Genome Biology | Volume 3 Issue 1

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 3 Issue 1
	Comment
	Editorial Editorial Genome Biology 2001, 3:comment0001-comment0001.1 (21 December 2001) Abstract \| Full text \| Editor’s summary In its one-and-a-half year history Genome Biology has witnessed the publication of the first plant genome, the first draft of the human genome (twice) and a more than doubling of the number of completed microbial sequences. There has also been a shift in 'functional genomics' away from simple microarray data and towards studies of the expression, structure and function of proteins, pathway and network analysis, and harnessing the power of comparative genomics. Debate has also raged over the past year on the importance and merits of providing immediate world-wide, barrier-free open access to the full text of research articles.
	Comment A Christmas Carol Gregory A Petsko Genome Biology 2001, 3:comment1001-comment1001.2 (28 December 2001) Full text \| PDF \| PubMed
	Review
	Review Dating branches on the Tree of Life using DNA Gregory A Wray Genome Biology 2001, 3:reviews0001-reviews0001.7 (20 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Protein family review The synucleins Julia M George Genome Biology 2001, 3:reviews3002-reviews3002.6 (20 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Synucleins are small, soluble proteins expressed primarily in brain tissue, the peripheral nervous system, the retina and certain tumors. Their functions are not clear, although some data suggest a role in the regulation of membrane stability and/or turnover, and α-synuclein protein accumulates abnormally in several neurodegenerative illnesses.
	Protein family review The Wnts Jeffrey R Miller Genome Biology 2001, 3:reviews3001-reviews3001.15 (28 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Wnts are a large family of secreted protein growth factors with diverse developmental roles governing cell fate, proliferation, migration, polarity, and death. In adults, Wnts function in homeostasis, and inappropriate activation of the Wnt pathway is implicated in a variety of cancers.
	Minireview Evolution of the initiating enzymes of the complement system Masaru Nonaka, Seita Miyazawa Genome Biology 2001, 3:reviews1001-reviews1001.5 (14 December 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the human MASP-1/3 gene, which encodes two proteases of the lectin-triggered complement cascade, has revealed alternatively used serine-protease-encoding regions for the gene's two protein products. Phylogenetic studies indicate that one arose by retrotransposition early in vertebrate evolution, supporting the idea that the lectin branch of the complement cascade arose earlier than the 'classical' pathway.
	Minireview Functional genomics in the study of seed germination Jérôme Bove, Marc Jullien, Philippe Grappin Genome Biology 2001, 3:reviews1002-reviews1002.5 (21 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent proteomic analysis of germinating Arabidopsis thaliana seeds demonstrates the effectiveness of functional genomics for investigating the complexity of developmental regulatory networks, such as the development of the embryo into a young plant.
	Report
	Web report Monte Carlo cell simulations Chaitanya Athale Genome Biology 2001, 3:reports2001 (21 December 2001) Abstract \| Full text
	Web report Cell-simulations portal Chaitanya Athale Genome Biology 2001, 3:reports2002 (21 December 2001) Abstract \| Full text
	Web report Where to look for steroid receptor information Eliezer Kopf Genome Biology 2001, 3:reports2003 (21 December 2001) Abstract \| Full text
	Web report Tracking down pathways and molecular interactions Eliezer Kopf Genome Biology 2001, 3:reports2004 (21 December 2001) Abstract \| Full text
	Web report Unraveling worm biology in the post-genomic era Chang-Su Lim Genome Biology 2001, 3:reports2005 (21 December 2001) Abstract \| Full text \| Editor’s summary WormBase aims to provide scientists with easily accessible and timely information on the genetics and biology of the nematode Caenorhabditis elegans as well as on some closely related nematodes.
