Genome Biology | Volume 4 Issue 1

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	Volume 4 Issue 1
	Comment
	Editorial Editorial Genome Biology 2002, 4:101 (31 December 2002) Abstract \| Full text \| PDF \| Editor’s summary In keeping with its promise to evolve in response to the needs of readers, Genome Biology is making a number of practical changes with the beginning of 2003.
	Comment Everything I need to know about genomics, I learned from Yogi Berra Gregory A Petsko Genome Biology 2002, 4:102 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As 2002 draws to a close, I find myself contemplating the future of biology with hope, but also with uncertainty and some apprehension. When I find myself in such a spiritual quandary, I usually turn to a guru.
	Review
	Protein family review The σ⁷⁰ family of sigma factors Mark SB Paget, John D Helmann Genome Biology 2003, 4:203 (3 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Members of the σ⁷⁰ family of sigma factors are components of the RNA polymerase holoenzyme that direct bacterial or plastid core RNA polymerase to specific promoter elements upstream of the transcription-initiation points. They can broadly be divided into four main groups on the basis of gene structure and function.
	Minireview Post-genomic insights into plant nodulation symbioses Peter M Gresshoff Genome Biology 2003, 4:201 (3 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several legume genes involved in establishing nitrogen fixation have been discovered using functional genomics; when mutated, the genes affect symbioses, and all encode receptor kinases.
	Minireview The genomics of insecticide resistance John G Oakeshott, Irene Home, Tara D Sutherland, Robyn J Russell Genome Biology 2003, 4:202 (3 January 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomic technologies are revealing mechanisms of insecticide resistance that had previously defied molecular analyses.
	Opinion A hat trick - Plasmodium, Anopheles and Homo Michael Ashburner Genome Biology 2002, 4:103 (17 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genomes of the malaria parasite, its vector and its host are now sequenced. But will it offer hope to the millions who die from malaria each year?
	Report
	Paper report Articles selected by Faculty of 1000: Human cis-regulatory evolution; recombination in rice; E. coli two-component systems; optimization of protein properties; maize chromosome 1. Genome Biology 2002, 4:304 (18 December 2002) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering cis-regulatory evolution in humans, homologous recombination in rice, analysis of all E. coli two-component regulatory system mutants, rapid optimization of protein properties and microsatellite diversity in maize chromosome 1.
	Meeting report Gene function in the mammalian genome, courtesy of the mouse Claire M Wade Genome Biology 2002, 4:302 (17 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Mouse Genome Conference, San Antonio, USA, 17-20 November, 2002.
	Meeting report The integrated world of functional genomics Itai Yanai Genome Biology 2002, 4:301 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the EMBO meeting 'Functional Genomics; The Future of Biology', Heidelberg, Germany, 13-16 October 2002.
	Meeting report The genome and the germ cell Kathleen Molyneaux, Christopher Wylie Genome Biology 2002, 4:303 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third biennial Cold Spring Harbor Laboratory meeting on Germ Cells, Cold Spring Harbor, USA, 9-13 October 2002.
	Research news Antibody fingerprint Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030102-01 (2 January 2003) Abstract \| Full text \| Editor’s summary Phage-based analysis of anti-tumour antibody repertoires has led to the identification of prostate cancer antigens.
	Research news Natural calcineurin inhibitor Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030103-01 (3 January 2003) Abstract \| Full text \| Editor’s summary The mitochondrial protein FKBP38 inhibits the phosphatase calcineurin and also targets Bcl-2, to regulate apoptosis.
	Research news Weeding out functions for Ku Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030106-02 (6 January 2003) Abstract \| Full text \| Editor’s summary Analysis of Arabidopsis mutants reveals that Ku70 regulates telomere maintenance and telomerase function in plants.
	Research news INK and ARF in chicks Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030106-01 (6 January 2003) Abstract \| Full text \| Editor’s summary The INK4a and ARF tumor suppressors are not well conserved in chickens.
	Research news Finishing fourteen Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030107-01 (7 January 2003) Abstract \| Full text \| Editor’s summary The sequencing of human chromosome 14 has been finished.
	Research news Generating robustness Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030108-02 (8 January 2003) Abstract \| Full text \| Editor’s summary Functional compensation between duplicate genes helps to create genetic robustness against mutation.
