Genome Biology | Volume 4 Issue 4

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	Volume 4 Issue 4
	Comment
	Comment Judgement call Gregory A Petsko Genome Biology 2003, 4:108 (28 March 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The editors of a number of life-science journals have released a new policy regarding the publication of reports of scientific research in areas that could potentially be of use to bioterrorists.
	Review
	Review Statistical tests for differential expression in cDNA microarray experiments Xiangqin Cui, Gary A Churchill Genome Biology 2003, 4:210 (17 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The simplest statistical method for extracting biological information from microarray data is the t test. Analysis of variance (ANOVA) and the mixed ANOVA model are general and powerful approaches for more complex microarray experiments.
	Protein family review Protein prenyltransferases Sebastian Maurer-Stroh, Stefan Washietl, Frank Eisenhaber Genome Biology 2003, 4:212 (1 April 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three different protein prenyltransferases catalyze the attachment of prenyl lipid anchors to a variety of eukaryotic proteins. Farnesyltransferase-inhibitor drugs have been developed as anti-cancer agents and may also be able to treat several other diseases.
	Minireview Modifications of histone cores and tails in V(D)J recombination Kathrin Muegge Genome Biology 2003, 4:211 (31 March 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study shows that methylated lysine 79 in the core region of histone H3 plays a role in regulating the rearrangement of V, D and J gene segments by providing a euchromatic 'mark' that may regulate access of the V(D)J recombinase.
	Opinion The mouse genome sequence - the end of the tail, or just the beginning? Janet Rossant, Stephen W Scherer Genome Biology 2003, 4:109 (1 April 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent flurry of papers on the mouse genome includes the description of the full genome assembly, analysis of the mouse transcriptome, the origin of interstrain variation, initial analysis of conserved non-coding regions and high-throughput expression analysis of a subset of genes. Each illustrates how the availability of the genome sequence will change the way mouse biologists do business in future.
	Report
	Paper report Articles selected by Faculty of 1000: Pseudomonas putida genome; SAGE analysis of cell death; array analysis of apoptosis; screen for phosphopeptide binding domain; using non-natural amino acids. Genome Biology 2003, 4:315 (6 March 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the Pseudomonas putida genome, SAGE and microarray analysis of cell death, a screen for phosphopeptide binding domains and an engineered bacterium that uses a non-natural amino acid.
	Paper report Articles selected by Faculty of 1000: proteomics of macromolecular complexes; verification of microarray data; chromosome 22 transcript map; arraying maize tissue-specific genes; profiling plant defense responses Genome Biology 2003, 4:316 (21 March 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the proteomics of macromolecular complexes, verification of microarray data, a transcript map of chromosome 22, arraying maize tissue-specific genes and profiling plant defense responses.
	Meeting report Survival strategies for transposons and genomes Sandra L Martin, David J Garfinkel Genome Biology 2003, 4:313 (28 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Keystone Symposium "Transposition and other genome rearrangements", Santa Fe, USA, 8-14 February 2003.
	Meeting report Microbial genome jambalaya Timothy D Read Genome Biology 2003, 4:314 (28 March 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third American Society of Microbiology (ASM) and The Institute for Genomic Research (TIGR) Microbial Genomes Conference, New Orleans, USA, 29 January to 1 February 2003.
	Deposited research article Extreme conservation of non-repetitive non-coding regions near HoxD complex of vertebrates Chilaka Sabarinadh, Subbaya Subramanian, Rakesh K Mishra Genome Biology 2003, 4:P2 (25 March 2003) Abstract \| Full text \| PDF \| Editor’s summary An unprecedented conservation of non-coding DNA sequences adjacent to the HoxD complex of vertebrates is reported here. Stretches of hundreds of base pairs in a 7kb region upstream of HoxD complex show 100% conservation from fish to human, suggesting a critical function for these sequences in the regulation of the HoxD complex.
	Research news Recombinant Vaccinia infects lab worker Ricki Lewis Genome Biology 2003, 4:spotlight-20030401-01 (1 April 2003) Abstract \| Full text \| Editor’s summary Development of pox-like lesions suggests vaccination doesn't protect against altered viruses.
	Research news Biomics Centre opens in UK Laura Spinney Genome Biology 2003, 4:spotlight-20030401-03 (1 April 2003) Abstract \| Full text \| Editor’s summary New research center brings together four "-omics" to tackle clinical problems.
