspects of a regulatory network controlling neuronal-specific expression in presynaptic neurons.
		Minireview A passport to neurotransmitter identity Marten P Smidt, J Peter H Burbach Genome Biology 2009, 10:229 (1 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A conserved gene regulatory circuit for dopaminergic neuron differentiation.
		Research Genomic linkage map of the human blood fluke Schistosoma mansoni Charles D Criscione, Claudia LL Valentim, Hirohisa Hirai, Philip T LoVerde, Timothy JC Anderson Genome Biology 2009, 10:R71 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genetic linkage map of Schistosoma mansoni reveals insights into higher female recombination, confirms ZW inheritance patterns and recombination hotspots.
		Minireview Genetics and genomics converge on the human blood fluke Andy Tait Genome Biology 2009, 10:225 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genetic map of the human infective blood fluke Schistosoma mansoni offers new approaches for research on this important parasitic worm.

	All
		Research High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans Arun K Ramani, Andrew C Nelson, Philipp Kapranov, Ian Bell, Thomas R Gingeras, Andrew G Fraser Genome Biology 2009, 10:R101 (24 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high-resolution transcriptome of wild-type and nonsense-mediated decay (NMD) defective C. elegans during development reveals insights into the NMD pathway and it’s role in development.
		Research Many LINE1 elements contribute to the transcriptome of human somatic cells Sanjida H Rangwala, Lili Zhang, Haig H Kazazian Genome Biology 2009, 10:R100 (22 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome.
		Research A cell surface interaction network of neural leucine-rich repeat receptors Christian Söllner, Gavin J Wright Genome Biology 2009, 10:R99 (18 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A network of Zebrafish extracellular neuroreceptor interactions are revealed using AVEXIS, a highly stringent interaction assay.
		Software Simultaneous alignment of short reads against multiple genomes Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel Genome Biology 2009, 10:R98 (17 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New software for the alignment of short-read sequence data to multiple genomes allows identification of polymorphisms that cannot be identified by alignment to a single reference genome.
		Research Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function James C Costello, Mehmet M Dalkilic, Scott M Beason, Jeff R Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D Eads, Justen R Andrews Genome Biology 2009, 10:R97 (16 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes.
		Research Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Santiago F Elena Genome Biology 2009, 10:R96 (15 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An Arabidopsis thaliana transcriptional network reveals regulatory mechanisms for the control of genes related to stress adaptation.
		Research Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae Sandra Merz, Benedikt Westermann Genome Biology 2009, 10:R95 (14 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide deletion mutant analysis in budding yeast reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis.
		Method De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra, Richard C Hamelin, Jörg Bohlmann, Colette Breuil, Steven JM Jones Genome Biology 2009, 10:R94 (11 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data
		Research Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection Nicoletta Bivi, Milena Romanello, Richard Harrison, Ian Clarke, David C Hoyle, Luigi Moro, Fulvia Ortolani, Antonella Bonetti, Franco Quadrifoglio, Gianluca Tell, Daniela Delneri Genome Biology 2009, 10:R93 (10 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Growth competition assays using barcoded yeast deletion-mutants reveal the molecular targets of nitrogen containing bisphosphonates used for the treatment of bone cancers and osteoporosis.
		Research A global survey identifies novel upstream components of the Ath5 neurogenic network Marcel Souren, Juan Martinez-Morales, Panagiota Makri, Beate Wittbrodt, Joachim Wittbrodt Genome Biology 2009, 10:R92 (7 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Regulators of vertebrate Ath5 expression were identified by high-throughput screening; extending the current gene regulatory model network controlling retinal neurogenesis.
		Method Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network Bolan Linghu, Evan S Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi Genome Biology 2009, 10:R91 (3 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes
		Minireview Predicting drug side-effects by chemical systems biology Nicholas P Tatonetti, Tianyun Liu, Russ B Altman Genome Biology 2009, 10:238 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chemical systems biology approaches can explain unexpected observations of drug inefficacy or side-effects.
		Minireview The promise and reality of personal genomics Bryndis Yngvadottir, Daniel G MacArthur, Hanjun Jin, Chris Tyler-Smith Genome Biology 2009, 10:237 (2 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The second personal genome sequence of a Korean tells something about genetic ancestry but still little of medical relevance.
		Research mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer Chao Cheng, Xuping Fu, Pedro Alves, Mark Gerstein Genome Biology 2009, 10:R90 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers
		Research Nucleosome deposition and DNA methylation at coding region boundaries Jung Choi, Jae-Bum Bae, Jaemyun Lyu, Tae-Yoon Kim, Young-Joon Kim Genome Biology 2009, 10:R89 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nucleosomes and methylation have been observed to peak at both ends of protein coding units in a genome-wide survey.