	Research news Thawing stem cells Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030108-01 (8 January 2003) Abstract \| Full text \| Editor’s summary Stem cells can be effectively recovered from cord blood that has been frozen for 15 years.
	Research news Phospho-profiling Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030109-02 (9 January 2003) Abstract \| Full text \| Editor’s summary Mass spectrometry can monitor global changes in tyrosine phosphorylation patterns that are attributable to signalling pathways in leukocytes.
	Research news Symbiont genome Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030109-01 (9 January 2003) Abstract \| Full text \| Editor’s summary The genome of Buchnera aphidicola, isolated from aphids, has been sequenced.
	Research news Filamentous forms go foraging Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030110-01 (10 January 2003) Abstract \| Full text \| Editor’s summary Kinase signalling pathways regulate the filamentous growth of budding yeast.
	Research news Radiodurans' rings and radioresistance Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030113-01 (13 January 2003) Abstract \| Full text \| Editor’s summary Genomic ring-like structures may account for the impressive radioresistance of the bacterium Deinococcus radiodurans.
	Research news Integrative genomics finds disease genes Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030114-01 (14 January 2003) Abstract \| Full text \| Editor’s summary Disease-gene discovery is accelerated by combining global information about DNA, mRNA and proteins.
	Research news Dissecting dyskerin Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030115-01 (15 January 2003) Abstract \| Full text \| Editor’s summary Premature aging and cancer is seen in mice with reduced levels of a pseudouridine synthase enzyme.
	Research news Reaping the rewards of RNAi Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030116-01 (16 January 2003) Abstract \| Full text \| Editor’s summary A systematic screen for worm phenotypes using RNA interference has now covered most of the genome.
	Research news The ESSENCE of exon inclusion Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030117-01 (17 January 2003) Abstract \| Full text \| Editor’s summary Synthetic proteins can repair aberrant splicing mutations.
	Research news Myc targets Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030120-01 (20 January 2003) Abstract \| Full text \| Editor’s summary The c-Myc oncoprotein binds to TFIIIB and activates RNA polymerase III transcriptional targets.
	Research news Investigating insulin Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030121-01 (21 January 2003) Abstract \| Full text \| Editor’s summary Insulin staining of differentiated stem cells may be due to insulin uptake from the medium rather than insulin production.
	Research news Haematopoietic stem cells Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030122-01 (22 January 2003) Abstract \| Full text \| Editor’s summary Experiments using knockout mice show that different factors are required for the generation and the maintenance of haematopoietic stem cells.
	Research news Discovering metabolic loci Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030123-01 (23 January 2003) Abstract \| Full text \| Editor’s summary Comparative genomics can uncover hidden metabolic potential and biosynthetic pathways.
	Research news ATM, telomeres and aging Jonathan Weitzman Genome Biology 2003, 4:spotlight-20030124-01 (24 January 2003) Abstract \| Full text \| Editor’s summary Analysis of double knockout mice demonstrates the link between ATM and the state of telomeres in causing disease.
	Research news PAR for the course Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030127-01 (27 January 2003) Abstract \| Full text \| Editor’s summary LKB1, a Drosophila PAR homolog, plays an important role in cell polarity.
	Research news Polyglutamine oligomers Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030128-01 (28 January 2003) Abstract \| Full text \| Editor’s summary Preventing oligomerization of polyglutamine repeats can reverse the symptoms of neurodegenerative disorders such as Huntington's disease.
	Research news The genetics of metamorphosis Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030130-01 (30 January 2003) Abstract \| Full text \| Editor’s summary Comparative genomics reveals the variation in developmental gene expression during the metamorphosis of flies.
	Research news Genetically-modified milk Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030131-01 (31 January 2003) Abstract \| Full text \| Editor’s summary Cloned cows expressing casein transgenes produce improved dairy milk.
