Genome Biology | Volume 3 Issue 4

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	Volume 3 Issue 4
	Comment
	Comment Life sentences: Ontology recapitulates philology Sydney Brenner Genome Biology 2002, 3:comment1006-comment1006.2 (19 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ontology is a structured vocabulary in the form of a directed acyclic graph such that each term is descended from its parent by some defined relationship such as "part of". The network we should be interested in is not the network of names but the network of the objects themselves.
	Comment What's in a name? Gregory A Petsko Genome Biology 2002, 3:comment1005-comment1005.2 (26 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nothing seems to engender more passion and provoke more quarrels than the matter of assigning names to things. Cell biologists seem to have about as much imagination as the American actor/screenplay writer/director Sylvester Stallone, who came up with Rocky; Rocky II; Rocky III and Rocky IV: ... and then Rambo; Rambo II; Rambo III.
	Review
	Protein family review ATP-dependent DNA ligases Ina V Martin, Stuart A MacNeill Genome Biology 2002, 3:reviews3005-reviews3005.7 (19 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DNA ligases catalyze the joining of breaks in the phosphodiester backbone of duplex DNA. Of the three known classes, DNA ligases I and III are important for various processes in DNA replication, recombination repair and DNA ligase IV functions in non-homologous end joining.
	Protein family review Retroviral proteases Ben M Dunn, Maureen M Goodenow, Alla Gustchina, Alexander Wlodawer Genome Biology 2002, 3:reviews3006-reviews3006.7 (26 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The proteases of retroviruses are key enzymes in viral propagation and are initially synthesized as polyprotein precursors that are subsequently cleaved at specific sites. Active retroviral proteases are homodimers, with each dimer structurally related to the larger class of single-chain aspartic peptidases. The need to develop new drugs against HIV will continue to be a driving force behind further characterization of retroviral proteases.
	Minireview Organellar proteomics: the prizes and pitfalls of opening the nuclear envelope Eric C Schirmer, Larry Gerace Genome Biology 2002, 3:reviews1008-reviews1008.4 (13 March 2002) Abstract \| Full text \| PDF \| PubMed
	Minireview Screening the yeast genome for new DNA-repair genes Ali Jazayeri, Stephen P Jackson Genome Biology 2002, 3:reviews1009-reviews1009.5 (13 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Studies of DNA repair and the maintenance of genomic integrity are essential to understanding the etiology and pathology of cancer. The availability of the complete genome sequence of Saccharomyces cerevissiae has greatly facilitated the discovery of new genes important for DNA repair.
	Minireview Screening the fruitfly immune system Marc S Dionne, David S Schneider Genome Biology 2002, 3:reviews1010-reviews1010.2 (27 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The anti-microbial defense system of Drosophila shows functional similarities with the vertebrate innate immune system. Two recent gene-expression profiling studies of fruitflies challenged with infectious agents have identified key molecular players in the fruitfly's response to bacterial and fungal infection, as well as a large number of immune-regulated genes with unknown immunological function.
	Minireview Genome scans and microarrays: converging on genes for schizophrenia? Nigel M Williams, Michael C O'Donovan, Michael J Owen Genome Biology 2002, 3:reviews1011-reviews1011.5 (27 March 2002) Abstract \| Full text \| PDF \| PubMed
	Opinion Is 'big biology' a commercial enterprise? Mark Swindells Genome Biology 2002, 3:comment2004-comment2004.4 (26 March 2002) Abstract \| Full text \| PDF \| PubMed
	Report
	Web report A pictorial resource for mammalian development Eliezer Kopf Genome Biology 2002, 3:reports2012 (25 March 2002) Abstract \| Full text
	Paper report Mimics in Listeria Wim D'Haeze Genome Biology 2002, 3:reports0019 (15 March 2002) Abstract \| Full text \| Editor’s summary A Listeria monocytogenes glucose-6-phosphate translocase shows how parasitic bacteria can use molecular mimicry to survive within eukaryotic host cells
	Paper report Brucella genome fever Wim D'Haeze Genome Biology 2002, 3:reports0020 (15 March 2002) Abstract \| Full text \| Editor’s summary The entire Brucella melitensis genome sequence could pave the way to a vaccine against brucellosis in humans
	Paper report Fruitfly fucosylation Wim D'Haeze Genome Biology 2002, 3:reports0021 (15 March 2002) Abstract \| Full text \| Editor’s summary A biocomputational study of the fruitfly genome reveals the presence of new genes putatively involved in fucosylation
	Paper report Flesh eater sequenced Wim D'Haeze Genome Biology 2002, 3:reports0022 (15 March 2002) Abstract \| Full text \| Editor’s summary Analysis of the entire genome sequence of Clostridium perfringens will help explain how gas gangrene develops in humans
	Paper report Hyperthermophile genome Wim D'Haeze Genome Biology 2002, 3:reports0023 (21 March 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of Pyrobaculum aerophilum reveals clues to how organisms can adapt to extreme temperatures
	Meeting report Use of genomic data in risk assessment John C Rockett Genome Biology 2002, 3:reports4011-reports4011.3 (22 March 2002) Abstract \| Full text \| PDF \| PubMed
	Meeting report Protein structure and function by the sea Trevor Lithgow Genome Biology 2002, 3:reports4008-reports4008.2 (27 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 27th Annual Lorne Conference on Protein Structure and Function, Lorne, Australia, 9-13 February 2002.
