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Volume 6 Issue 9
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Comment |
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Trinity
Gregory A Petsko Genome Biology 2005, 6:118 (30 August 2005)
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Editor’s summary
Our bright young biologists should start thinking now about the ethical issues of what we can do and will be able to do in the future. |
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Network security and data integrity in academia: an assessment and a proposal for large-scale archiving
Andrew Smith, Dov Greenbaum, Shawn M Douglas, Morrow Long, Mark Gerstein Genome Biology 2005, 6:119 (30 August 2005)
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Editor’s summary
A direct impediment to the optimal use of online databases is the increasing prevalence, severity, and toll of computer and network security incidents. Funding agencies should set up working groups that can provide essential services such as universal backup, archival storage, and mirroring of community resources, consistent with the key goal of security in academia: to preserve data and results for posterity. |
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Review |
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Phosphoproteomics: new insights into cellular signaling
Marc Mumby, Deirdre Brekken Genome Biology 2005, 6:230 (17 August 2005)
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Editor’s summary
This article presents a brief review of phosphoproteomics with an emphasis on the biological insights into signaling networks that have been derived so far. |
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Canonical Wnt signaling: high-throughput RNAi widens the path
Anthony MC Brown Genome Biology 2005, 6:231 (31 August 2005)
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Editor’s summary
Although Wnt signaling has been the subject of extensive genetic analysis in the past, some 200 genes have now been identified as candidate modulators of this pathway by a recent study using high-throughput RNAi screening. |
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Using genomics to deliver natural products from symbiotic bacteria
Jon Clardy Genome Biology 2005, 6:232 (31 August 2005)
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Editor’s summary
Recent research has identified the clusters of bacterial genes responsible for the synthesis of some natural products with promising anticancer activity, making it possible for these molecules to be synthesized in easily cultured bacteria. |
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Report |
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Articles selected by Faculty of 1000: Profiling honeybee brains; phylogenetic analysis in legumes; marine and freshwater bacterioplankton transcriptomes; RNA secondary structure prediction; unraveling the tissue origin of cancer samples
Genome Biology 2005, 6:345 (12 August 2005)
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Editor’s summary
A selection of evaluations from Faculty of 1000 covering profiling honeybee brains; phylogenetic analysis in legumes; marine and freshwater bacterioplankton transcriptomes; RNA secondary structure prediction; unraveling the tissue origin of cancer samples. |
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Articles selected by Faculty of 1000: profiling human embryonic stem cells; rearrangements in orthologous genomic regions; profiling the aging primate brain; conserved elements in eukaryotes; diversity of phytoplankton-associated bacteria
Genome Biology 2005, 6:346 (1 September 2005)
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Editor’s summary
A selection of evaluations from Faculty of 1000 covering profiling human embryonic stem cells; rearrangements in orthologous genomic regions; profiling the aging primate brain; conserved elements in eukaryotes; diversity of phytoplankton-associated bacteria. |
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The first decade of microbial genomics: what have we learned and where are we going next?