	Research news NIH revises conflict rules Ted Agres Genome Biology 2004, 4:spotlight-20040113-01 (13 January 2004) Abstract \| Full text \| Editor’s summary Congress will review allegations of financial wrongdoing
	Research news NSF roadmap urged Ted Agres Genome Biology 2004, 4:spotlight-20040116-01 (16 January 2004) Abstract \| Full text \| Editor’s summary Mechanism would set criteria, priorities for large-scale research facilities
	Research news New T-cell epitope mathematics David Secko Genome Biology 2004, 4:spotlight-20040119-01 (19 January 2004) Abstract \| Full text \| Editor’s summary Posttranslational protein fragment splicing can generate many more epitopes than thought
	Research news US Senate likely to pass budget Ted Agres Genome Biology 2004, 4:spotlight-20040121-01 (21 January 2004) Abstract \| Full text \| Editor’s summary The outlook for the NIH in the fiscal year of 2005: 'another really tough year,' say advocates
	Research news European Research Council doubts Andrew Scott Genome Biology 2004, 4:spotlight-20040123-01 (23 January 2004) Abstract \| Full text \| Editor’s summary Prominent European scientists echo concerns from the UK Royal Society
	Research news European Virtual Institute for Genome Annotation receives €12 million Genome Biology Genome Biology 2004, 4:spotlight-20040127-01 (27 January 2004) Abstract \| Full text \| Editor’s summary The European Union has awarded 12 million euros (approximately US $15 million) to a consortium of 24 bioinformatics research groups from 14 European countries, to create the "BioSapiens Network of Excellence in Bioinformatics".
	Research news Bdellovibrio genome sequenced David Secko Genome Biology 2004, 4:spotlight-20040130-01 (30 January 2004) Abstract \| Full text \| Editor’s summary The Bdellovibrio bacteriovorus genome provides insight into its predatory lifestyle
	Research
	Research Computational comparison of two mouse draft genomes and the human golden path Zhenyu Xuan, Jinhua Wang, Michael Q Zhang Genome Biology 2002, 4:R1 (5 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A comparison of the newly completed, publicly available, genome sequence of the mouse with the prior sequence of the mouse from Celera Genomics Inc. and with the human genome provides a consensus view of the mouse and important insights into human gene numbers.
	Research Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state Romeo Lascaris, Harmen J Bussemaker, André Boorsma, Matt Piper, Hans van der Spek, Les Grivell, Jolanda Blom Genome Biology 2002, 4:R3 (17 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To understand why overexpression of HAP4 is able to override the signals that normally result in glucose repression of mitochondrial function, changes that occur in these cells were analyzed.
	Research A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes David N Baldwin, Veena Vanchinathan, Patrick O Brown, Julie A Theriot Genome Biology 2002, 4:R2 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptional response of cultured human intestinal epithelial cells, the first line of host defense, to infection by Listeria monocytogenes has been examined. The predominant response to infection was mediated by NFκB. The response to two bacterial mutants - actA which is defective in actin-based motility and prfA, which is defective in the expression of all L. monocytogenes virulence genes - revealed no detectable difference in the host transcriptional response to the wild-type and mutant bacteria.
	Research Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level Jose L Jiménez, Michael P Mitchell, John G Sgouros Genome Biology 2002, 4:R4 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The extent to which protein subcellular localization and functional categories established from clustering of orthologous genes agree with gene-expression data has been investigated in Saccharomyces cerevisiae. An increase in the resolution of biologically meaningful classes is observed upon the combination of experiments under different conditions. Differences and similarities in the expression between cytoplasmic-mitochondrial and interspecies translation machineries complement evolutionary information from sequence similarity.
	Research Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays Hong-Ying Wang, Renae L Malek, Anne E Kwitek, Andrew S Greene, Truong V Luu, Babak Behbahani, Bryan Frank, John Quackenbush, Norman H Lee Genome Biology 2003, 4:R5 (6 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long oligonucleotide microarrays are potentially more cost- and management efficient than cDNA microarrays. Unmodified sense and antisense 70-mer oligonucleotides were synthesized and compared with PCR-amplified cDNA clones corresponding to the same genes. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80.
	Research Towards reconstruction of gene networks from expression data by supervised learning Lev A Soinov, Maria A Krestyaninova, Alvis Brazma Genome Biology 2003, 4:R6 (6 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary One of the most important problems in gene network reconstruction is finding, for each gene in the network, which genes can affect it. A supervised learning approach was used to address this question in budding yeast by building decision-tree-related classifiers, which predict gene expression from the expression data of other genes.
	Method MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data Scott W Doniger, Nathan Salomonis, Kam D Dahlquist, Karen Vranizan, Steven C Lawlor, Bruce R Conklin Genome Biology 2003, 4:R7 (6 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP.