	Meeting report Genome informatics for data-driven biology Kenta Nakai, Jean-Philippe Vert Genome Biology 2002, 3:reports4010-reports4010.3 (27 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 12th International Conference on Genome Informatics, Tokyo, Japan, 17-19 December 2001.
	Meeting report Cell-cycle regulation Needhi Bhalla Genome Biology 2002, 3:reports4009-reports4009.4 (28 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'cell-cycle regulation' minisymposium at the 41st Annual Meeting of the American Society for Cell Biology, Washington DC, USA, 8-12 December 2001.
	Meeting report Chips to hits Krishnarao Appasani Genome Biology 2002, 3:reports4012-reports4012.2 (3 April 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the IBC USA International Microtechnology Conference 'Chips to hits', San Diego, USA, 27 October to 1 November 2001.
	Research news Linkage analysis in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020402-02 (2 April 2002) Abstract \| Full text \| Editor’s summary Combining expression profiling with linkage analysis reveals the complexity of regulatory programs in yeast strains.
	Research news Senescence tale Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020402-01 (2 April 2002) Abstract \| Full text \| Editor’s summary Replicative senescence appears to be controlled by changes in the telomeric protein complex rather than telomere loss.
	Research news Where do jaws come from? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020403-02 (3 April 2002) Abstract \| Full text \| Editor’s summary Loss of Hox gene expression may have played a role in the evolution of the vertebrate jaw.
	Research news Strep genomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020403-01 (3 April 2002) Abstract \| Full text \| Editor’s summary Comparative genomics identifies genes associated with Streptococcus strains that cause acute rheumatic fever.
	Research news Publication with a pinch of privatization Pete Moore Genome Biology 2002, 3:spotlight-20020404-02 (4 April 2002) Abstract \| Full text \| Editor’s summary As Science yet again bends the accepted rules on data release, when publishing the rice genome, opinions are strongly divided on whether this should be the shape of things to come.
	Research news Protein polymorphisms Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020404-01 (4 April 2002) Abstract \| Full text \| Editor’s summary Combining genetics with proteomics to analyse protein variations in mouse brains.
	Research news The genome that feeds the world Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020405-01 (5 April 2002) Abstract \| Full text \| Editor’s summary Two independent groups report draft sequences of the rice genome.
	Research news BAC to BAC Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020408-02 (8 April 2002) Abstract \| Full text \| Editor’s summary Spotting modified DNA directly onto untreated glass surfaces offers an efficient system for identifying genomic abnormalities in tumor samples.
	Research news The silencing team Tudor Toma Genome Biology 2002, 3:spotlight-20020408-01 (8 April 2002) Abstract \| Full text \| Editor’s summary Two enzymes cooperate to silence genes and maintain DNA methylation in human cancer cells.
	Research news Cloning like rabbits Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020409-02 (9 April 2002) Abstract \| Full text \| Editor’s summary French scientists have succeeded in generating cloned rabbits by nuclear transfer.
	Research news Bop controls ventricle formation Tudor Toma Genome Biology 2002, 3:spotlight-20020409-01 (9 April 2002) Abstract \| Full text \| Editor’s summary Bop encodes a muscle-restricted protein essential for cardiac differentiation and right ventricle morphogenesis.
