Genome Biology | Volume 5 Issue 2

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	Volume 5 Issue 2
	Comment
	Comment Bad chemistry Gregory A Petsko Genome Biology 2004, 5:102 (2 February 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary General chemistry courses haven't changed significantly in forty years. Because most basic chemistry students are premedical students, medical schools have enormous influence and could help us start all over again to create undergraduate chemistry education that works.
	Review
	Protein family review Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes Liam P Keegan, Anne Leroy, Duncan Sproul, Mary A O'Connell Genome Biology 2004, 5:209 (2 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Adenosine deaminases acting on RNA (ADARs), which are found in animals but are not known in other organisms, deaminate adenosines site-specifically within the coding sequences of transcripts encoding ion-channel subunits, increasing the diversity of these proteins in the central nervous system.
	Minireview Rewiring the transcriptional regulatory circuits of cells Devin R Scannell, Ken Wolfe Genome Biology 2004, 5:206 (29 January 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New data from yeast species show that both changing the cis-acting DNA elements in promoters, and replacing the trans-acting regulatory proteins can regulate gene expression.
	Minireview The diversity of endothelial cells: a challenge for therapeutic angiogenesis Edward M Conway, Peter Carmeliet Genome Biology 2004, 5:207 (29 January 2004) Abstract \| Full text \| PDF \| Editor’s summary Molecular characterization of endothelial-cell diversity will facilitate the development of novel, highly specific and safe therapies for many diseases.
	Minireview Spreading silence with Sid Peter van Roessel, Andrea H Brand Genome Biology 2004, 5:208 (30 January 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A membrane channel, encoded by the gene sid-1, is responsible for the spreading of RNA interference between cells in plants and in Caenorhabditis elegans.
	Report
	Paper report Articles selected by Faculty of 1000: Geobacter sulfurreducens genome sequence; studying protein-protein interactions in planta; screening peptoid libraries; human protein reference database; cell-type control in Candida albicans Genome Biology 2004, 5:311 (13 January 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the Geobacter sulfurreducens genome sequence, studying protein-protein interactions in planta, screening peptoid libraries, a human protein reference database and a study of the circuitry underlying cell-type control in Candida albicans.
	Paper report Articles selected by Faculty of 1000: transcriptome of Plasmodium falciparum; species-specific proteomic signatures; predicting protein subcellular localization; in vivo expression profiling of Borrelia burgdorferi; cell fate during Arabidopsis embryogenesis Genome Biology 2004, 5:312 (27 January 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the transcriptome of Plasmodium falciparum, species- and phyla-specific proteomic signatures, predicting protein subcellular localization, in vivo expression profiling of Borrelia burgdorferi in the central nervous system of non-human primates, cell fate decisions during early embryonic patterning in Arabidopsis .
	Meeting report The post-genomic era for a select few Paul Cliften Genome Biology 2004, 5:308 (15 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report of the 4th Colmar Scientific Symposium 'Biology in the Post-genomic Era', Colmar, France, 16-17 October 2003.
	Meeting report Functional genomics: strict tempo and hierarchical vocabularies Thomas Preiss Genome Biology 2004, 5:307 (16 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Comparative and Functional Genomics Workshop, Hinxton, UK, 2-5 November 2003.
	Meeting report Making sense of lung-cancer gene-expression profiles Dennis A Wigle, Ming Tsao, Igor Jurisica Genome Biology 2004, 5:309 (30 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Critical Assessment of Microarray Data Analysis (CAMDA'03) meeting and competition, Durham, USA, 12-14 November 2003.
	Meeting report Mouse genomics gets the royal treatment F Buaas Genome Biology 2004, 5:310 (30 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Genetics Society autumn meeting 'The mouse: genetics and genome', The Royal Society, London, UK, 14 November 2003.
	Deposited research article Extracellular genomic DNA protects mice against radiation and chemical mutagens Leonid A Yakubov, Nelly A Popova, Valery P Nikolin, Dmitry V Semenov, Sergei S Bogachev, Irina N Oskina Genome Biology 2003, 5:P3 (30 December 2003) Abstract \| Full text \| PDF \| Editor’s summary DNA fragments mutated by irradiation or chemical mutagens may be released by dying cells and incorporated into the genome of healthy cells, thereby inducing genomic instability. We show that injection of normal mouse DNA, but not human DNA, into lethally irradiated mice dramatically increased their survival.