	Volume 4 Issue 1
	Comment
	Editorial Editorial Genome Biology 2002, 4:101 (31 December 2002) Abstract \| Full text \| PDF \| Editor’s summary In keeping with its promise to evolve in response to the needs of readers, Genome Biology is making a number of practical changes with the beginning of 2003.
	Comment Everything I need to know about genomics, I learned from Yogi Berra Gregory A Petsko Genome Biology 2002, 4:102 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As 2002 draws to a close, I find myself contemplating the future of biology with hope, but also with uncertainty and some apprehension. When I find myself in such a spiritual quandary, I usually turn to a guru.
	Review
	Protein family review The σ⁷⁰ family of sigma factors Mark SB Paget, John D Helmann Genome Biology 2003, 4:203 (3 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Members of the σ⁷⁰ family of sigma factors are components of the RNA polymerase holoenzyme that direct bacterial or plastid core RNA polymerase to specific promoter elements upstream of the transcription-initiation points. They can broadly be divided into four main groups on the basis of gene structure and function.
	Minireview Post-genomic insights into plant nodulation symbioses Peter M Gresshoff Genome Biology 2003, 4:201 (3 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several legume genes involved in establishing nitrogen fixation have been discovered using functional genomics; when mutated, the genes affect symbioses, and all encode receptor kinases.
	Minireview The genomics of insecticide resistance John G Oakeshott, Irene Home, Tara D Sutherland, Robyn J Russell Genome Biology 2003, 4:202 (3 January 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomic technologies are revealing mechanisms of insecticide resistance that had previously defied molecular analyses.
	Opinion A hat trick - Plasmodium, Anopheles and Homo Michael Ashburner Genome Biology 2002, 4:103 (17 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genomes of the malaria parasite, its vector and its host are now sequenced. But will it offer hope to the millions who die from malaria each year?
	Report
	Paper report Articles selected by Faculty of 1000: Human cis-regulatory evolution; recombination in rice; E. coli two-component systems; optimization of protein properties; maize chromosome 1. Genome Biology 2002, 4:304 (18 December 2002) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering cis-regulatory evolution in humans, homologous recombination in rice, analysis of all E. coli two-component regulatory system mutants, rapid optimization of protein properties and microsatellite diversity in maize chromosome 1.
	Meeting report Gene function in the mammalian genome, courtesy of the mouse Claire M Wade Genome Biology 2002, 4:302 (17 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 16th International Mouse Genome Conference, San Antonio, USA, 17-20 November, 2002.
	Meeting report The integrated world of functional genomics Itai Yanai Genome Biology 2002, 4:301 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the EMBO meeting 'Functional Genomics; The Future of Biology', Heidelberg, Germany, 13-16 October 2002.
	Meeting report The genome and the germ cell Kathleen Molyneaux, Christopher Wylie Genome Biology 2002, 4:303 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third biennial Cold Spring Harbor Laboratory meeting on Germ Cells, Cold Spring Harbor, USA, 9-13 October 2002.
	Research news Antibody fingerprint Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030102-01 (2 January 2003) Abstract \| Full text \| Editor’s summary Phage-based analysis of anti-tumour antibody repertoires has led to the identification of prostate cancer antigens.
	Research news Natural calcineurin inhibitor Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030103-01 (3 January 2003) Abstract \| Full text \| Editor’s summary The mitochondrial protein FKBP38 inhibits the phosphatase calcineurin and also targets Bcl-2, to regulate apoptosis.
	Research news Weeding out functions for Ku Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030106-02 (6 January 2003) Abstract \| Full text \| Editor’s summary Analysis of Arabidopsis mutants reveals that Ku70 regulates telomere maintenance and telomerase function in plants.
	Research news INK and ARF in chicks Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030106-01 (6 January 2003) Abstract \| Full text \| Editor’s summary The INK4a and ARF tumor suppressors are not well conserved in chickens.
	Research news Finishing fourteen Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030107-01 (7 January 2003) Abstract \| Full text \| Editor’s summary The sequencing of human chromosome 14 has been finished.
	Research news Generating robustness Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030108-02 (8 January 2003) Abstract \| Full text \| Editor’s summary Functional compensation between duplicate genes helps to create genetic robustness against mutation.