David A Rasko, Emmanuel F Mongodin Genome Biology 2005, 6:341 (30 August 2005)
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Editor’s summary
A report on the International Conference on Microbial Genomics, Halifax, Canada, 13-16 April 2005. |
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The biology of genomes: sequence gives way to function
David A Hinds Genome Biology 2005, 6:342 (30 August 2005)
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Editor’s summary
A report on the meeting 'The Biology of Genomes', Cold Spring Harbor, USA, 11-15 May 2005. |
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Human genetics moves from clinic to bench - and back
Miroslava Ogorelkova, Xavier Estivill Genome Biology 2005, 6:343 (31 August 2005)
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Editor’s summary
A report on the European Society of Human Genetics Conference 2005, Prague, Czech Republic, 7-10 May 2005. |
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Transcriptional networking
Sarah A Teichmann, Erich Bornberg-Bauer, Nicholas M Luscombe Genome Biology 2005, 6:344 (31 August 2005)
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Editor’s summary
A report on the European Science Foundation workshop 'Transcription Networks: A Global View' Madrid, Spain, 26-28 May 2005. |
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Research |
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Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
JV Chamary, Laurence D Hurst Genome Biology 2005, 6:R75 (16 August 2005)
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Editor’s summary
Simulating evolution and reallocating the substitutions observed in mouse genes revealed that in mammals synonymous sites do not evolve neutrally and synonymous mutations may be under selection because of their effects on the thermodynamic stability of mRNA. |
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Identification of cyanobacterial non-coding RNAs by comparative genome analysis
Ilka M Axmann, Philip Kensche, Jörg Vogel, Stefan Kohl, Hanspeter Herzel, Wolfgang R Hess Genome Biology 2005, 6:R73 (17 August 2005)
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Editor’s summary
The first genome-wide and systematic screen for non-coding RNAs (ncRNAs) in cyanobacteria. Several ncRNAs were computationally predicted and their presence was biochemically verified. These ncRNAs may have regulatory functions, and each shows a distinct phylogenetic distribution. |
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Differential gene expression in anatomical compartments of the human eye
Jennifer J Diehn, Maximilian Diehn, Michael F Marmor, Patrick O Brown Genome Biology 2005, 6:R74 (17 August 2005)
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Editor’s summary
DNA microarrays (representing approximately 30,000 human genes) were used to analyze gene expression in six different human eye compartments, revealing candidate genes for diseases affecting the cornea, lens and retina. |
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A molecular map of mesenchymal tumors
Stephen R Henderson, David Guiliano, Nadege Presneau, Sean McLean, Richard Frow, Sonja Vujovic, John Anderson, Neil Sebire, Jeremy Whelan, Nick Athanasou, Adrienne M Flanagan, Chris Boshoff Genome Biology 2005, 6:R76 (26 August 2005)
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Editor’s summary
A comprehensive study of the gene expression profile of 96 mesenchymal tumors identifies molecular fingerprints for most tumors in this group. |
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Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae
David J Eide, Suzanne Clark, T Murlidharan Nair, Mathias Gehl, Michael Gribskov, Mary Guerinot, Jeffrey F Harper Genome Biology 2005, 6:R77 (30 August 2005)
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| F1000 Biology
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Editor’s summary
The accumulation of thirteen minerals was assayed in 4,385 yeast mutant strains, identifying 212 strains that showed altered ionome (mineral accumulation) profiles. |
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E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns
Anatoly Urisman, Kael F Fischer, Charles Y Chiu, Amy L Kistler, Shoshannah Beck, David Wang, Joseph L DeRisi Genome Biology 2005, 6:R78 (30 August 2005)
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Editor’s summary
An algorithm, E-Predict, for microarray-based species identification is presented. E-Predict compares an observed hybridization pattern with a set of theoretical energy profiles. Each profile represents a species that may be identified. |
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A computational method to predict genetically encoded rare amino acids in proteins
Barnali N Chaudhuri, Todd O Yeates Genome Biology 2005, 6:R79 (31 August 2005)
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Editor’s summary
A new method for predicting recoding by rare amino acids such as selenocysteine and pyrrolysine was used to survey a set of microbial genomes. |
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PubNet: a flexible system for visualizing literature derived networks
Shawn M Douglas, Gaetano T Montelione, Mark Gerstein Genome Biology 2005, 6:R80 (16 August 2005)
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Editor’s summary
PubNet is a web-based tool to extract several types of relationships returned by PubMed queries and map them into networks. |
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L2L: a simple tool for discovering the hidden significance in microarray expression data
John C Newman, Alan M Weiner Genome Biology 2005, 6:R81 (31 August 2005)
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Editor’s summary
A database with lists of differentially expressed genes from published microarray studies is presented together with an application for mining the database with the user’s own microarray data, allowing the identification of novel biological patterns in microarray data. |
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Correspondence |
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Correction: A DNA microarray survey of gene expression in normal human tissues
Radha Shyamsundar, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, Jonathan R Pollack Genome Biology 2005, 6:404 (19 August 2005)
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