	Research news Promega wins Taq patent round Peg Brickley Genome Biology 2003, 4:spotlight-20030102-03 (1 April 2003) Abstract \| Full text \| Editor’s summary Court confirms fudged science behind Roche PCR patent, but fight for enzyme rights is not over.
	Research news Bacteria help plants grow C L Bishop Genome Biology 2003, 4:spotlight-20030402-01 (2 April 2003) Abstract \| Full text \| Editor’s summary Volatiles released by soil microorganisms stimulate growth of Arabidopsis.
	Research news PAC-p53 interactions Tudor P Toma Genome Biology 2003, 4:spotlight-20030403-01 (3 April 2003) Abstract \| Full text \| Editor’s summary p53 uses a specific binding site to regulate both its target gene PAC1 and apoptosis.
	Research news tmRNA to the rescue Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030404-01 (4 April 2003) Abstract \| Full text \| Editor’s summary Cryo-EM sheds light on tmRNA-mediated ribosomal rescue during stalled protein production.
	Research news Latest SARS evidence Robert Walgate Genome Biology 2003, 4:spotlight-20030407-01 (7 April 2003) Abstract \| Full text \| Editor’s summary SARS almost certainly caused by new type of coronavirus - diagnostic tests being prepared.
	Research news Biobank debate heats up Pat Hagan Genome Biology 2003, 4:spotlight-20030408-02 (8 April 2003) Abstract \| Full text \| Editor’s summary New head of UK gene bank project tries to woo critics.
	Research news Science police needed? Peg Brickley Genome Biology 2003, 4:spotlight-20030408-01 (8 April 2003) Abstract \| Full text \| Editor’s summary Security specialist proposes international regulation of potentially dangerous research
	Research news Counting tillers Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030410-02 (10 April 2003) Abstract \| Full text \| Editor’s summary A novel gene, MOC1, controls branching and bud formation in rice.
	Research news Quick custom flu vaccines Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030410-01 (10 April 2003) Abstract \| Full text \| Editor’s summary Technique used to craft new H5N1 vaccine could speed development for all new strains.
	Research news 2003 Gairdner International Awards announced David Bruce Genome Biology 2003, 4:spotlight-20030411-02 (11 April 2003) Abstract \| Full text \| Editor’s summary The 2003 awards hail advances in neuroscience and immunology.
	Research news Compromise reached over German copyright bill Martina Habeck Genome Biology 2003, 4:spotlight-20030411-01 (11 April 2003) Abstract \| Full text \| Editor’s summary New law to allow access to digital scientific information should be passed this week.
	Research news Seven up Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030414-01 (14 April 2003) Abstract \| Full text \| Editor’s summary Completion of the sequence of human chromosome 7 enables the identification of candidate genes related to diseases such as autism.
	Research news Sobriety amid the celebration Peg Brickley Genome Biology 2003, 4:spotlight-20030414-02 (14 April 2003) Abstract \| Full text \| Editor’s summary In a week of landmark events for genomics, we survey the landscape.
	Research news Human genome project completed Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030415-01 (15 April 2003) Abstract \| Full text \| Editor’s summary The "final" version includes 99% of gene-containing DNA, and variation between individuals is identified as the next big challenge.
	Research news MRC scientists revolt Pat Hagan Genome Biology 2003, 4:spotlight-20030416-01 (16 April 2003) Abstract \| Full text \| Editor’s summary Staff are demanding the withdrawal of proposals to relocate the UK's National Institute of Medical Research.
	Research news WHO says coronavirus causes SARS Robert Walgate Genome Biology 2003, 4:spotlight-20030417-01 (17 April 2003) Abstract \| Full text \| Editor’s summary WHO announces the cause of SARS, and the genome sequence confirms its uniqueness and link to the disease.
	Research news Whither NHGRI? Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030417-02 (17 April 2003) Abstract \| Full text \| Editor’s summary Although the human genome is done, the genome institute still has plenty to do.
	Research news Postcard from the party Brendan Maher Genome Biology 2003, 4:spotlight-20030122-01 (22 April 2003) Abstract \| Full text \| Editor’s summary Celebrations for DNA and its sequence in humans.
	Research news Charles A. Janeway, Jr Diane Martindale Genome Biology 2003, 4:spotlight-20030122-02 (22 April 2003) Abstract \| Full text \| Editor’s summary The father of innate immunity has died, aged 60.
