In this issue - Hindawi Publishing Corporationdownloads.hindawi.com/journals/ijg/2002/842186.pdf ·...
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Comparative and Functional Genomics Comp Funct Genom 2002; 3: 397. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.210 In this issue Upstream — news in genomics In this issue we report on important papers pub- lished from May to July, highlighting break- throughs on several important genomes, includ- ing mouse, zebrafish, Fugu and Plasmodium. Other recent papers have reported on a mech- anism for genome size reduction in Arabidop- sis, comparisons and verifications of large-scale protein-protein interaction datasets, developments in RNA interference approaches for mammalian systems and a solid-phase peptide tagging method for proteomics. A mathematical analysis of suppression subtraction hybridisation Chetan Gadgil et al. present a mathematical model of SSH based on DNA hybridization kinetics. They have used their model to assess the effects of vari- ous experimental parameters (such as mRNA abun- dance in the cDNA sample and the reaction time used) on the chances of detecting messages from different abundance classes, and on the number of false positives obtained, to facilitate optimisation of the approach. They also use the model to look at the best way to spike a sequence into the driver cDNA pool. A computational strategy for protein function assignment that deals with the domain problem Antonio Perez and colleagues describe and demon- strate an automated approach to protein function classification that combines the keyword (KW) and feature (FT) fields of SWISS-PROT entries to build up a database of protomotifs. When a novel pro- tein shows similarity to an annotated protein, the functional information from a protomotif is only transferred to the novel protein if the match is in the correct region of the protein. Meeting Review: ESF — Impact of nucleic acid chemistry on gene function analysis Kathrin Heermeier et al. report on the ESF pro- gramme on Integrated Approaches for Functional Genomics workshop “Impact of Nucleic Acid Chemistry on Gene Function Analysis: Antisense, Aptamers, Ribozymes and RNAi”. Meeting Review: From genotype to phenotype: Linking Bioinformatics and Medical Informatics Ontologies In first of two reports from Manchester Bioinfor- matics Week, Ele Holloway reviews the ontologies workshop that launched the conference. The talks covered issues in nomenclature and data standards and profiled a range of existing ontologies and projects currently in development. Meeting Review: CCP11 Group Meeting: Towards the Functional Analysis of Microarrays Clare Sansom reports on the CCP11 group microar- ray analysis meeting from Manchester Bioinfor- matics Week. The meeting focussed mainly on statistical methods and analysis, with some presen- tations on modelling of networks, and profiles of a selection of microarray projects. Meeting Review: The 50 th American Society for Mass Spectrometry meeting Francesco Brancia brings us a report from the annual meeting of the ASMS: ‘Mass Spectrometry and Allied Topics’. The development of new mass spectrometers and implementation of new analyt- ical methods were the central themes of the con- ference, and, as last year, the application of mass spectrometry to proteomics was a hot topic. Copyright 2002 John Wiley & Sons, Ltd.
Transcript of In this issue - Hindawi Publishing Corporationdownloads.hindawi.com/journals/ijg/2002/842186.pdf ·...
Comparative and Functional GenomicsComp Funct Genom 2002; 3: 397.Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.210
In this issue
Upstream — news in genomics
In this issue we report on important papers pub-lished from May to July, highlighting break-throughs on several important genomes, includ-ing mouse, zebrafish, Fugu and Plasmodium.Other recent papers have reported on a mech-anism for genome size reduction in Arabidop-sis, comparisons and verifications of large-scaleprotein-protein interaction datasets, developmentsin RNA interference approaches for mammaliansystems and a solid-phase peptide tagging methodfor proteomics.
A mathematical analysis of suppressionsubtraction hybridisation
Chetan Gadgil et al. present a mathematical modelof SSH based on DNA hybridization kinetics. Theyhave used their model to assess the effects of vari-ous experimental parameters (such as mRNA abun-dance in the cDNA sample and the reaction timeused) on the chances of detecting messages fromdifferent abundance classes, and on the number offalse positives obtained, to facilitate optimisationof the approach. They also use the model to lookat the best way to spike a sequence into the drivercDNA pool.
A computational strategy for proteinfunction assignment that deals with thedomain problem
Antonio Perez and colleagues describe and demon-strate an automated approach to protein functionclassification that combines the keyword (KW) andfeature (FT) fields of SWISS-PROT entries to buildup a database of protomotifs. When a novel pro-tein shows similarity to an annotated protein, thefunctional information from a protomotif is onlytransferred to the novel protein if the match is inthe correct region of the protein.
Meeting Review: ESF — Impact of nucleicacid chemistry on gene function analysis
Kathrin Heermeier et al. report on the ESF pro-gramme on Integrated Approaches for FunctionalGenomics workshop “Impact of Nucleic AcidChemistry on Gene Function Analysis: Antisense,Aptamers, Ribozymes and RNAi”.
Meeting Review: From genotype tophenotype: Linking Bioinformatics andMedical Informatics Ontologies
In first of two reports from Manchester Bioinfor-matics Week, Ele Holloway reviews the ontologiesworkshop that launched the conference. The talkscovered issues in nomenclature and data standardsand profiled a range of existing ontologies andprojects currently in development.
Meeting Review: CCP11 Group Meeting:Towards the Functional Analysis ofMicroarrays
Clare Sansom reports on the CCP11 group microar-ray analysis meeting from Manchester Bioinfor-matics Week. The meeting focussed mainly onstatistical methods and analysis, with some presen-tations on modelling of networks, and profiles of aselection of microarray projects.
Meeting Review: The 50th AmericanSociety for Mass Spectrometry meeting
Francesco Brancia brings us a report from theannual meeting of the ASMS: ‘Mass Spectrometryand Allied Topics’. The development of new massspectrometers and implementation of new analyt-ical methods were the central themes of the con-ference, and, as last year, the application of massspectrometry to proteomics was a hot topic.
Copyright 2002 John Wiley & Sons, Ltd.
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