	Deposited research article A statistical approach predicts human microRNA targets Neil R Smalheiser, Vetle I Torvik Genome Biology 2004, 5:P4 (14 January 2004) Abstract \| Full text \| PDF \| Editor’s summary We carried out a population-wide statistical analysis of how human microRNAs interact complementarily with human mRNAs. The 72 candidate mRNA targets identified predict a significant number of well-known and novel human genes that warrant experimental validation.
	Deposited research article Computational identification of microRNA targets Nikolaus Rajewsky, Nicholas D Socci Genome Biology 2004, 5:P5 (14 January 2004) Abstract \| Full text \| PDF \| Editor’s summary We present a new computational method to identify microRNA target sites that incorporates both kinetic and thermodynamic components of target recognition.
	Deposited research article Prediction for Target Sites of Small Interfering RNA Duplexes in SARS Coronavirus Fengmin Ji, Liaofu Luo Genome Biology 2004, 5:P6 (16 January 2004) Abstract \| Full text \| PDF \| Editor’s summary RNA interference is used for SARS-related pharmaceutical research and development. Using a bioinformatic method twenty seven, 21-25-base sequence segments in the SARS-coronavirus genome are predicted as the optimal target sites of small interfering RNA duplexes.
	Research news Rita Colwell leaves NSF Maria Anderson Genome Biology 2004, 5:spotlight-20040216-03 (16 February 2004) Abstract \| Full text \| Editor’s summary National Institute of Standards and Technology director Arden Bement to be acting director
	Research news European boost for structural genomics Genome Biology Genome Biology 2004, 5:spotlight-20040216-01 (16 February 2004) Abstract \| Full text \| Editor’s summary The European Commission has given 10 million euros (approximately US $12.5 million) to the European Molecular Biology Laboratory (EMBL) and over 20 partners from 9 European countries, to create BIOXHIT, a "Biocrystallography on a Highly Integrated Technology Platform" project to expedite structural genomics.
	Research news Bioinformatics network cheered Andrew Scott Genome Biology 2004, 5:spotlight-20040216-02 (16 February 2004) Abstract \| Full text \| Editor’s summary European Virtual Institute for Genome Annotation will have a global impact
	Research
	Research A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale Genome Biology 2004, 5:R7 (15 January 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes.
	Research Genome-wide investigation of light and carbon signaling interactions in Arabidopsis Karen E Thum, Michael J Shin, Peter M Palenchar, Andrei Kouranov, Gloria M Coruzzi Genome Biology 2004, 5:R10 (27 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This study uses microarrays to identify Arabidopsis thaliana genes involved in light and carbon-signaling pathways. The data are classified and regulatory motifs in the promoters of co-regulated genes predicted.
	Research In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection Kathleen Marchal, Sigrid De Keersmaecker, Pieter Monsieurs, Nadja van Boxel, Karen Lemmens, Gert Thijs, Jos Vanderleyden, Bart De Moor Genome Biology 2004, 5:R9 (29 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide computational screen for targets of the PmrA transcription factor in Salmonella typhimurium has identified novel target genes.
	Research An unappreciated role for RNA surveillance R Tyler Hillman, Richard E Green, Steven E Brenner Genome Biology 2004, 5:R8 (2 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Following the hypothesis that the public databases contain cloned mRNAs that would be degraded in vivo by the nonsense-mediated mRNA decay mechanism, 144 isoform sequences deposited in SWISS-PROT have been identified that derive from mRNAs with premature termination codons
	Method Predicting specificity in bZIP coiled-coil protein interactions Jessica H Fong, Amy E Keating, Mona Singh Genome Biology 2004, 5:R11 (16 January 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A method to predict interactions between coiled-coil dominas, which is based on sequence and biophysical data.
	Software Versatile and open software for comparing large genomes Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg Genome Biology 2004, 5:R12 (30 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.