	Web report A novel approach to analyzing SNPs Chang-Su Lim Genome Biology 2001, 3:reports2006 (21 December 2001) Abstract \| Full text
	Web report Gateway to the worm community Chang-Su Lim Genome Biology 2001, 3:reports2007 (21 December 2001) Abstract \| Full text
	Paper report Puzzling out transcriptional networks on a genomic scale Reiner Veitia Genome Biology 2001, 3:reports0001 (18 December 2001) Abstract \| Full text \| Editor’s summary In silico searches of promoter sequence motifs, combined with analysis of microarray data, have revealed potential synergistic interactions within the yeast transcriptional regulatory network
	Paper report Transcriptional regulation of the cell cycle Agnieszka M Lichanska Genome Biology 2001, 3:reports0004 (18 December 2001) Abstract \| Full text
	Paper report AT targets for anti-tumor drugs Agnieszka M Lichanska Genome Biology 2001, 3:reports0002 (20 December 2001) Abstract \| Full text \| Editor’s summary Binding sites for the anti-tumor drug bizelesin in DNA are identified by in silico and in vitro analysis of AT-rich islands
	Paper report Enzyme active-site prediction Agnieszka M Lichanska Genome Biology 2001, 3:reports0003 (20 December 2001) Abstract \| Full text
	Paper report Signatures of tumor origin John C Rockett Genome Biology 2001, 3:reports0005 (20 December 2001) Abstract \| Full text
	Paper report A recipe for resurrection John C Rockett Genome Biology 2001, 3:reports0006 (20 December 2001) Abstract \| Full text
	Paper report Human TSIX - an evolutionary relic? Cathy Holding Genome Biology 2001, 3:reports0007 (20 December 2001) Abstract \| Full text \| Editor’s summary Analysis of the human TSIX transcript shows it to be a truncated and probably non-functional evolutionary relic
	Meeting report Post-genomic Pseudomonas Shawn Lewenza, Robert EW Hancock Genome Biology 2001, 3:reports4002-reports4002.2 (7 December 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the Pseudomonas 2001 Meeting, Brussels, Belgium, 17-21 September 2001.
	Meeting report SNPing variation from genomes David A Liberles Genome Biology 2001, 3:reports4001-reports4001.4 (12 December 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the fourth International Meeting on Single Nucleotide Polymorphisms and Complex Genome Analysis, Stockholm, Sweden, 10-13 October 2001.
	Meeting report The pleiotropic dividends of genomics Ann Schlesinger Genome Biology 2001, 3:reports4003-reports4003.2 (12 December 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the 19th Whitehead Institute Symposium, Cambridge, USA, 14-16 October 2001.
	Tutorial Tools and resources for identifying protein families, domains and motifs Nicola J Mulder, Rolf Apweiler Genome Biology 2001, 3:reviews2001-reviews2001.8 (19 December 2001) Abstract \| Full text \| PDF \| PubMed
	Deposited research article Characterization of the expression ratio noise structure in high-density oligonucleotide arrays Felix Naef, Coleen R Hacker, Nila Patil, Marcelo Magnasco Genome Biology 2001, 3:preprint0001-preprint0001.24 (7 December 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New scoring functions for expression ratios and associated quality measures provide a powerful method for assessing the significance of differential gene expression results from high-density oligonucleotide arrays, relative to the noise resulting from the enzymatic and hybridization steps.
	Research news Miniature Genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020102-01 (2 January 2002) Abstract \| Full text \| Editor’s summary The short-lived chordate Oikopleura dioica has a small and compact genome.
	Research news Re-evaluating the yeast genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020103-01 (3 January 2002) Abstract \| Full text \| Editor’s summary An integrated bioinformatic and functional genomic strategy has been used to discover 137 new genes within the yeast genome.
	Research news Monkey map Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020104-01 (4 January 2002) Abstract \| Full text \| Editor’s summary Japanese researchers have constructed a human-chimpanzee comparative clone map.
	Research news Damage in worms Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020107-01 (7 January 2002) Abstract \| Full text \| Editor’s summary Combined functional genomics approaches help to identify novel genes involved in the DNA damage response pathway in nematodes.
	Research news Variation on the fourth Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020108-01 (8 January 2002) Abstract \| Full text \| Editor’s summary Researchers have discovered evidence for sequence variation and recombination on the fourth chromosome of Drosophila.
	Research news SMaRT correction Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020109-01 (9 January 2002) Abstract \| Full text \| Editor’s summary Gene therapists have developed a RNA-mediated technique for correcting gene defects that cause cystic fibrosis.
	Research news Systematic proteomics in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020110-01 (10 January 2002) Abstract \| Full text \| Editor’s summary Large-scale purification and mass spectrometry has been used to characterize hundreds of multiprotein complexes in yeast.