	Research news Control of Flowering C L Bishop Genome Biology 2003, 4:spotlight-20030422-03 (22 April 2003) Abstract \| Full text \| Editor’s summary Identifying the differences in flowering regulation between short- and long-day plants
	Research news Amino-acid cycling drives nitrogen fixation C L Bishop Genome Biology 2003, 4:spotlight-20030422-04 (22 April 2003) Abstract \| Full text \| Editor’s summary A complex amino-acid cycle is essential for symbiotic nitrogen fixation in pea nodules
	Research news Life cycle control of Chlamydomonas reinhardtii C L Bishop Genome Biology 2003, 4:spotlight-20030423-01 (23 April 2003) Abstract \| Full text \| Editor’s summary The photoreceptor phototropin controls the sexual life cycle of C. reinhardtii
	Research news Whole-genome sequencing of a spirochaete Cathy Holding Genome Biology 2003, 4:spotlight-20030424-01 (24 April 2003) Abstract \| Full text \| Editor’s summary The genome of the causative agent of leptospirosis has beeen sequenced.
	Research news Maternal impact of chromatin reorganization Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030425-01 (25 April 2003) Abstract \| Full text \| Editor’s summary An oocyte-derived protein, NPM2, is essential for mammalian zygotic development.
	Research news Who'll sweep the Gene Sweepstake? Charles Q Choi Genome Biology 2003, 4:spotlight-20030430-01 (30 April 2003) Abstract \| Full text \| Editor’s summary Betting is still open on the long-debated number of genes in the human genome
	Research news Sequencers come together Cathy Holding Genome Biology 2004, 4:spotlight-20040401-01 (1 April 2004) Abstract \| Full text \| Editor’s summary The Brown Norway rat genome sequence is obtained from the whole genome shotgun and clone-by-clone approach
	Research news Bacterial genomics in Spain Xavier Bosch Genome Biology 2004, 4:spotlight-20040405-01 (5 April 2004) Abstract \| Full text \| Editor’s summary Scientists set up a research network to focus on an 'underappreciated' discipline
	Research news Minding the genome gap Stephen Pincock Genome Biology 2004, 4:spotlight-20040405-01 (6 April 2004) Abstract \| Full text \| Editor’s summary HUGO conference opens with plea to refocus efforts on differences, not disease genotypes
	Research news Comparing relatives Stephen Pincock Genome Biology 2004, 4:spotlight-20040406-02 (6 April 2004) Abstract \| Full text \| Editor’s summary Developments in chimp and kangaroo genomics offer different insights into human genetics
	Research news Genes constantly evolve Cathy Holding Genome Biology 2004, 4:spotlight-20040407-01 (7 April 2004) Abstract \| Full text \| Editor’s summary Drosophila fixed coding regions duplicate and degenerate to rapidly create new genes
	Research news Chlamydial evolution probed Cathy Holding Genome Biology 2004, 4:spotlight-20040413-01 (13 April 2004) Abstract \| Full text \| Editor’s summary Species evolved within primitive eukaryotic cells and had virulence factors now widespread
	Research news Copies are key for gene networks Cathy Holding Genome Biology 2004, 4:spotlight-20040415-01 (15 April 2004) Abstract \| Full text \| Editor’s summary The majority of network evolution appears to have occurred by duplication and divergence
	Research news Can sequence predict function? Cathy Holding Genome Biology 2004, 4:spotlight-20040419-01 (19 April 2004) Abstract \| Full text \| Editor’s summary An algorithm could provide the framework for the confirmation of protein function
	Research news Human genome database unveiled Tabitha M Powledge Genome Biology 2004, 4:spotlight-20040421-01 (21 April 2004) Abstract \| Full text \| Editor’s summary A new resource emphasizes the need for multiple genomic datasets to increase clarity
	Research news UK risks 'losing science data' Robert Walgate Genome Biology 2004, 4:spotlight-20040422-01 (22 April 2004) Abstract \| Full text \| Editor’s summary British Library says its digital storage plan is critical to underpin science
	Research news Finding recombination hotspots Cathy Holding Genome Biology 2004, 4:spotlight-20040423-01 (23 April 2004) Abstract \| Full text \| Editor’s summary A mathematical method is valid at low and fine resolution, but its use for disease mapping is doubted
	Research news John Maynard Smith dies Catherine Brahic Genome Biology 2004, 4:spotlight-20040427-01 (27 April 2004) Abstract \| Full text \| Editor’s summary The evolutionary biologist applied game theory to evolution, and defended neo-Darwinism