	Volume 5 Issue 2
	Comment
	Comment Bad chemistry Gregory A Petsko Genome Biology 2004, 5:102 (2 February 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary General chemistry courses haven't changed significantly in forty years. Because most basic chemistry students are premedical students, medical schools have enormous influence and could help us start all over again to create undergraduate chemistry education that works.
	Review
	Protein family review Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes Liam P Keegan, Anne Leroy, Duncan Sproul, Mary A O'Connell Genome Biology 2004, 5:209 (2 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Adenosine deaminases acting on RNA (ADARs), which are found in animals but are not known in other organisms, deaminate adenosines site-specifically within the coding sequences of transcripts encoding ion-channel subunits, increasing the diversity of these proteins in the central nervous system.
	Minireview Rewiring the transcriptional regulatory circuits of cells Devin R Scannell, Ken Wolfe Genome Biology 2004, 5:206 (29 January 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New data from yeast species show that both changing the cis-acting DNA elements in promoters, and replacing the trans-acting regulatory proteins can regulate gene expression.
	Minireview The diversity of endothelial cells: a challenge for therapeutic angiogenesis Edward M Conway, Peter Carmeliet Genome Biology 2004, 5:207 (29 January 2004) Abstract \| Full text \| PDF \| Editor’s summary Molecular characterization of endothelial-cell diversity will facilitate the development of novel, highly specific and safe therapies for many diseases.
	Minireview Spreading silence with Sid Peter van Roessel, Andrea H Brand Genome Biology 2004, 5:208 (30 January 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A membrane channel, encoded by the gene sid-1, is responsible for the spreading of RNA interference between cells in plants and in Caenorhabditis elegans.
	Report
	Paper report Articles selected by Faculty of 1000: Geobacter sulfurreducens genome sequence; studying protein-protein interactions in planta; screening peptoid libraries; human protein reference database; cell-type control in Candida albicans Genome Biology 2004, 5:311 (13 January 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the Geobacter sulfurreducens genome sequence, studying protein-protein interactions in planta, screening peptoid libraries, a human protein reference database and a study of the circuitry underlying cell-type control in Candida albicans.
	Paper report Articles selected by Faculty of 1000: transcriptome of Plasmodium falciparum; species-specific proteomic signatures; predicting protein subcellular localization; in vivo expression profiling of Borrelia burgdorferi; cell fate during Arabidopsis embryogenesis Genome Biology 2004, 5:312 (27 January 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the transcriptome of Plasmodium falciparum, species- and phyla-specific proteomic signatures, predicting protein subcellular localization, in vivo expression profiling of Borrelia burgdorferi in the central nervous system of non-human primates, cell fate decisions during early embryonic patterning in Arabidopsis .
	Meeting report The post-genomic era for a select few Paul Cliften Genome Biology 2004, 5:308 (15 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report of the 4th Colmar Scientific Symposium 'Biology in the Post-genomic Era', Colmar, France, 16-17 October 2003.
	Meeting report Functional genomics: strict tempo and hierarchical vocabularies Thomas Preiss Genome Biology 2004, 5:307 (16 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Comparative and Functional Genomics Workshop, Hinxton, UK, 2-5 November 2003.
	Meeting report Making sense of lung-cancer gene-expression profiles Dennis A Wigle, Ming Tsao, Igor Jurisica Genome Biology 2004, 5:309 (30 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Critical Assessment of Microarray Data Analysis (CAMDA'03) meeting and competition, Durham, USA, 12-14 November 2003.
	Meeting report Mouse genomics gets the royal treatment F Buaas Genome Biology 2004, 5:310 (30 January 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Genetics Society autumn meeting 'The mouse: genetics and genome', The Royal Society, London, UK, 14 November 2003.
	Deposited research article Extracellular genomic DNA protects mice against radiation and chemical mutagens Leonid A Yakubov, Nelly A Popova, Valery P Nikolin, Dmitry V Semenov, Sergei S Bogachev, Irina N Oskina Genome Biology 2003, 5:P3 (30 December 2003) Abstract \| Full text \| PDF \| Editor’s summary DNA fragments mutated by irradiation or chemical mutagens may be released by dying cells and incorporated into the genome of healthy cells, thereby inducing genomic instability. We show that injection of normal mouse DNA, but not human DNA, into lethally irradiated mice dramatically increased their survival.