	Research news Plasmodium Py235 profiles Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020111-01 (11 January 2002) Abstract \| Full text \| Editor’s summary The malaria parasite expresses genes encoding different rhoptry proteins at specific stages of its life cycle.
	Research news Keeping an eye on gene expression Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020114-01 (14 January 2002) Abstract \| Full text \| Editor’s summary Gene profiling has identified sets of genes associated with different cell types within the human eye.
	Research news p53 mysteries Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020115-02 (15 January 2002) Abstract \| Full text \| Editor’s summary Researchers explore models for p53 function using chromatin immunoprecipitation methodology.
	Research news Finding the bug in the system Tudor Toma Genome Biology 2002, 3:spotlight-20020115-01 (15 January 2002) Abstract \| Full text \| Editor’s summary Computational subtraction uses the human genome to detect possible microbial causes for infectious diseases.
	Research news Analysing Xist Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020116-01 (16 January 2002) Abstract \| Full text \| Editor’s summary Different domains of the Xist RNA are involved in chromosomal localization and gene silencing during X inactivation.
	Research news Crenarchaeon sequence Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020117-01 (17 January 2002) Abstract \| Full text \| Editor’s summary The genome sequence of Pyrobaculum aerophilum gives clues about its unusual biology and its sulfur intolerance.
	Research news 'Flesh-eater' genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020118-01 (18 January 2002) Abstract \| Full text \| Editor’s summary Japanese researchers report the complete genome sequence of the gangrene-causing pathogen Clostridium perfringens.
	Research news In silico chromosome staining Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020121-01 (21 January 2002) Abstract \| Full text \| Editor’s summary A computation method can re-create the chromosomal banding patterns characteristic of Giemsa staining.
	Research news Hybrid vigor in rock pools Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020122-01 (22 January 2002) Abstract \| Full text \| Editor’s summary A study of Daphnia water flea populations in rock pools emphasises the importance of interbreeding and gene flow.
	Research news cis-regulatory modules Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020123-01 (23 January 2002) Abstract \| Full text \| Editor’s summary Clusters of transcription factor binding sites can predict developmentally regulated genes in Drosophila.
	Research news Smelly T-shirts Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020124-01 (24 January 2002) Abstract \| Full text \| Editor’s summary A woman may choose a mate who smells like her father.
	Research news Antisense RNA Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020125-01 (25 January 2002) Abstract \| Full text \| Editor’s summary Short antisense RNA molecules can induce gene-silencing in worms.
	Research news Microsatellites in plant genomes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020128-01 (28 January 2002) Abstract \| Full text \| Editor’s summary Analysis of several plant genomes reveals that microsatellites are associated with non-repetitive, transcribed genome sequences.
	Research news Mitochondrial mutations Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020129-01 (29 January 2002) Abstract \| Full text \| Editor’s summary Homoplasmic mutations in mitochondrial DNA cause severe respiratory chain defects.
	Research news Transgenic frogs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020130-01 (30 January 2002) Abstract \| Full text \| Editor’s summary A binary transgenic system used often in flies has been successfully adapted to drive transgene expression in Xenopus.
	Research news Plant pathogen genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020131-01 (31 January 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of the plant pathogen Ralstonia solanacearum reveals clues about its pathogenicity.
	Research
	Research From genome to function: the Arabidopsis aquaporins Francoise Quigley, Joshua M Rosenberg, Yair Shachar-Hill, Hans J Bohnert Genome Biology 2001, 3:research0001-research0001.17 (7 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The aquaporins are membrane proteins that have been characterized as facilitators of water flux. The Arabidopsis genome contains 38 sequences with homology to aquaporin in four subfamilies. Using the A. thaliana genome sequence, aquaporin family structure and expression have been analyzed.
	Research The Spin/Ssty repeat: a new motif identified in proteins involved in vertebrate development from gamete to embryo Eike Staub, Detlev Mennerich, André Rosenthal Genome Biology 2001, 3:research0003-research0003.6 (7 December 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Spin/Ssty genes might be important in the transition from sperm cells and oocytes to the early embryo. The discovery of a new protein motif of around 50 amino acids in length, the Spin/Ssty repeat is reported. Each repeat resides in its own exon, supporting the view that Spin/Ssty repeats are independent functional units.