		Meeting report New tricks for an old-favorite model Charalampos Rallis Genome Biology 2009, 10:315 (1 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 24th International Conference on Yeast Genetics and Molecular Biology, Manchester, UK, 19-24 July 2009.
		Comment Nation of twits Gregory A Petsko Genome Biology 2009, 10:110 (28 August 2009) Abstract \| Full text \| PDF \| Editor’s summary Gregory Petsko bemoans the rise of the Twittering classes.
		Method Assisted assembly: how to improve a de novo genome assembly by using related species Sante Gnerre, Eric S Lander, Kerstin Lindblad-Toh, David B Jaffe Genome Biology 2009, 10:R88 (27 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is described for improving low sequence coverage genome assemblies
		Research Depletion of T-cell intracellular antigen proteins promotes cell proliferation Raquel Reyes, José Alcalde, José M Izquierdo Genome Biology 2009, 10:R87 (26 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptome of TIA-1/TIAR-depleted cells indicates roles in inflammation, cell-cell signaling, immune suppression, angiogenesis, metabolism and cell proliferation.
		Protein family review The claudins Madhu Lal-Nag, Patrice J Morin Genome Biology 2009, 10:235 (26 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Claudins are crucial components of tight junctions and are important in regulating permeability and maintaining cell polarity in cell sheets.
		Minireview Reprogramming the epigenome during germline and seed development Mark A Johnson, Judith Bender Genome Biology 2009, 10:232 (24 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene silencing by DNA methylation and small RNAs is globally reconfigured during gametogenesis in Arabidopsis.
		Software Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes Xianjun Dong, David Fredman, Boris Lenhard Genome Biology 2009, 10:R86 (21 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Synorth is a web resource for exploring and categorizing the syntenic relationships in gene regulatory blocks across multiple genomes.
		Research Community-wide analysis of microbial genome sequence signatures Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members.
		Software MouseCyc: a curated biochemical pathways database for the laboratory mouse Alexei V Evsikov, Mary E Dolan, Michael P Genrich, Emily Patek, Carol J Bult Genome Biology 2009, 10:R84 (14 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MouseCyc is a database of curated metabolic pathways for the laboratory mouse.
		Software Improved base calling for the Illumina Genome Analyzer using machine learning strategies Martin Kircher, Udo Stenzel, Janet Kelso Genome Biology 2009, 10:R83 (14 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ibis is an accurate, fast and easy-to-use base caller for the Illumina Genome Analyzer that reduces error rates and increases output of usable reads.
		Meeting report Malaria genomics meets drug-resistance phenotyping in the field Paul Hunt, Bronwyn MacInnis, Cally Roper Genome Biology 2009, 10:314 (11 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report of the 2nd Wellcome Trust Conference on Genomic Epidemiology of Malaria, Hinxton, UK, 14-17 June 2009.
		Minireview Virus-mediated mRNA decay by hyperadenylation Kevin J Sokoloski, Emily L Chaskey, Jeffrey Wilusz Genome Biology 2009, 10:234 (11 August 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Degradation of cellular mRNAs in Kaposi's sarcoma-associated herpesvirus infection is associated with hyperadenylation of transcripts.
		Research Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery Sebastian H Eck, Anna Benet-Pagès, Krzysztof Flisikowski, Thomas Meitinger, Ruedi Fries, Tim M Strom Genome Biology 2009, 10:R82 (6 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The next generation sequencing of a single cow genome with low-to-medium coverage has revealed 2.44 million new SNPs.
		Meeting report Phenotypic variation meets systems biology Teresa M Przytycka Genome Biology 2009, 10:313 (3 August 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 18th Annual Growth Factor and Signal Transduction Symposium, Ames, USA, 11-14 June 2009.
		Minireview New levels of sophistication in the transcriptional landscape of bacteria Arnoud HM van Vliet, Brendan W Wren Genome Biology 2009, 10:233 (3 August 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Previously unanticipated roles of noncoding and antisense RNAs give the regulation of gene expression in bacteria an extra layer of complexity.
		Research Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine Katharine J Webb, William HJ Norton, Dietrich Trümbach, Annemarie H Meijer, Jovica Ninkovic, Stefanie Topp, Daniel Heck, Carsten Marr, Wolfgang Wurst, Fabian J Theis, Herman P Spaink, Laure Bally-Cuif Genome Biology 2009, 10:R81 (31 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptome analysis of a zebrafish mutant that does not respond to amphetamine identifies a network of coordinated gene regulation that may underlie the susceptibility to addiction.
		Minireview Amphetamine recapitulates developmental programs in the zebrafish Jean Lud Cadet Genome Biology 2009, 10:231 (31 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The zebrafish as a model for drug addiction.
