Genome Biology | Volume 2 Issue 12

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 2 Issue 12
	Comment
	Comment A piece of the action Gregory A Petsko Genome Biology 2001, 2:comment1014-comment1014.2 (22 November 2001) Full text \| PDF \| PubMed \| Editor’s summary On the one hand we have an embarrassment of riches in terms of NIH budget, while on the other we have people who leave science for want of a small amount of initial funding.
	Review
	Protein family review Family-B G-protein-coupled receptors Anthony J Harmar Genome Biology 2001, 2:reviews3013-reviews3013.10 (23 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary G-protein-coupled receptors of family B (also called the secretin-receptor family) include receptors for polypeptide hormones, molecules thought to mediate intercellular interactions and proteins that regulate stress responses and longevity. They share a common molecular architecture (with seven putative transmembrane segments) with other G-protein-coupled receptors and are found in all animals.
	Protein family review Granzymes: a family of lymphocyte granule serine proteases Joseph A Trapani Genome Biology 2001, 2:reviews3014-reviews3014.7 (23 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Granzymes, a family of serine proteases, are expressed exclusively by cytotoxic T lymphocytes and natural killer (NK) cells, of the immune system and generally induce apoptosis. They can be grouped into three subfamilies according to substrate specificity and genomic location.
	Minireview Genome interdependence in insect-bacterium symbioses Evelyn Zientz, Francisco J Silva, Roy Gross Genome Biology 2001, 2:reviews1032-reviews1032.6 (22 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Modern genomic techniques are providing exciting new information about the molecular basis and the biological roles of symbioses between unicellular and multicellular organisms
	Minireview Muscular expressions: profiling genes in complex tissues Richard Hampson, Simon M Hughes Genome Biology 2001, 2:reviews1033-reviews1033.3 (22 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Four recent gene-expression studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to fundamental new insights.
	Report
	Web report Comparative analyses of biomolecules Vasudeva Ginjala Genome Biology 2001, 2:reports2018 (9 November 2001) Abstract \| Full text
	Paper report Polymorphisms in drug metabolism John C Rockett Genome Biology 2001, 2:reports0044 (28 November 2001) Abstract \| Full text \| Editor’s summary Systematic examination of the gene encoding CYP2B6, a human cytochrome P450, has characterized genetic polymorphisms that might account for its variability in expression and function between individuals.
	Paper report Two species of African elephants John C Rockett Genome Biology 2001, 2:reports0045 (28 November 2001) Abstract \| Full text
	Paper report Predicting drug sensitivity Agnieszka M Lichanska Genome Biology 2001, 2:reports0046 (28 November 2001) Abstract \| Full text
	Paper report Secreted bacterial proteins Agnieszka M Lichanska Genome Biology 2001, 2:reports0047 (28 November 2001) Abstract \| Full text \| Editor’s summary Predicted extracellular proteins of Bacillus subtilis have been compared with the experimental identification of the extracellular proteome by two-dimensional gel electrophoresis, peptide sequencing and mass spectrometry.
	Paper report Molecular diversity of a family of pain receptors Maria Östergård Genome Biology 2001, 2:reports0048 (28 November 2001) Abstract \| Full text \| Editor’s summary A large family of G-protein-coupled receptors, with sequence homology to the oncoprotein MAS1, has been shown to be specifically expressed in nociceptive sensory neurons.
	Meeting report Chromosome replication: from ORC to fork Conrad A Nieduszynski, Anne D Donaldson, J Julian Blow Genome Biology 2001, 2:reports4030-reports4030.3 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2001 Eukaryotic DNA Replication meeting, Cold Spring Harbor Laboratory, New York, 5-9 September 2001.
	Meeting report Chromosomal vectors for gene therapy: castles in the air? Wendy A Bickmore Genome Biology 2001, 2:reports4031-reports4031.2 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the ESF/LESC Exploratory Workshop 'Understanding Chromosome Behaviour: Prospects for Constructing Chromosome-Based Vectors for Gene Therapy', Elmau, Germany, 27-30 September 2001.
	Meeting report Mycobacteria: from genomes to disease control M Jo Colston Genome Biology 2001, 2:reports4032-reports4032.3 (21 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'Mycobacteria - new developments' at the 149th meeting of Society for General Microbiology, University of East Anglia, Norwich, UK, 10-13 September 2001.