	Research news Zooming in on micrometastases Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020410-01 (10 April 2002) Abstract \| Full text \| Editor’s summary Researchers have developed an optimized procedure for analyzing the genome and transcriptome of single tumour cells.
	Research news Male mutations Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020411-02 (11 April 2002) Abstract \| Full text \| Editor’s summary Comparative genetic analysis of humans and apes supports the suggested higher mutation rates in hominid males.
	Research news Controlling CFTR protein folding Tudor Toma Genome Biology 2002, 3:spotlight-20020411-01 (11 April 2002) Abstract \| Full text \| Editor’s summary Proline residues promote correct folding of the cystic fibrosis conductance regulator by preventing the formation of misfolded structures.
	Research news Monkey business Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020412-01 (12 April 2002) Abstract \| Full text \| Editor’s summary Comparative transcriptome and proteome analysis highlights the differences between the brains of humans and monkeys.
	Research news African cows Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020415-01 (15 April 2002) Abstract \| Full text \| Editor’s summary Genetic analysis provides clues into the history of cattle pastoralism in Africa.
	Research news Mitochondrial DNA homoplasmy Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020416-01 (16 April 2002) Abstract \| Full text \| Editor’s summary Point mutations in the mitochondrial genome are very common in aged cells and undergo rapid clonal expansion.
	Research news Short hairpins to silence genes SPIS MedWire Genome Biology 2002, 3:spotlight-20020417-01 (17 April 2002) Abstract \| Full text \| Editor’s summary Short hairpin RNAs can be engineered to suppress specific gene expression in cultured Drosophila and mammalian cells
	Research news CDK7 in C. elegans Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020418-01 (18 April 2002) Abstract \| Full text \| Editor’s summary Characterization of the worm ortholog of the cyclin-dependent kinase CDK7 confirms its dual role in transcription and cell-cycle regulation.
	Research news Green revolution Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020419-01 (19 April 2002) Abstract \| Full text \| Editor’s summary Mutation of a gene in the gibberellin metabolic pathway played a part in the green revolution.
	Research news Pseudomonas switch to resistance Tudor Toma Genome Biology 2002, 3:spotlight-20020422-01 (22 April 2002) Abstract \| Full text \| Editor’s summary Pseudomonas aeruginosa biofilm formation and antibiotic resistance in cystic fibrosis are linked
	Research news FOXO transcription factor stimulates repair Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020422-02 (22 April 2002) Abstract \| Full text \| Editor’s summary A member of the FOXO family of forkhead transcription factors regulates cell-cycle and DNA repair pathways under stress.
	Research news Retroviral risk Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020423-01 (23 April 2002) Abstract \| Full text \| Editor’s summary Gene therapy with retroviral vectors can increase the risk of developing leukemia.
	Research news 2002 Gairdner International Awards announced David Bruce Genome Biology 2002, 3:spotlight-20020424-01 (24 April 2002) Abstract \| Full text \| Editor’s summary The 2002 awards recognize the impact of genomics, proteomics and bioinformatics.
	Research news Keeping a CHEK on breast cancer Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020424-02 (24 April 2002) Abstract \| Full text \| Editor’s summary CHEK2, like BRCA1 and BRCA2, is a susceptibility gene for breast cancer.
	Research news Tick tock Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020425-01 (25 April 2002) Abstract \| Full text \| Editor’s summary Microarray analysis of murine circadian gene regulation reveals remarkable divergence between different tissues.
	Research news Schizophrenia surprise Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020426-01 (26 April 2002) Abstract \| Full text \| Editor’s summary A large-scale study fails to find a genetic link between schizophrenia and chromosome 1q.
	Research news Bee behavior Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020429-01 (29 April 2002) Abstract \| Full text \| Editor’s summary Changes in enzyme expression levels affect bee food-searching behavior.
	Research news Grass genomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020430-01 (30 April 2002) Abstract \| Full text \| Editor’s summary Comparison of genomic sequences from maize and rice identifies conserved non-coding sequences that may control grass gene expression.