	Research news NIH misconduct rules reviewed Ted Agres Genome Biology 2004, 4:spotlight-20040427-02 (27 April 2004) Abstract \| Full text \| Editor’s summary Professional societies support revisions to rules on whistleblowers and research misconduct
	Research news SARS escaped Beijing lab twice Robert Walgate Genome Biology 2004, 4:spotlight-20040427-03 (27 April 2004) Abstract \| Full text \| Editor’s summary Laboratory safety at the Chinese Institute of Virology is under close scrutiny
	Research news Swiss computing center opens Martina Habeck Genome Biology 2004, 4:spotlight-20040428-02 (28 April 2004) Abstract \| Full text \| Editor’s summary Scientists hope to develop life sciences computing tools of the future
	Research news Open-access journals rank well Alison McCook Genome Biology 2004, 4:spotlight-20040422-01 (28 April 2004) Abstract \| Full text \| Editor’s summary Report suggests similar impact factors for open-access and traditional journals
	Research news Genome analysis without compare David Secko Genome Biology 2004, 4:spotlight-20040429-01 (29 April 2004) Abstract \| Full text \| Editor’s summary A method measures selection pressures on a single genome without the use of comparative genomics
	Research news Viral micro RNAs identified Cathy Holding Genome Biology 2004, 4:spotlight-20040430-01 (30 April 2004) Abstract \| Full text \| Editor’s summary Genome-encoded micro RNAs isolated from Epstein-Barr virus, but their functions are unclear
	Research
	Research Haplotypic analysis of the TNF locus by association efficiency and entropy Hans Ackerman, Stanley Usen, Richard Mott, Anna Richardson, Fatoumatta Sisay-Joof, Pauline Katundu, Terrie Taylor, Ryk Ward, Malcolm Molyneux, Margaret Pinder, Dominic P Kwiatkowski Genome Biology 2003, 4:R24 (17 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To understand the causal basis of TNF associations with disease, it is necessary to understand the haplotypic structure of this locus. The TNF locus in Gambian and Malawi human samples is haplotypically diverse and has a rich history of intragenic recombination. As a consequence, a large proportion of TNF single nucleotide polymorphisms (SNPs) must be typed to detect a disease-modifying SNP at this locus. The most informative subset of SNPs to genotype differs between the two populations.
	Research Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence Joseph Cheung, Xavier Estivill, Razi Khaja, Jeffrey R MacDonald, Ken Lau, Lap-Chee Tsui, Stephen W Scherer Genome Biology 2003, 4:R25 (17 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Rapid computational heuristics have been developed based on BLAST analysis to detect segmental duplications, as well as regions containing potential sequence misassignments in the human genome assemblies. Most of the sequences in the human genome that have undergone recent segmental duplications have now been identified.
	Research Analysis and functional classification of transcripts from the nematode Meloidogyne incognita James P McCarter, Makedonka Dautova Mitreva, John Martin, Mike Dante, Todd Wylie, Uma Rao, Deana Pape, Yvette Bowers, Brenda Theising, Claire V Murphy, Andrew P Kloek, Brandi J Chiapelli, Sandra W Clifton, David Mck Bird, Robert H Waterston Genome Biology 2003, 4:R26 (31 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary As an entrée to characterizing plant parasitic nematode genomes, 5,700 expressed sequence tags (ESTs) from the infective second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita have been analyzed. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes.
	Software ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data Hsien-Da Huang, Jorng-Tzong Horng, Chau-Chin Lee, Baw-Jhiune Liu Genome Biology 2003, 4:R29 (14 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences.
	Software MatchMiner: a tool for batch navigation among gene and gene product identifiers Kimberly J Bussey, David Kane, Margot Sunshine, Sudar Narasimhan, Satoshi Nishizuka, William C Reinhold, Barry Zeeberg, Ajay, John N Weinstein Genome Biology 2003, 4:R27 (25 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research.
	Software GoMiner: a resource for biological interpretation of genomic and proteomic data Barry R Zeeberg, Weimin Feng, Geoffrey Wang, May D Wang, Anthony T Fojo, Margot Sunshine, Sudarshan Narasimhan, David W Kane, William C Reinhold, Samir Lababidi, Kimberly J Bussey, Joseph Riss, J Barrett, John N Weinstein Genome Biology 2003, 4:R28 (25 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GoMiner, a program package that organizes lists of 'interesting' genes for biological interpretation in the context of the Gene Ontology, has been developed.