	Meeting report The life of brine: halophiles in 2001 Mike Dyall-Smith, Michael Danson Genome Biology 2001, 2:reports4033-reports4033.3 (21 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the International conference on Halophilic Microorganisms, Sevilla, Spain, 23-27 September 2001.
	Deposited research article Microarray data analysis: a practical approach for selecting differentially expressed genes David M Mutch, Alvin Berger, Robert Mansourian, Andreas Rytz, Matthew-Alan Roberts Genome Biology 2001, 2:preprint0009-preprint0009.29 (16 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for extracting differentially expressed genes across any number of experimental samples by evaluating the maximum fold change across all experimental conditions and all absolute expression levels has been tested using expression data from livers of mice in a nutritional experiment.
	Research news Wood genomics Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011203-01 (3 December 2001) Abstract \| Full text \| Editor’s summary Transcript profiling identifies groups of genes associated with different developmental stages during the formation of wood in trees.
	Research news Genes repressed by GDNF Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011204-01 (4 December 2001) Abstract \| Full text \| Editor’s summary The genes down-regulated by the glial cell-line-derived neurotrophic factor may account for the factor's inhibition of neurite growth.
	Research news Guarding the Giardia genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011205-01 (5 December 2001) Abstract \| Full text \| Editor’s summary Two active transposons in the Giardia genome are found in subtelomeric regions and may prevent telomere decay.
	Research news End-joining in yeast Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011206-01 (6 December 2001) Abstract \| Full text \| Editor’s summary Two genes have been found to down-regulate the non-homologous end-joining pathway in meiotic diploid yeast cells.
	Research news Leukemia translocations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011207-01 (7 December 2001) Abstract \| Full text \| Editor’s summary Expression profiling defines a distinct class of lymphoblastic leukemia caused by translocations within the MLL gene.
	Research news Amplifying the signal Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011210-01 (10 December 2001) Abstract \| Full text \| Editor’s summary A two-step approach can be used to amplify marker gene expression for non-invasive imaging.
	Research news Regulating adeno-associated virus Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011211-01 (11 December 2001) Abstract \| Full text \| Editor’s summary A genetic screen has identified a cellular protein that can regulate the replication and production of the potential gene therapy-vector, adeno-associated virus.
	Research news Bugs in flies Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011212-01 (12 December 2001) Abstract \| Full text \| Editor’s summary Microarray analysis has identified a number of novel Drosophila genes that are induced by microbial infection.
	Research news Telomere capping Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011213-01 (13 December 2001) Abstract \| Full text \| Editor’s summary Analysis of knockout mice has revealed a role for DNA-PK in mammalian telomere capping.
	Research news Double mutations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011214-01 (14 December 2001) Abstract \| Full text \| Editor’s summary A high-throughput strategy identifies synthetic lethality of thousands of yeast genes.
	Research news Mono-allelic expression in trypanosomes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011217-02 (17 December 2001) Abstract \| Full text \| Editor’s summary Localization to an extranucleolar body containing RNA polymerase I determines expression of active trypanosome loci during infection.
	Research news Wellcome Trust buys Crick's archives Pat Hagan Genome Biology 2001, 2:spotlight-20011217-01 (17 December 2001) Abstract \| Full text \| Editor’s summary The Wellcome Trust and Heritage Lottery Fund have combined to secure open access to Francis Crick's papers.
	Research news Evolving without sex Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011218-01 (18 December 2001) Abstract \| Full text \| Editor’s summary Some asexual fungi have evolved distinct genomes within a single individual, accumulating mutations without the need for recombination.
	Research news Green flies Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011219-01 (19 December 2001) Abstract \| Full text \| Editor’s summary A fluorescent protein-trap strategy identifies new Drosophila genes with different subcellular distributions.
	Research news Death domains, dysplasia and development Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011220-01 (20 December 2001) Abstract \| Full text \| Editor’s summary The mouse crinkled locus encodes a death-domain adaptor protein associated with hypohidrotic ectodermal dysplasia.