	Research
	Research Evolutionary conservation of otd/Otx2 transcription factor action: a genome-wide microarray analysis in Drosophila Haiqiong Montalta-He, Ronny Leemans, Thomas Loop, Martin Strahm, Ulrich Certa, Michael Primig, Dario Acampora, Antonio Simeone, Heinrich Reichert Genome Biology 2002, 3:research0015.1-research0015.15 (14 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes of the orthodenticle (otd)/Otx transcription factor family have conserved roles in the embryogenesis of head and brain. Quantitative transcript imaging was used to analyze the functional equivalence of Drosophila otd and mammalian Otx gene action at a genomic level. Approximately one third of the otd-regulated transcripts also respond to overexpression of the human Otx2 gene in Drosophila.
	Research Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome Peter Kosarev, Klaus FX Mayer, Christian S Hardtke Genome Biology 2002, 3:research0016-research0016.12 (14 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Inspection of the Arabidopsis proteome with InterPro predicts 446 RING domains. Each domain was evaluated and 59 false positives were eliminated. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement.
	Research New feature subset selection procedures for classification of expression profiles Trond Bø, Inge Jonassen Genome Biology 2002, 3:research0017-research0017.11 (14 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New methods are presented for finding gene sets from microarrays that are well suited for distinguishing experiment classes, such as healthy versus diseased tissues. These methods are based on evaluating genes in pairs and evaluating how well a pair in combination distinguishes two experiment classes. The gene sets selected by our methods outperform the standard methods, in some cases by a large margin.
	Research Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays Felix Naef, Coleen R Hacker, Nila Patil, Marcelo Magnasco Genome Biology 2002, 3:research0018-research0018.11 (22 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A statistical analysis of a large number of duplicate high-density oligonucleotide arrays experiments showed that the noise inherent in these investigations is characteristically dependent on intensity and can be well described in terms of local normalization of log-ratio distributions. Robust estimates of the local standard deviation of these distributions provide a simple and powerful way to assess significance in differential gene expression experiments.
	Research Permutation-validated principal components analysis of microarray data Jobst Landgrebe, Wolfgang Wurst, Gerhard Welzl Genome Biology 2002, 3:research0019-research0019.11 (22 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to assess reliability in multivariate microarray data analysis using permutation-validated principal components analysis has been used to extract the leading sources of variance from microarray data, to visualize relationships between genes and hybridizations and to select informative genes in a statistically reliable manner.

	Volume 3 Issue 4
	Comment
	Comment Life sentences: Ontology recapitulates philology Sydney Brenner Genome Biology 2002, 3:comment1006-comment1006.2 (19 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ontology is a structured vocabulary in the form of a directed acyclic graph such that each term is descended from its parent by some defined relationship such as "part of". The network we should be interested in is not the network of names but the network of the objects themselves.
	Comment What's in a name? Gregory A Petsko Genome Biology 2002, 3:comment1005-comment1005.2 (26 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nothing seems to engender more passion and provoke more quarrels than the matter of assigning names to things. Cell biologists seem to have about as much imagination as the American actor/screenplay writer/director Sylvester Stallone, who came up with Rocky; Rocky II; Rocky III and Rocky IV: ... and then Rambo; Rambo II; Rambo III.
	Review
	Protein family review ATP-dependent DNA ligases Ina V Martin, Stuart A MacNeill Genome Biology 2002, 3:reviews3005-reviews3005.7 (19 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DNA ligases catalyze the joining of breaks in the phosphodiester backbone of duplex DNA. Of the three known classes, DNA ligases I and III are important for various processes in DNA replication, recombination repair and DNA ligase IV functions in non-homologous end joining.
	Protein family review Retroviral proteases Ben M Dunn, Maureen M Goodenow, Alla Gustchina, Alexander Wlodawer Genome Biology 2002, 3:reviews3006-reviews3006.7 (26 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The proteases of retroviruses are key enzymes in viral propagation and are initially synthesized as polyprotein precursors that are subsequently cleaved at specific sites. Active retroviral proteases are homodimers, with each dimer structurally related to the larger class of single-chain aspartic peptidases. The need to develop new drugs against HIV will continue to be a driving force behind further characterization of retroviral proteases.