	Volume 4 Issue 4
	Comment
	Comment Judgement call Gregory A Petsko Genome Biology 2003, 4:108 (28 March 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The editors of a number of life-science journals have released a new policy regarding the publication of reports of scientific research in areas that could potentially be of use to bioterrorists.
	Review
	Review Statistical tests for differential expression in cDNA microarray experiments Xiangqin Cui, Gary A Churchill Genome Biology 2003, 4:210 (17 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The simplest statistical method for extracting biological information from microarray data is the t test. Analysis of variance (ANOVA) and the mixed ANOVA model are general and powerful approaches for more complex microarray experiments.
	Protein family review Protein prenyltransferases Sebastian Maurer-Stroh, Stefan Washietl, Frank Eisenhaber Genome Biology 2003, 4:212 (1 April 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three different protein prenyltransferases catalyze the attachment of prenyl lipid anchors to a variety of eukaryotic proteins. Farnesyltransferase-inhibitor drugs have been developed as anti-cancer agents and may also be able to treat several other diseases.
	Minireview Modifications of histone cores and tails in V(D)J recombination Kathrin Muegge Genome Biology 2003, 4:211 (31 March 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study shows that methylated lysine 79 in the core region of histone H3 plays a role in regulating the rearrangement of V, D and J gene segments by providing a euchromatic 'mark' that may regulate access of the V(D)J recombinase.
	Opinion The mouse genome sequence - the end of the tail, or just the beginning? Janet Rossant, Stephen W Scherer Genome Biology 2003, 4:109 (1 April 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent flurry of papers on the mouse genome includes the description of the full genome assembly, analysis of the mouse transcriptome, the origin of interstrain variation, initial analysis of conserved non-coding regions and high-throughput expression analysis of a subset of genes. Each illustrates how the availability of the genome sequence will change the way mouse biologists do business in future.
	Report
	Paper report Articles selected by Faculty of 1000: Pseudomonas putida genome; SAGE analysis of cell death; array analysis of apoptosis; screen for phosphopeptide binding domain; using non-natural amino acids. Genome Biology 2003, 4:315 (6 March 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the Pseudomonas putida genome, SAGE and microarray analysis of cell death, a screen for phosphopeptide binding domains and an engineered bacterium that uses a non-natural amino acid.
	Paper report Articles selected by Faculty of 1000: proteomics of macromolecular complexes; verification of microarray data; chromosome 22 transcript map; arraying maize tissue-specific genes; profiling plant defense responses Genome Biology 2003, 4:316 (21 March 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the proteomics of macromolecular complexes, verification of microarray data, a transcript map of chromosome 22, arraying maize tissue-specific genes and profiling plant defense responses.
	Meeting report Survival strategies for transposons and genomes Sandra L Martin, David J Garfinkel Genome Biology 2003, 4:313 (28 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Keystone Symposium "Transposition and other genome rearrangements", Santa Fe, USA, 8-14 February 2003.
	Meeting report Microbial genome jambalaya Timothy D Read Genome Biology 2003, 4:314 (28 March 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third American Society of Microbiology (ASM) and The Institute for Genomic Research (TIGR) Microbial Genomes Conference, New Orleans, USA, 29 January to 1 February 2003.
	Deposited research article Extreme conservation of non-repetitive non-coding regions near HoxD complex of vertebrates Chilaka Sabarinadh, Subbaya Subramanian, Rakesh K Mishra Genome Biology 2003, 4:P2 (25 March 2003) Abstract \| Full text \| PDF \| Editor’s summary An unprecedented conservation of non-coding DNA sequences adjacent to the HoxD complex of vertebrates is reported here. Stretches of hundreds of base pairs in a 7kb region upstream of HoxD complex show 100% conservation from fish to human, suggesting a critical function for these sequences in the regulation of the HoxD complex.
	Research news Recombinant Vaccinia infects lab worker Ricki Lewis Genome Biology 2003, 4:spotlight-20030401-01 (1 April 2003) Abstract \| Full text \| Editor’s summary Development of pox-like lesions suggests vaccination doesn't protect against altered viruses.
	Research news Biomics Centre opens in UK Laura Spinney Genome Biology 2003, 4:spotlight-20030401-03 (1 April 2003) Abstract \| Full text \| Editor’s summary New research center brings together four "-omics" to tackle clinical problems.