	Research news Three-spined sticklebacks Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011221-01 (21 December 2001) Abstract \| Full text \| Editor’s summary A linkage map for three-spined stickleback fish provides a reference for studies of morphological and behavioural changes during vertebrate evolution.
	Research news Primitive microbe enlightens evolution Tudor Toma Genome Biology 2001, 2:spotlight-20011227-01 (27 December 2001) Abstract \| Full text \| Editor’s summary Single-celled choanoflagellates have a unique receptor tyrosine kinase that may be linked to the origin of multicellular animals.
	Research news Sir inhibitor Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011228-01 (28 December 2001) Abstract \| Full text \| Editor’s summary Splitomicin is a small molecule that inhibits the Sir2p silencing protein and phenocopies sir2 deletion in yeast.
	Research news Chromosome countdown: 22...21...20... Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011228-02 (28 December 2001) Abstract \| Full text \| Editor’s summary British scientists have added the sequence of chromosome 20 to the list of 'finished' human chromosomes.
	Research
	Research Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences Lakshminarayan M Iyer, L Aravind, Peer Bork, Kay Hofmann, Arcady R Mushegian, Igor B Zhulin, Eugene V Koonin Genome Biology 2001, 2:research0051-research0051.11 (13 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Six cases where application of novel or conventional computational methods for protein sequence and structure analysis led to non-trivial predictions that were subsequently supported by direct experiments were analyzed. On all occasions, the original prediction seemed unjustified, and in at least three cases an alternative, well-supported computational prediction, incompatible with the original one, could be derived.
	Research Computational prediction of membrane-tethered transcription factors Joel Zupicich, Steven E Brenner, William C Skarnes Genome Biology 2001, 2:research0050-research0050.6 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A handful of membrane-spanning transcription factors has been previously identified. To investigate the existence of other transmembrane transcription factors all proteins in SWISS-PROT/TrEMBL were computationally analyzed; 76 factors were identifed.
	Research The process of genome shrinkage in the obligate symbiont Buchnera aphidicola Nancy A Moran, Alex Mira Genome Biology 2001, 2:research0054-research0054.12 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To examine the process of genome reduction in symbionts, the tiny genome of the endosymbiont Buchnera aphidicola was compared to a reconstructed larger ancestral genome. On the basis of this comparison, 503 genes were eliminated from the Buchnera genome within syntenic fragments, and 1,403 genes were lost from the gaps between syntenic fragments, probably in connection with genome rearrangements.
	Research Development of an optimized interaction-mating protocol for large-scale yeast two-hybrid analyses Tim-Robert Soellick, Joachim F Uhrig Genome Biology 2001, 2:research0052-research0052.7 (15 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An optimized interaction mating protocol for the yeast two-hybrid system, which gives increased mating efficiencies has been devloped. This significantly reduces the effort and cost of cDNA library screening and allows multiple parallel approaches.
	Research Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins I King Jordan, Fyodor A Kondrashov, Igor B Rogozin, Roman L Tatusov, Yuri I Wolf, Eugene V Koonin Genome Biology 2001, 2:research0053-research0053.9 (20 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A simple relative rates test that attempts to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins has been developed. Relative rates of protein evolution are remarkably constant for the three species groups analyzed.
	Research Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls Andrew A Hill, Eugene L Brown, Maryann Z Whitley, Greg Tucker-Kellogg, Craig P Hunter, Donna K Slonim Genome Biology 2001, 2:research0055-research0055.13 (21 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparability of array results is necessary for the creation of large-scale gene expression databases. Normalization procedures for oligonucleotide arrays based on a common pool of known biotin-labeled cRNAs spiked into each hybridization are described and evaluated. Scaled frequency is as reproducible and accurate as global normalization.
	Correspondence
	Correspondence Flip-flop around the origin and terminus of replication in prokaryotic genomes Paweł Mackiewicz, Dorota Mackiewicz, Maria Kowalczuk, Stanisław Cebrat Genome Biology 2001, 2:interactions1004-interactions1004.4 (15 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Evidence for symmetric chromosomal inversions around the replication origin in bacteria by JA Eisen, JF Heidelberg, O White, SL Salzberg. Genome Biology 2000, 1:research0011.1-0011.9.