	Deposited research article A statistical approach predicts human microRNA targets Neil R Smalheiser, Vetle I Torvik Genome Biology 2004, 5:P4 (14 January 2004) Abstract \| Full text \| PDF \| Editor’s summary We carried out a population-wide statistical analysis of how human microRNAs interact complementarily with human mRNAs. The 72 candidate mRNA targets identified predict a significant number of well-known and novel human genes that warrant experimental validation.
	Deposited research article Computational identification of microRNA targets Nikolaus Rajewsky, Nicholas D Socci Genome Biology 2004, 5:P5 (14 January 2004) Abstract \| Full text \| PDF \| Editor’s summary We present a new computational method to identify microRNA target sites that incorporates both kinetic and thermodynamic components of target recognition.
	Deposited research article Prediction for Target Sites of Small Interfering RNA Duplexes in SARS Coronavirus Fengmin Ji, Liaofu Luo Genome Biology 2004, 5:P6 (16 January 2004) Abstract \| Full text \| PDF \| Editor’s summary RNA interference is used for SARS-related pharmaceutical research and development. Using a bioinformatic method twenty seven, 21-25-base sequence segments in the SARS-coronavirus genome are predicted as the optimal target sites of small interfering RNA duplexes.
	Research news Rita Colwell leaves NSF Maria Anderson Genome Biology 2004, 5:spotlight-20040216-03 (16 February 2004) Abstract \| Full text \| Editor’s summary National Institute of Standards and Technology director Arden Bement to be acting director
	Research news European boost for structural genomics Genome Biology Genome Biology 2004, 5:spotlight-20040216-01 (16 February 2004) Abstract \| Full text \| Editor’s summary The European Commission has given 10 million euros (approximately US $12.5 million) to the European Molecular Biology Laboratory (EMBL) and over 20 partners from 9 European countries, to create BIOXHIT, a "Biocrystallography on a Highly Integrated Technology Platform" project to expedite structural genomics.
	Research news Bioinformatics network cheered Andrew Scott Genome Biology 2004, 5:spotlight-20040216-02 (16 February 2004) Abstract \| Full text \| Editor’s summary European Virtual Institute for Genome Annotation will have a global impact
	Research
	Research A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale Genome Biology 2004, 5:R7 (15 January 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes.
	Research Genome-wide investigation of light and carbon signaling interactions in Arabidopsis Karen E Thum, Michael J Shin, Peter M Palenchar, Andrei Kouranov, Gloria M Coruzzi Genome Biology 2004, 5:R10 (27 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This study uses microarrays to identify Arabidopsis thaliana genes involved in light and carbon-signaling pathways. The data are classified and regulatory motifs in the promoters of co-regulated genes predicted.
	Research In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection Kathleen Marchal, Sigrid De Keersmaecker, Pieter Monsieurs, Nadja van Boxel, Karen Lemmens, Gert Thijs, Jos Vanderleyden, Bart De Moor Genome Biology 2004, 5:R9 (29 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide computational screen for targets of the PmrA transcription factor in Salmonella typhimurium has identified novel target genes.
	Research An unappreciated role for RNA surveillance R Tyler Hillman, Richard E Green, Steven E Brenner Genome Biology 2004, 5:R8 (2 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Following the hypothesis that the public databases contain cloned mRNAs that would be degraded in vivo by the nonsense-mediated mRNA decay mechanism, 144 isoform sequences deposited in SWISS-PROT have been identified that derive from mRNAs with premature termination codons
	Method Predicting specificity in bZIP coiled-coil protein interactions Jessica H Fong, Amy E Keating, Mona Singh Genome Biology 2004, 5:R11 (16 January 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary A method to predict interactions between coiled-coil dominas, which is based on sequence and biophysical data.
	Software Versatile and open software for comparing large genomes Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg Genome Biology 2004, 5:R12 (30 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.

Explore Genome Biology

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Volume 5 Issue 2

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