	Research news Thawing stem cells Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030108-01 (8 January 2003) Abstract \| Full text \| Editor’s summary Stem cells can be effectively recovered from cord blood that has been frozen for 15 years.
	Research news Phospho-profiling Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030109-02 (9 January 2003) Abstract \| Full text \| Editor’s summary Mass spectrometry can monitor global changes in tyrosine phosphorylation patterns that are attributable to signalling pathways in leukocytes.
	Research news Symbiont genome Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030109-01 (9 January 2003) Abstract \| Full text \| Editor’s summary The genome of Buchnera aphidicola, isolated from aphids, has been sequenced.
	Research news Filamentous forms go foraging Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030110-01 (10 January 2003) Abstract \| Full text \| Editor’s summary Kinase signalling pathways regulate the filamentous growth of budding yeast.
	Research news Radiodurans' rings and radioresistance Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030113-01 (13 January 2003) Abstract \| Full text \| Editor’s summary Genomic ring-like structures may account for the impressive radioresistance of the bacterium Deinococcus radiodurans.
	Research news Integrative genomics finds disease genes Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030114-01 (14 January 2003) Abstract \| Full text \| Editor’s summary Disease-gene discovery is accelerated by combining global information about DNA, mRNA and proteins.
	Research news Dissecting dyskerin Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030115-01 (15 January 2003) Abstract \| Full text \| Editor’s summary Premature aging and cancer is seen in mice with reduced levels of a pseudouridine synthase enzyme.
	Research news Reaping the rewards of RNAi Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030116-01 (16 January 2003) Abstract \| Full text \| Editor’s summary A systematic screen for worm phenotypes using RNA interference has now covered most of the genome.
	Research news The ESSENCE of exon inclusion Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030117-01 (17 January 2003) Abstract \| Full text \| Editor’s summary Synthetic proteins can repair aberrant splicing mutations.
	Research news Myc targets Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030120-01 (20 January 2003) Abstract \| Full text \| Editor’s summary The c-Myc oncoprotein binds to TFIIIB and activates RNA polymerase III transcriptional targets.
	Research news Investigating insulin Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030121-01 (21 January 2003) Abstract \| Full text \| Editor’s summary Insulin staining of differentiated stem cells may be due to insulin uptake from the medium rather than insulin production.
	Research news Haematopoietic stem cells Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030122-01 (22 January 2003) Abstract \| Full text \| Editor’s summary Experiments using knockout mice show that different factors are required for the generation and the maintenance of haematopoietic stem cells.
	Research news Discovering metabolic loci Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030123-01 (23 January 2003) Abstract \| Full text \| Editor’s summary Comparative genomics can uncover hidden metabolic potential and biosynthetic pathways.
	Research news ATM, telomeres and aging Jonathan Weitzman Genome Biology 2003, 4:spotlight-20030124-01 (24 January 2003) Abstract \| Full text \| Editor’s summary Analysis of double knockout mice demonstrates the link between ATM and the state of telomeres in causing disease.
	Research news PAR for the course Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030127-01 (27 January 2003) Abstract \| Full text \| Editor’s summary LKB1, a Drosophila PAR homolog, plays an important role in cell polarity.
	Research news Polyglutamine oligomers Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030128-01 (28 January 2003) Abstract \| Full text \| Editor’s summary Preventing oligomerization of polyglutamine repeats can reverse the symptoms of neurodegenerative disorders such as Huntington's disease.
	Research news The genetics of metamorphosis Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030130-01 (30 January 2003) Abstract \| Full text \| Editor’s summary Comparative genomics reveals the variation in developmental gene expression during the metamorphosis of flies.
	Research news Genetically-modified milk Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030131-01 (31 January 2003) Abstract \| Full text \| Editor’s summary Cloned cows expressing casein transgenes produce improved dairy milk.