	Volume 2 Issue 12
	Comment
	Comment A piece of the action Gregory A Petsko Genome Biology 2001, 2:comment1014-comment1014.2 (22 November 2001) Full text \| PDF \| PubMed \| Editor’s summary On the one hand we have an embarrassment of riches in terms of NIH budget, while on the other we have people who leave science for want of a small amount of initial funding.
	Review
	Protein family review Family-B G-protein-coupled receptors Anthony J Harmar Genome Biology 2001, 2:reviews3013-reviews3013.10 (23 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary G-protein-coupled receptors of family B (also called the secretin-receptor family) include receptors for polypeptide hormones, molecules thought to mediate intercellular interactions and proteins that regulate stress responses and longevity. They share a common molecular architecture (with seven putative transmembrane segments) with other G-protein-coupled receptors and are found in all animals.
	Protein family review Granzymes: a family of lymphocyte granule serine proteases Joseph A Trapani Genome Biology 2001, 2:reviews3014-reviews3014.7 (23 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Granzymes, a family of serine proteases, are expressed exclusively by cytotoxic T lymphocytes and natural killer (NK) cells, of the immune system and generally induce apoptosis. They can be grouped into three subfamilies according to substrate specificity and genomic location.
	Minireview Genome interdependence in insect-bacterium symbioses Evelyn Zientz, Francisco J Silva, Roy Gross Genome Biology 2001, 2:reviews1032-reviews1032.6 (22 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Modern genomic techniques are providing exciting new information about the molecular basis and the biological roles of symbioses between unicellular and multicellular organisms
	Minireview Muscular expressions: profiling genes in complex tissues Richard Hampson, Simon M Hughes Genome Biology 2001, 2:reviews1033-reviews1033.3 (22 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Four recent gene-expression studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to fundamental new insights.
	Report
	Web report Comparative analyses of biomolecules Vasudeva Ginjala Genome Biology 2001, 2:reports2018 (9 November 2001) Abstract \| Full text
	Paper report Polymorphisms in drug metabolism John C Rockett Genome Biology 2001, 2:reports0044 (28 November 2001) Abstract \| Full text \| Editor’s summary Systematic examination of the gene encoding CYP2B6, a human cytochrome P450, has characterized genetic polymorphisms that might account for its variability in expression and function between individuals.
	Paper report Two species of African elephants John C Rockett Genome Biology 2001, 2:reports0045 (28 November 2001) Abstract \| Full text
	Paper report Predicting drug sensitivity Agnieszka M Lichanska Genome Biology 2001, 2:reports0046 (28 November 2001) Abstract \| Full text
	Paper report Secreted bacterial proteins Agnieszka M Lichanska Genome Biology 2001, 2:reports0047 (28 November 2001) Abstract \| Full text \| Editor’s summary Predicted extracellular proteins of Bacillus subtilis have been compared with the experimental identification of the extracellular proteome by two-dimensional gel electrophoresis, peptide sequencing and mass spectrometry.
	Paper report Molecular diversity of a family of pain receptors Maria Östergård Genome Biology 2001, 2:reports0048 (28 November 2001) Abstract \| Full text \| Editor’s summary A large family of G-protein-coupled receptors, with sequence homology to the oncoprotein MAS1, has been shown to be specifically expressed in nociceptive sensory neurons.
	Meeting report Chromosome replication: from ORC to fork Conrad A Nieduszynski, Anne D Donaldson, J Julian Blow Genome Biology 2001, 2:reports4030-reports4030.3 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2001 Eukaryotic DNA Replication meeting, Cold Spring Harbor Laboratory, New York, 5-9 September 2001.
	Meeting report Chromosomal vectors for gene therapy: castles in the air? Wendy A Bickmore Genome Biology 2001, 2:reports4031-reports4031.2 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the ESF/LESC Exploratory Workshop 'Understanding Chromosome Behaviour: Prospects for Constructing Chromosome-Based Vectors for Gene Therapy', Elmau, Germany, 27-30 September 2001.
	Meeting report Mycobacteria: from genomes to disease control M Jo Colston Genome Biology 2001, 2:reports4032-reports4032.3 (21 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'Mycobacteria - new developments' at the 149th meeting of Society for General Microbiology, University of East Anglia, Norwich, UK, 10-13 September 2001.
