Genome Biology | Volume 10 Issue 7

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 10 Issue 7
	Comment
	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.
	Review
	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.
	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.
	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.
	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.
	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.
	Report
	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.
	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
	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.
	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.
	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.
	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 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.
	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
	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.
	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.
	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.
	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.

	Volume 10 Issue 7
	Comment
	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.
	Review
	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.
	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.
	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.
	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.
	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.
	Report
	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.
	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
	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.
	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.
	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.
	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 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.
	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
	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.
	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.
	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.
	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.

Explore Genome Biology

Articles

Volume 10 Issue 7

Comment

Review

Report

Research