	Minireview Organellar proteomics: the prizes and pitfalls of opening the nuclear envelope Eric C Schirmer, Larry Gerace Genome Biology 2002, 3:reviews1008-reviews1008.4 (13 March 2002) Abstract \| Full text \| PDF \| PubMed
	Minireview Screening the yeast genome for new DNA-repair genes Ali Jazayeri, Stephen P Jackson Genome Biology 2002, 3:reviews1009-reviews1009.5 (13 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Studies of DNA repair and the maintenance of genomic integrity are essential to understanding the etiology and pathology of cancer. The availability of the complete genome sequence of Saccharomyces cerevissiae has greatly facilitated the discovery of new genes important for DNA repair.
	Minireview Screening the fruitfly immune system Marc S Dionne, David S Schneider Genome Biology 2002, 3:reviews1010-reviews1010.2 (27 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The anti-microbial defense system of Drosophila shows functional similarities with the vertebrate innate immune system. Two recent gene-expression profiling studies of fruitflies challenged with infectious agents have identified key molecular players in the fruitfly's response to bacterial and fungal infection, as well as a large number of immune-regulated genes with unknown immunological function.
	Minireview Genome scans and microarrays: converging on genes for schizophrenia? Nigel M Williams, Michael C O'Donovan, Michael J Owen Genome Biology 2002, 3:reviews1011-reviews1011.5 (27 March 2002) Abstract \| Full text \| PDF \| PubMed
	Opinion Is 'big biology' a commercial enterprise? Mark Swindells Genome Biology 2002, 3:comment2004-comment2004.4 (26 March 2002) Abstract \| Full text \| PDF \| PubMed
	Report
	Web report A pictorial resource for mammalian development Eliezer Kopf Genome Biology 2002, 3:reports2012 (25 March 2002) Abstract \| Full text
	Paper report Mimics in Listeria Wim D'Haeze Genome Biology 2002, 3:reports0019 (15 March 2002) Abstract \| Full text \| Editor’s summary A Listeria monocytogenes glucose-6-phosphate translocase shows how parasitic bacteria can use molecular mimicry to survive within eukaryotic host cells
	Paper report Brucella genome fever Wim D'Haeze Genome Biology 2002, 3:reports0020 (15 March 2002) Abstract \| Full text \| Editor’s summary The entire Brucella melitensis genome sequence could pave the way to a vaccine against brucellosis in humans
	Paper report Fruitfly fucosylation Wim D'Haeze Genome Biology 2002, 3:reports0021 (15 March 2002) Abstract \| Full text \| Editor’s summary A biocomputational study of the fruitfly genome reveals the presence of new genes putatively involved in fucosylation
	Paper report Flesh eater sequenced Wim D'Haeze Genome Biology 2002, 3:reports0022 (15 March 2002) Abstract \| Full text \| Editor’s summary Analysis of the entire genome sequence of Clostridium perfringens will help explain how gas gangrene develops in humans
	Paper report Hyperthermophile genome Wim D'Haeze Genome Biology 2002, 3:reports0023 (21 March 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of Pyrobaculum aerophilum reveals clues to how organisms can adapt to extreme temperatures
	Meeting report Use of genomic data in risk assessment John C Rockett Genome Biology 2002, 3:reports4011-reports4011.3 (22 March 2002) Abstract \| Full text \| PDF \| PubMed
	Meeting report Protein structure and function by the sea Trevor Lithgow Genome Biology 2002, 3:reports4008-reports4008.2 (27 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 27th Annual Lorne Conference on Protein Structure and Function, Lorne, Australia, 9-13 February 2002.
	Meeting report Genome informatics for data-driven biology Kenta Nakai, Jean-Philippe Vert Genome Biology 2002, 3:reports4010-reports4010.3 (27 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 12th International Conference on Genome Informatics, Tokyo, Japan, 17-19 December 2001.
	Meeting report Cell-cycle regulation Needhi Bhalla Genome Biology 2002, 3:reports4009-reports4009.4 (28 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 'cell-cycle regulation' minisymposium at the 41st Annual Meeting of the American Society for Cell Biology, Washington DC, USA, 8-12 December 2001.
	Meeting report Chips to hits Krishnarao Appasani Genome Biology 2002, 3:reports4012-reports4012.2 (3 April 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the IBC USA International Microtechnology Conference 'Chips to hits', San Diego, USA, 27 October to 1 November 2001.
	Research news Linkage analysis in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020402-02 (2 April 2002) Abstract \| Full text \| Editor’s summary Combining expression profiling with linkage analysis reveals the complexity of regulatory programs in yeast strains.