	Meeting report The life of brine: halophiles in 2001 Mike Dyall-Smith, Michael Danson Genome Biology 2001, 2:reports4033-reports4033.3 (21 November 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the International conference on Halophilic Microorganisms, Sevilla, Spain, 23-27 September 2001.
	Deposited research article Microarray data analysis: a practical approach for selecting differentially expressed genes David M Mutch, Alvin Berger, Robert Mansourian, Andreas Rytz, Matthew-Alan Roberts Genome Biology 2001, 2:preprint0009-preprint0009.29 (16 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method for extracting differentially expressed genes across any number of experimental samples by evaluating the maximum fold change across all experimental conditions and all absolute expression levels has been tested using expression data from livers of mice in a nutritional experiment.
	Research news Wood genomics Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011203-01 (3 December 2001) Abstract \| Full text \| Editor’s summary Transcript profiling identifies groups of genes associated with different developmental stages during the formation of wood in trees.
	Research news Genes repressed by GDNF Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011204-01 (4 December 2001) Abstract \| Full text \| Editor’s summary The genes down-regulated by the glial cell-line-derived neurotrophic factor may account for the factor's inhibition of neurite growth.
	Research news Guarding the Giardia genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011205-01 (5 December 2001) Abstract \| Full text \| Editor’s summary Two active transposons in the Giardia genome are found in subtelomeric regions and may prevent telomere decay.
	Research news End-joining in yeast Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011206-01 (6 December 2001) Abstract \| Full text \| Editor’s summary Two genes have been found to down-regulate the non-homologous end-joining pathway in meiotic diploid yeast cells.
	Research news Leukemia translocations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011207-01 (7 December 2001) Abstract \| Full text \| Editor’s summary Expression profiling defines a distinct class of lymphoblastic leukemia caused by translocations within the MLL gene.
	Research news Amplifying the signal Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011210-01 (10 December 2001) Abstract \| Full text \| Editor’s summary A two-step approach can be used to amplify marker gene expression for non-invasive imaging.
	Research news Regulating adeno-associated virus Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011211-01 (11 December 2001) Abstract \| Full text \| Editor’s summary A genetic screen has identified a cellular protein that can regulate the replication and production of the potential gene therapy-vector, adeno-associated virus.
	Research news Bugs in flies Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011212-01 (12 December 2001) Abstract \| Full text \| Editor’s summary Microarray analysis has identified a number of novel Drosophila genes that are induced by microbial infection.
	Research news Telomere capping Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011213-01 (13 December 2001) Abstract \| Full text \| Editor’s summary Analysis of knockout mice has revealed a role for DNA-PK in mammalian telomere capping.
	Research news Double mutations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011214-01 (14 December 2001) Abstract \| Full text \| Editor’s summary A high-throughput strategy identifies synthetic lethality of thousands of yeast genes.
	Research news Mono-allelic expression in trypanosomes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011217-02 (17 December 2001) Abstract \| Full text \| Editor’s summary Localization to an extranucleolar body containing RNA polymerase I determines expression of active trypanosome loci during infection.
	Research news Wellcome Trust buys Crick's archives Pat Hagan Genome Biology 2001, 2:spotlight-20011217-01 (17 December 2001) Abstract \| Full text \| Editor’s summary The Wellcome Trust and Heritage Lottery Fund have combined to secure open access to Francis Crick's papers.
	Research news Evolving without sex Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011218-01 (18 December 2001) Abstract \| Full text \| Editor’s summary Some asexual fungi have evolved distinct genomes within a single individual, accumulating mutations without the need for recombination.
	Research news Green flies Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011219-01 (19 December 2001) Abstract \| Full text \| Editor’s summary A fluorescent protein-trap strategy identifies new Drosophila genes with different subcellular distributions.
	Research news Death domains, dysplasia and development Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011220-01 (20 December 2001) Abstract \| Full text \| Editor’s summary The mouse crinkled locus encodes a death-domain adaptor protein associated with hypohidrotic ectodermal dysplasia.
	Research news Three-spined sticklebacks Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011221-01 (21 December 2001) Abstract \| Full text \| Editor’s summary A linkage map for three-spined stickleback fish provides a reference for studies of morphological and behavioural changes during vertebrate evolution.