	Research news Promega wins Taq patent round Peg Brickley Genome Biology 2003, 4:spotlight-20030102-03 (1 April 2003) Abstract \| Full text \| Editor’s summary Court confirms fudged science behind Roche PCR patent, but fight for enzyme rights is not over.
	Research news Bacteria help plants grow C L Bishop Genome Biology 2003, 4:spotlight-20030402-01 (2 April 2003) Abstract \| Full text \| Editor’s summary Volatiles released by soil microorganisms stimulate growth of Arabidopsis.
	Research news PAC-p53 interactions Tudor P Toma Genome Biology 2003, 4:spotlight-20030403-01 (3 April 2003) Abstract \| Full text \| Editor’s summary p53 uses a specific binding site to regulate both its target gene PAC1 and apoptosis.
	Research news tmRNA to the rescue Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030404-01 (4 April 2003) Abstract \| Full text \| Editor’s summary Cryo-EM sheds light on tmRNA-mediated ribosomal rescue during stalled protein production.
	Research news Latest SARS evidence Robert Walgate Genome Biology 2003, 4:spotlight-20030407-01 (7 April 2003) Abstract \| Full text \| Editor’s summary SARS almost certainly caused by new type of coronavirus - diagnostic tests being prepared.
	Research news Biobank debate heats up Pat Hagan Genome Biology 2003, 4:spotlight-20030408-02 (8 April 2003) Abstract \| Full text \| Editor’s summary New head of UK gene bank project tries to woo critics.
	Research news Science police needed? Peg Brickley Genome Biology 2003, 4:spotlight-20030408-01 (8 April 2003) Abstract \| Full text \| Editor’s summary Security specialist proposes international regulation of potentially dangerous research
	Research news Counting tillers Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030410-02 (10 April 2003) Abstract \| Full text \| Editor’s summary A novel gene, MOC1, controls branching and bud formation in rice.
	Research news Quick custom flu vaccines Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030410-01 (10 April 2003) Abstract \| Full text \| Editor’s summary Technique used to craft new H5N1 vaccine could speed development for all new strains.
	Research news 2003 Gairdner International Awards announced David Bruce Genome Biology 2003, 4:spotlight-20030411-02 (11 April 2003) Abstract \| Full text \| Editor’s summary The 2003 awards hail advances in neuroscience and immunology.
	Research news Compromise reached over German copyright bill Martina Habeck Genome Biology 2003, 4:spotlight-20030411-01 (11 April 2003) Abstract \| Full text \| Editor’s summary New law to allow access to digital scientific information should be passed this week.
	Research news Seven up Jonathan B Weitzman Genome Biology 2003, 4:spotlight-20030414-01 (14 April 2003) Abstract \| Full text \| Editor’s summary Completion of the sequence of human chromosome 7 enables the identification of candidate genes related to diseases such as autism.
	Research news Sobriety amid the celebration Peg Brickley Genome Biology 2003, 4:spotlight-20030414-02 (14 April 2003) Abstract \| Full text \| Editor’s summary In a week of landmark events for genomics, we survey the landscape.
	Research news Human genome project completed Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030415-01 (15 April 2003) Abstract \| Full text \| Editor’s summary The "final" version includes 99% of gene-containing DNA, and variation between individuals is identified as the next big challenge.
	Research news MRC scientists revolt Pat Hagan Genome Biology 2003, 4:spotlight-20030416-01 (16 April 2003) Abstract \| Full text \| Editor’s summary Staff are demanding the withdrawal of proposals to relocate the UK's National Institute of Medical Research.
	Research news WHO says coronavirus causes SARS Robert Walgate Genome Biology 2003, 4:spotlight-20030417-01 (17 April 2003) Abstract \| Full text \| Editor’s summary WHO announces the cause of SARS, and the genome sequence confirms its uniqueness and link to the disease.
	Research news Whither NHGRI? Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030417-02 (17 April 2003) Abstract \| Full text \| Editor’s summary Although the human genome is done, the genome institute still has plenty to do.
	Research news Postcard from the party Brendan Maher Genome Biology 2003, 4:spotlight-20030122-01 (22 April 2003) Abstract \| Full text \| Editor’s summary Celebrations for DNA and its sequence in humans.
	Research news Charles A. Janeway, Jr Diane Martindale Genome Biology 2003, 4:spotlight-20030122-02 (22 April 2003) Abstract \| Full text \| Editor’s summary The father of innate immunity has died, aged 60.