		Comment Wimps? What wimps? Gregory A Petsko Genome Biology 2009, 10:109 (29 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Older scientists should give researchers starting out on their careers more support and encouragement.
		Meeting report Defining and targeting transcription factors in cancer Aisling M Redmond, Jason S Carroll Genome Biology 2009, 10:311 (24 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the Keystone Symposium on Molecular and Cellular Biology, 'Deregulation of transcription in cancer: controlling cell fate decisions', Killarney, Ireland, 21-26 July 2009.
		Research Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen Genome Biology 2009, 10:R80 (23 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.
		Method Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen Genome Biology 2009, 10:R79 (22 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.
		Meeting report microRNAs mature with help from cancer biology Zain Paroo, Alexander Pertsemlidis Genome Biology 2009, 10:310 (20 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium on Molecular and Cellular Biology, 'MicroRNA and Cancer', Keystone, Colorado, USA, 10-15 June 2009.
		Research Identification and characterization of novel amphioxus microRNAs by Solexa sequencing Xi Chen, Qibin Li, Jin Wang, Xing Guo, Xiangrui Jiang, Zhiji Ren, Chunyue Weng, Guoxun Sun, Xiuqiang Wang, Yaping Liu, Lijia Ma, Jun-Yuan Chen, Jun Wang, Ke Zen, Junfeng Zhang, Chen-Yu Zhang Genome Biology 2009, 10:R78 (17 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of amphioxus miRNAs suggests an expansion of miRNAs played a key role in the evolution of chordates to vertebrates
		Method Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies Essi Laajala, Tero Aittokallio, Riitta Lahesmaa, Laura L Elo Genome Biology 2009, 10:R77 (16 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel statistical procedure is presented that uses probe-level information on Affymetrix exon arrays to detect differential splicing.
		Research A transcriptional network associated with natural variation in Drosophila aggressive behavior Alexis C Edwards, Julien F Ayroles, Eric A Stone, Mary Carbone, Richard F Lyman, Trudy FC Mackay Genome Biology 2009, 10:R76 (16 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide screen of inbred Drosophila lines together with transcriptional network modeling reveals insights into the genetic bases of heritable aggression.
		Review How to build a paraspeckle Yasnory TF Sasaki, Tetsuro Hirose Genome Biology 2009, 10:227 (16 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Noncoding RNAs have recently been identified as essential components of the enigmatic nuclear suborganelles called paraspeckles.
		Research Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans Vaishali Katju, James C Farslow, Ulfar Bergthorsson Genome Biology 2009, 10:R75 (13 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differences between yeast and worm duplicates result from differences in mechanisms of duplication and effective population size.
		Research Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals Shanye Yin, Ping Wang, Wenjun Deng, Hancheng Zheng, Landian Hu, Laurence D Hurst, Xiangyin Kong Genome Biology 2009, 10:R74 (13 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of gene expression variation in autosomal and X-linked genes reveals that high transcriptional noise is not a necessary consequence of haploid expression.
		Minireview A Candida-based view of fungal sex and pathogenesis Richard J Bennett Genome Biology 2009, 10:230 (10 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparisons of the genomes of multiple Candida species reveals several shared traits associated with pathogenesis, but striking differences in sexual reproduction.
		Research Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler Genome Biology 2009, 10:R73 (9 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions.
		Minireview Floral induction and monocarpic versus polycarpic life histories Richard Amasino Genome Biology 2009, 10:228 (2 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Subtle differences in control of flowering-induction genes might contribute to the annual versus perennial growth habits of related plant species.
		Research Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons Rui Liu, Sridhar Hannenhalli, Maja Bucan Genome Biology 2009, 10:R72 (1 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative strategy of comparative genomics, experimental and computational approaches reveals aspects of a regulatory network controlling neuronal-specific expression in presynaptic neurons.
		Minireview A passport to neurotransmitter identity Marten P Smidt, J Peter H Burbach Genome Biology 2009, 10:229 (1 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A conserved gene regulatory circuit for dopaminergic neuron differentiation.
		Research Genomic linkage map of the human blood fluke Schistosoma mansoni Charles D Criscione, Claudia LL Valentim, Hirohisa Hirai, Philip T LoVerde, Timothy JC Anderson Genome Biology 2009, 10:R71 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genetic linkage map of Schistosoma mansoni reveals insights into higher female recombination, confirms ZW inheritance patterns and recombination hotspots.
		Minireview Genetics and genomics converge on the human blood fluke Andy Tait Genome Biology 2009, 10:225 (30 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genetic map of the human infective blood fluke Schistosoma mansoni offers new approaches for research on this important parasitic worm.