	Research news Primitive microbe enlightens evolution Tudor Toma Genome Biology 2001, 2:spotlight-20011227-01 (27 December 2001) Abstract \| Full text \| Editor’s summary Single-celled choanoflagellates have a unique receptor tyrosine kinase that may be linked to the origin of multicellular animals.
	Research news Sir inhibitor Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011228-01 (28 December 2001) Abstract \| Full text \| Editor’s summary Splitomicin is a small molecule that inhibits the Sir2p silencing protein and phenocopies sir2 deletion in yeast.
	Research news Chromosome countdown: 22...21...20... Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011228-02 (28 December 2001) Abstract \| Full text \| Editor’s summary British scientists have added the sequence of chromosome 20 to the list of 'finished' human chromosomes.
	Research
	Research Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences Lakshminarayan M Iyer, L Aravind, Peer Bork, Kay Hofmann, Arcady R Mushegian, Igor B Zhulin, Eugene V Koonin Genome Biology 2001, 2:research0051-research0051.11 (13 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Six cases where application of novel or conventional computational methods for protein sequence and structure analysis led to non-trivial predictions that were subsequently supported by direct experiments were analyzed. On all occasions, the original prediction seemed unjustified, and in at least three cases an alternative, well-supported computational prediction, incompatible with the original one, could be derived.
	Research Computational prediction of membrane-tethered transcription factors Joel Zupicich, Steven E Brenner, William C Skarnes Genome Biology 2001, 2:research0050-research0050.6 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A handful of membrane-spanning transcription factors has been previously identified. To investigate the existence of other transmembrane transcription factors all proteins in SWISS-PROT/TrEMBL were computationally analyzed; 76 factors were identifed.
	Research The process of genome shrinkage in the obligate symbiont Buchnera aphidicola Nancy A Moran, Alex Mira Genome Biology 2001, 2:research0054-research0054.12 (14 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To examine the process of genome reduction in symbionts, the tiny genome of the endosymbiont Buchnera aphidicola was compared to a reconstructed larger ancestral genome. On the basis of this comparison, 503 genes were eliminated from the Buchnera genome within syntenic fragments, and 1,403 genes were lost from the gaps between syntenic fragments, probably in connection with genome rearrangements.
	Research Development of an optimized interaction-mating protocol for large-scale yeast two-hybrid analyses Tim-Robert Soellick, Joachim F Uhrig Genome Biology 2001, 2:research0052-research0052.7 (15 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An optimized interaction mating protocol for the yeast two-hybrid system, which gives increased mating efficiencies has been devloped. This significantly reduces the effort and cost of cDNA library screening and allows multiple parallel approaches.
	Research Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins I King Jordan, Fyodor A Kondrashov, Igor B Rogozin, Roman L Tatusov, Yuri I Wolf, Eugene V Koonin Genome Biology 2001, 2:research0053-research0053.9 (20 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A simple relative rates test that attempts to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins has been developed. Relative rates of protein evolution are remarkably constant for the three species groups analyzed.
	Research Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls Andrew A Hill, Eugene L Brown, Maryann Z Whitley, Greg Tucker-Kellogg, Craig P Hunter, Donna K Slonim Genome Biology 2001, 2:research0055-research0055.13 (21 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparability of array results is necessary for the creation of large-scale gene expression databases. Normalization procedures for oligonucleotide arrays based on a common pool of known biotin-labeled cRNAs spiked into each hybridization are described and evaluated. Scaled frequency is as reproducible and accurate as global normalization.
	Correspondence
	Correspondence Flip-flop around the origin and terminus of replication in prokaryotic genomes Paweł Mackiewicz, Dorota Mackiewicz, Maria Kowalczuk, Stanisław Cebrat Genome Biology 2001, 2:interactions1004-interactions1004.4 (15 November 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A response to Evidence for symmetric chromosomal inversions around the replication origin in bacteria by JA Eisen, JF Heidelberg, O White, SL Salzberg. Genome Biology 2000, 1:research0011.1-0011.9.

Explore Genome Biology

Articles

Volume 2 Issue 12

Comment

Review

Report

Research

Correspondence