	Research news Control of Flowering C L Bishop Genome Biology 2003, 4:spotlight-20030422-03 (22 April 2003) Abstract \| Full text \| Editor’s summary Identifying the differences in flowering regulation between short- and long-day plants
	Research news Amino-acid cycling drives nitrogen fixation C L Bishop Genome Biology 2003, 4:spotlight-20030422-04 (22 April 2003) Abstract \| Full text \| Editor’s summary A complex amino-acid cycle is essential for symbiotic nitrogen fixation in pea nodules
	Research news Life cycle control of Chlamydomonas reinhardtii C L Bishop Genome Biology 2003, 4:spotlight-20030423-01 (23 April 2003) Abstract \| Full text \| Editor’s summary The photoreceptor phototropin controls the sexual life cycle of C. reinhardtii
	Research news Whole-genome sequencing of a spirochaete Cathy Holding Genome Biology 2003, 4:spotlight-20030424-01 (24 April 2003) Abstract \| Full text \| Editor’s summary The genome of the causative agent of leptospirosis has beeen sequenced.
	Research news Maternal impact of chromatin reorganization Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030425-01 (25 April 2003) Abstract \| Full text \| Editor’s summary An oocyte-derived protein, NPM2, is essential for mammalian zygotic development.
	Research news Who'll sweep the Gene Sweepstake? Charles Q Choi Genome Biology 2003, 4:spotlight-20030430-01 (30 April 2003) Abstract \| Full text \| Editor’s summary Betting is still open on the long-debated number of genes in the human genome
	Research news Sequencers come together Cathy Holding Genome Biology 2004, 4:spotlight-20040401-01 (1 April 2004) Abstract \| Full text \| Editor’s summary The Brown Norway rat genome sequence is obtained from the whole genome shotgun and clone-by-clone approach
	Research news Bacterial genomics in Spain Xavier Bosch Genome Biology 2004, 4:spotlight-20040405-01 (5 April 2004) Abstract \| Full text \| Editor’s summary Scientists set up a research network to focus on an 'underappreciated' discipline
	Research news Minding the genome gap Stephen Pincock Genome Biology 2004, 4:spotlight-20040405-01 (6 April 2004) Abstract \| Full text \| Editor’s summary HUGO conference opens with plea to refocus efforts on differences, not disease genotypes
	Research news Comparing relatives Stephen Pincock Genome Biology 2004, 4:spotlight-20040406-02 (6 April 2004) Abstract \| Full text \| Editor’s summary Developments in chimp and kangaroo genomics offer different insights into human genetics
	Research news Genes constantly evolve Cathy Holding Genome Biology 2004, 4:spotlight-20040407-01 (7 April 2004) Abstract \| Full text \| Editor’s summary Drosophila fixed coding regions duplicate and degenerate to rapidly create new genes
	Research news Chlamydial evolution probed Cathy Holding Genome Biology 2004, 4:spotlight-20040413-01 (13 April 2004) Abstract \| Full text \| Editor’s summary Species evolved within primitive eukaryotic cells and had virulence factors now widespread
	Research news Copies are key for gene networks Cathy Holding Genome Biology 2004, 4:spotlight-20040415-01 (15 April 2004) Abstract \| Full text \| Editor’s summary The majority of network evolution appears to have occurred by duplication and divergence
	Research news Can sequence predict function? Cathy Holding Genome Biology 2004, 4:spotlight-20040419-01 (19 April 2004) Abstract \| Full text \| Editor’s summary An algorithm could provide the framework for the confirmation of protein function
	Research news Human genome database unveiled Tabitha M Powledge Genome Biology 2004, 4:spotlight-20040421-01 (21 April 2004) Abstract \| Full text \| Editor’s summary A new resource emphasizes the need for multiple genomic datasets to increase clarity
	Research news UK risks 'losing science data' Robert Walgate Genome Biology 2004, 4:spotlight-20040422-01 (22 April 2004) Abstract \| Full text \| Editor’s summary British Library says its digital storage plan is critical to underpin science
	Research news Finding recombination hotspots Cathy Holding Genome Biology 2004, 4:spotlight-20040423-01 (23 April 2004) Abstract \| Full text \| Editor’s summary A mathematical method is valid at low and fine resolution, but its use for disease mapping is doubted
	Research news John Maynard Smith dies Catherine Brahic Genome Biology 2004, 4:spotlight-20040427-01 (27 April 2004) Abstract \| Full text \| Editor’s summary The evolutionary biologist applied game theory to evolution, and defended neo-Darwinism
	Research news NIH misconduct rules reviewed Ted Agres Genome Biology 2004, 4:spotlight-20040427-02 (27 April 2004) Abstract \| Full text \| Editor’s summary Professional societies support revisions to rules on whistleblowers and research misconduct