	Research news Senescence tale Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020402-01 (2 April 2002) Abstract \| Full text \| Editor’s summary Replicative senescence appears to be controlled by changes in the telomeric protein complex rather than telomere loss.
	Research news Where do jaws come from? Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020403-02 (3 April 2002) Abstract \| Full text \| Editor’s summary Loss of Hox gene expression may have played a role in the evolution of the vertebrate jaw.
	Research news Strep genomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020403-01 (3 April 2002) Abstract \| Full text \| Editor’s summary Comparative genomics identifies genes associated with Streptococcus strains that cause acute rheumatic fever.
	Research news Publication with a pinch of privatization Pete Moore Genome Biology 2002, 3:spotlight-20020404-02 (4 April 2002) Abstract \| Full text \| Editor’s summary As Science yet again bends the accepted rules on data release, when publishing the rice genome, opinions are strongly divided on whether this should be the shape of things to come.
	Research news Protein polymorphisms Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020404-01 (4 April 2002) Abstract \| Full text \| Editor’s summary Combining genetics with proteomics to analyse protein variations in mouse brains.
	Research news The genome that feeds the world Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020405-01 (5 April 2002) Abstract \| Full text \| Editor’s summary Two independent groups report draft sequences of the rice genome.
	Research news BAC to BAC Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020408-02 (8 April 2002) Abstract \| Full text \| Editor’s summary Spotting modified DNA directly onto untreated glass surfaces offers an efficient system for identifying genomic abnormalities in tumor samples.
	Research news The silencing team Tudor Toma Genome Biology 2002, 3:spotlight-20020408-01 (8 April 2002) Abstract \| Full text \| Editor’s summary Two enzymes cooperate to silence genes and maintain DNA methylation in human cancer cells.
	Research news Cloning like rabbits Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020409-02 (9 April 2002) Abstract \| Full text \| Editor’s summary French scientists have succeeded in generating cloned rabbits by nuclear transfer.
	Research news Bop controls ventricle formation Tudor Toma Genome Biology 2002, 3:spotlight-20020409-01 (9 April 2002) Abstract \| Full text \| Editor’s summary Bop encodes a muscle-restricted protein essential for cardiac differentiation and right ventricle morphogenesis.
	Research news Zooming in on micrometastases Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020410-01 (10 April 2002) Abstract \| Full text \| Editor’s summary Researchers have developed an optimized procedure for analyzing the genome and transcriptome of single tumour cells.
	Research news Male mutations Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020411-02 (11 April 2002) Abstract \| Full text \| Editor’s summary Comparative genetic analysis of humans and apes supports the suggested higher mutation rates in hominid males.
	Research news Controlling CFTR protein folding Tudor Toma Genome Biology 2002, 3:spotlight-20020411-01 (11 April 2002) Abstract \| Full text \| Editor’s summary Proline residues promote correct folding of the cystic fibrosis conductance regulator by preventing the formation of misfolded structures.
	Research news Monkey business Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020412-01 (12 April 2002) Abstract \| Full text \| Editor’s summary Comparative transcriptome and proteome analysis highlights the differences between the brains of humans and monkeys.
	Research news African cows Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020415-01 (15 April 2002) Abstract \| Full text \| Editor’s summary Genetic analysis provides clues into the history of cattle pastoralism in Africa.
	Research news Mitochondrial DNA homoplasmy Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020416-01 (16 April 2002) Abstract \| Full text \| Editor’s summary Point mutations in the mitochondrial genome are very common in aged cells and undergo rapid clonal expansion.
	Research news Short hairpins to silence genes SPIS MedWire Genome Biology 2002, 3:spotlight-20020417-01 (17 April 2002) Abstract \| Full text \| Editor’s summary Short hairpin RNAs can be engineered to suppress specific gene expression in cultured Drosophila and mammalian cells
	Research news CDK7 in C. elegans Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020418-01 (18 April 2002) Abstract \| Full text \| Editor’s summary Characterization of the worm ortholog of the cyclin-dependent kinase CDK7 confirms its dual role in transcription and cell-cycle regulation.
	Research news Green revolution Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020419-01 (19 April 2002) Abstract \| Full text \| Editor’s summary Mutation of a gene in the gibberellin metabolic pathway played a part in the green revolution.