	Research news NIH revises conflict rules Ted Agres Genome Biology 2004, 4:spotlight-20040113-01 (13 January 2004) Abstract \| Full text \| Editor’s summary Congress will review allegations of financial wrongdoing
	Research news NSF roadmap urged Ted Agres Genome Biology 2004, 4:spotlight-20040116-01 (16 January 2004) Abstract \| Full text \| Editor’s summary Mechanism would set criteria, priorities for large-scale research facilities
	Research news New T-cell epitope mathematics David Secko Genome Biology 2004, 4:spotlight-20040119-01 (19 January 2004) Abstract \| Full text \| Editor’s summary Posttranslational protein fragment splicing can generate many more epitopes than thought
	Research news US Senate likely to pass budget Ted Agres Genome Biology 2004, 4:spotlight-20040121-01 (21 January 2004) Abstract \| Full text \| Editor’s summary The outlook for the NIH in the fiscal year of 2005: 'another really tough year,' say advocates
	Research news European Research Council doubts Andrew Scott Genome Biology 2004, 4:spotlight-20040123-01 (23 January 2004) Abstract \| Full text \| Editor’s summary Prominent European scientists echo concerns from the UK Royal Society
	Research news European Virtual Institute for Genome Annotation receives €12 million Genome Biology Genome Biology 2004, 4:spotlight-20040127-01 (27 January 2004) Abstract \| Full text \| Editor’s summary The European Union has awarded 12 million euros (approximately US $15 million) to a consortium of 24 bioinformatics research groups from 14 European countries, to create the "BioSapiens Network of Excellence in Bioinformatics".
	Research news Bdellovibrio genome sequenced David Secko Genome Biology 2004, 4:spotlight-20040130-01 (30 January 2004) Abstract \| Full text \| Editor’s summary The Bdellovibrio bacteriovorus genome provides insight into its predatory lifestyle
	Research
	Research Computational comparison of two mouse draft genomes and the human golden path Zhenyu Xuan, Jinhua Wang, Michael Q Zhang Genome Biology 2002, 4:R1 (5 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A comparison of the newly completed, publicly available, genome sequence of the mouse with the prior sequence of the mouse from Celera Genomics Inc. and with the human genome provides a consensus view of the mouse and important insights into human gene numbers.
	Research Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state Romeo Lascaris, Harmen J Bussemaker, André Boorsma, Matt Piper, Hans van der Spek, Les Grivell, Jolanda Blom Genome Biology 2002, 4:R3 (17 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To understand why overexpression of HAP4 is able to override the signals that normally result in glucose repression of mitochondrial function, changes that occur in these cells were analyzed.
	Research A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes David N Baldwin, Veena Vanchinathan, Patrick O Brown, Julie A Theriot Genome Biology 2002, 4:R2 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The transcriptional response of cultured human intestinal epithelial cells, the first line of host defense, to infection by Listeria monocytogenes has been examined. The predominant response to infection was mediated by NFκB. The response to two bacterial mutants - actA which is defective in actin-based motility and prfA, which is defective in the expression of all L. monocytogenes virulence genes - revealed no detectable difference in the host transcriptional response to the wild-type and mutant bacteria.
	Research Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level Jose L Jiménez, Michael P Mitchell, John G Sgouros Genome Biology 2002, 4:R4 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The extent to which protein subcellular localization and functional categories established from clustering of orthologous genes agree with gene-expression data has been investigated in Saccharomyces cerevisiae. An increase in the resolution of biologically meaningful classes is observed upon the combination of experiments under different conditions. Differences and similarities in the expression between cytoplasmic-mitochondrial and interspecies translation machineries complement evolutionary information from sequence similarity.
	Research Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays Hong-Ying Wang, Renae L Malek, Anne E Kwitek, Andrew S Greene, Truong V Luu, Babak Behbahani, Bryan Frank, John Quackenbush, Norman H Lee Genome Biology 2003, 4:R5 (6 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long oligonucleotide microarrays are potentially more cost- and management efficient than cDNA microarrays. Unmodified sense and antisense 70-mer oligonucleotides were synthesized and compared with PCR-amplified cDNA clones corresponding to the same genes. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80.
	Research Towards reconstruction of gene networks from expression data by supervised learning Lev A Soinov, Maria A Krestyaninova, Alvis Brazma Genome Biology 2003, 4:R6 (6 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary One of the most important problems in gene network reconstruction is finding, for each gene in the network, which genes can affect it. A supervised learning approach was used to address this question in budding yeast by building decision-tree-related classifiers, which predict gene expression from the expression data of other genes.
	Method MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data Scott W Doniger, Nathan Salomonis, Kam D Dahlquist, Karen Vranizan, Steven C Lawlor, Bruce R Conklin Genome Biology 2003, 4:R7 (6 January 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP.

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