	Research news SARS escaped Beijing lab twice Robert Walgate Genome Biology 2004, 4:spotlight-20040427-03 (27 April 2004) Abstract \| Full text \| Editor’s summary Laboratory safety at the Chinese Institute of Virology is under close scrutiny
	Research news Swiss computing center opens Martina Habeck Genome Biology 2004, 4:spotlight-20040428-02 (28 April 2004) Abstract \| Full text \| Editor’s summary Scientists hope to develop life sciences computing tools of the future
	Research news Open-access journals rank well Alison McCook Genome Biology 2004, 4:spotlight-20040422-01 (28 April 2004) Abstract \| Full text \| Editor’s summary Report suggests similar impact factors for open-access and traditional journals
	Research news Genome analysis without compare David Secko Genome Biology 2004, 4:spotlight-20040429-01 (29 April 2004) Abstract \| Full text \| Editor’s summary A method measures selection pressures on a single genome without the use of comparative genomics
	Research news Viral micro RNAs identified Cathy Holding Genome Biology 2004, 4:spotlight-20040430-01 (30 April 2004) Abstract \| Full text \| Editor’s summary Genome-encoded micro RNAs isolated from Epstein-Barr virus, but their functions are unclear
	Research
	Research Haplotypic analysis of the TNF locus by association efficiency and entropy Hans Ackerman, Stanley Usen, Richard Mott, Anna Richardson, Fatoumatta Sisay-Joof, Pauline Katundu, Terrie Taylor, Ryk Ward, Malcolm Molyneux, Margaret Pinder, Dominic P Kwiatkowski Genome Biology 2003, 4:R24 (17 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To understand the causal basis of TNF associations with disease, it is necessary to understand the haplotypic structure of this locus. The TNF locus in Gambian and Malawi human samples is haplotypically diverse and has a rich history of intragenic recombination. As a consequence, a large proportion of TNF single nucleotide polymorphisms (SNPs) must be typed to detect a disease-modifying SNP at this locus. The most informative subset of SNPs to genotype differs between the two populations.
	Research Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence Joseph Cheung, Xavier Estivill, Razi Khaja, Jeffrey R MacDonald, Ken Lau, Lap-Chee Tsui, Stephen W Scherer Genome Biology 2003, 4:R25 (17 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Rapid computational heuristics have been developed based on BLAST analysis to detect segmental duplications, as well as regions containing potential sequence misassignments in the human genome assemblies. Most of the sequences in the human genome that have undergone recent segmental duplications have now been identified.
	Research Analysis and functional classification of transcripts from the nematode Meloidogyne incognita James P McCarter, Makedonka Dautova Mitreva, John Martin, Mike Dante, Todd Wylie, Uma Rao, Deana Pape, Yvette Bowers, Brenda Theising, Claire V Murphy, Andrew P Kloek, Brandi J Chiapelli, Sandra W Clifton, David Mck Bird, Robert H Waterston Genome Biology 2003, 4:R26 (31 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary As an entrée to characterizing plant parasitic nematode genomes, 5,700 expressed sequence tags (ESTs) from the infective second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita have been analyzed. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes.
	Software ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data Hsien-Da Huang, Jorng-Tzong Horng, Chau-Chin Lee, Baw-Jhiune Liu Genome Biology 2003, 4:R29 (14 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences.
	Software MatchMiner: a tool for batch navigation among gene and gene product identifiers Kimberly J Bussey, David Kane, Margot Sunshine, Sudar Narasimhan, Satoshi Nishizuka, William C Reinhold, Barry Zeeberg, Ajay, John N Weinstein Genome Biology 2003, 4:R27 (25 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research.
	Software GoMiner: a resource for biological interpretation of genomic and proteomic data Barry R Zeeberg, Weimin Feng, Geoffrey Wang, May D Wang, Anthony T Fojo, Margot Sunshine, Sudarshan Narasimhan, David W Kane, William C Reinhold, Samir Lababidi, Kimberly J Bussey, Joseph Riss, J Barrett, John N Weinstein Genome Biology 2003, 4:R28 (25 March 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GoMiner, a program package that organizes lists of 'interesting' genes for biological interpretation in the context of the Gene Ontology, has been developed.

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