	Research news Pseudomonas switch to resistance Tudor Toma Genome Biology 2002, 3:spotlight-20020422-01 (22 April 2002) Abstract \| Full text \| Editor’s summary Pseudomonas aeruginosa biofilm formation and antibiotic resistance in cystic fibrosis are linked
	Research news FOXO transcription factor stimulates repair Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020422-02 (22 April 2002) Abstract \| Full text \| Editor’s summary A member of the FOXO family of forkhead transcription factors regulates cell-cycle and DNA repair pathways under stress.
	Research news Retroviral risk Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020423-01 (23 April 2002) Abstract \| Full text \| Editor’s summary Gene therapy with retroviral vectors can increase the risk of developing leukemia.
	Research news 2002 Gairdner International Awards announced David Bruce Genome Biology 2002, 3:spotlight-20020424-01 (24 April 2002) Abstract \| Full text \| Editor’s summary The 2002 awards recognize the impact of genomics, proteomics and bioinformatics.
	Research news Keeping a CHEK on breast cancer Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020424-02 (24 April 2002) Abstract \| Full text \| Editor’s summary CHEK2, like BRCA1 and BRCA2, is a susceptibility gene for breast cancer.
	Research news Tick tock Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020425-01 (25 April 2002) Abstract \| Full text \| Editor’s summary Microarray analysis of murine circadian gene regulation reveals remarkable divergence between different tissues.
	Research news Schizophrenia surprise Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020426-01 (26 April 2002) Abstract \| Full text \| Editor’s summary A large-scale study fails to find a genetic link between schizophrenia and chromosome 1q.
	Research news Bee behavior Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020429-01 (29 April 2002) Abstract \| Full text \| Editor’s summary Changes in enzyme expression levels affect bee food-searching behavior.
	Research news Grass genomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020430-01 (30 April 2002) Abstract \| Full text \| Editor’s summary Comparison of genomic sequences from maize and rice identifies conserved non-coding sequences that may control grass gene expression.
	Research
	Research Evolutionary conservation of otd/Otx2 transcription factor action: a genome-wide microarray analysis in Drosophila Haiqiong Montalta-He, Ronny Leemans, Thomas Loop, Martin Strahm, Ulrich Certa, Michael Primig, Dario Acampora, Antonio Simeone, Heinrich Reichert Genome Biology 2002, 3:research0015.1-research0015.15 (14 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes of the orthodenticle (otd)/Otx transcription factor family have conserved roles in the embryogenesis of head and brain. Quantitative transcript imaging was used to analyze the functional equivalence of Drosophila otd and mammalian Otx gene action at a genomic level. Approximately one third of the otd-regulated transcripts also respond to overexpression of the human Otx2 gene in Drosophila.
	Research Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome Peter Kosarev, Klaus FX Mayer, Christian S Hardtke Genome Biology 2002, 3:research0016-research0016.12 (14 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Inspection of the Arabidopsis proteome with InterPro predicts 446 RING domains. Each domain was evaluated and 59 false positives were eliminated. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement.
	Research New feature subset selection procedures for classification of expression profiles Trond Bø, Inge Jonassen Genome Biology 2002, 3:research0017-research0017.11 (14 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New methods are presented for finding gene sets from microarrays that are well suited for distinguishing experiment classes, such as healthy versus diseased tissues. These methods are based on evaluating genes in pairs and evaluating how well a pair in combination distinguishes two experiment classes. The gene sets selected by our methods outperform the standard methods, in some cases by a large margin.
	Research Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays Felix Naef, Coleen R Hacker, Nila Patil, Marcelo Magnasco Genome Biology 2002, 3:research0018-research0018.11 (22 March 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A statistical analysis of a large number of duplicate high-density oligonucleotide arrays experiments showed that the noise inherent in these investigations is characteristically dependent on intensity and can be well described in terms of local normalization of log-ratio distributions. Robust estimates of the local standard deviation of these distributions provide a simple and powerful way to assess significance in differential gene expression experiments.
	Research Permutation-validated principal components analysis of microarray data Jobst Landgrebe, Wolfgang Wurst, Gerhard Welzl Genome Biology 2002, 3:research0019-research0019.11 (22 March 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to assess reliability in multivariate microarray data analysis using permutation-validated principal components analysis has been used to extract the leading sources of variance from microarray data, to visualize relationships between genes and hybridizations and to select informative genes in a statistically reliable manner.

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