	Research Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins Donald Jones, Emily Crowe, Tracy A Stevens, E Peter M Candido Genome Biology 2001, 3:research0002-research0002.15 (12 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA interference experiments in Caenorhabditis elegans suggest functional overlap in many ubiquitin-conjugating enzymes (UBCs). Phylogenetic analysis of C. elegans, Drosophila, and human genes implies that the numbers of UBCs increases with developmental complexity.
	Research Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants Gary Xie, Christian Forst, Carol Bonner, Roy A Jensen Genome Biology 2001, 3:research0004-research0004.13 (14 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tryptophan synthase consists of two subunits, α and β. Two subgroups of β chain exist; the major group TrpEb_1 and the minor group, TrpEb_2. Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the α chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. at least six lineages of the Archaea are likely to use TrpEb_2 as the functional β chain.
	Research Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip^® arrays Eugene Chudin, Randal Walker, Alan Kosaka, Sue X Wu, Douglas Rabert, Thomas K Chang, Dirk E Kreder Genome Biology 2001, 3:research0005-research0005.10 (14 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Affymetrix microarrays have been shown to give a signal proportional to actual transcript concentration, to distinguish concentration levels within a factor of 2, and to detect transcript frequencies as low as 1 in 2,000,000. We assessed these representations through a series of 'spike-in' hybridizations involving four prokaryotic transcripts in the absence and presence of fixed eukaryotic background. A linear relationship between transcript abundance and signal was consistently observed between 1 pM and 10 pM transcripts. Landmark studies outlining an observed linear relationship between signal and transcript concentration may not extend to commercially available arrays under routine operating conditions.
	Research Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain Naoki Osada, Munetomo Hida, Jun Kusuda, Reiko Tanuma, Makoto Hirata, Momoki Hirai, Keiji Terao, Yutaka Suzuki, Sumio Sugano, Katsuyuki Hashimoto Genome Biology 2001, 3:research0006-research0006.5 (19 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Twenty-nine novel human genes were predicted with putative coding regions sharing an open reading frame with the cynomolgus monkey, and the expression of 21 pairs of genes was confirmed by reverse transcription-coupled polymerase chain reaction.

	Volume 3 Issue 1
	Comment
	Editorial Editorial Genome Biology 2001, 3:comment0001-comment0001.1 (21 December 2001) Abstract \| Full text \| Editor’s summary In its one-and-a-half year history Genome Biology has witnessed the publication of the first plant genome, the first draft of the human genome (twice) and a more than doubling of the number of completed microbial sequences. There has also been a shift in 'functional genomics' away from simple microarray data and towards studies of the expression, structure and function of proteins, pathway and network analysis, and harnessing the power of comparative genomics. Debate has also raged over the past year on the importance and merits of providing immediate world-wide, barrier-free open access to the full text of research articles.
	Comment A Christmas Carol Gregory A Petsko Genome Biology 2001, 3:comment1001-comment1001.2 (28 December 2001) Full text \| PDF \| PubMed
	Review
	Review Dating branches on the Tree of Life using DNA Gregory A Wray Genome Biology 2001, 3:reviews0001-reviews0001.7 (20 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	Protein family review The synucleins Julia M George Genome Biology 2001, 3:reviews3002-reviews3002.6 (20 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Synucleins are small, soluble proteins expressed primarily in brain tissue, the peripheral nervous system, the retina and certain tumors. Their functions are not clear, although some data suggest a role in the regulation of membrane stability and/or turnover, and α-synuclein protein accumulates abnormally in several neurodegenerative illnesses.
	Protein family review The Wnts Jeffrey R Miller Genome Biology 2001, 3:reviews3001-reviews3001.15 (28 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Wnts are a large family of secreted protein growth factors with diverse developmental roles governing cell fate, proliferation, migration, polarity, and death. In adults, Wnts function in homeostasis, and inappropriate activation of the Wnt pathway is implicated in a variety of cancers.
	Minireview Evolution of the initiating enzymes of the complement system Masaru Nonaka, Seita Miyazawa Genome Biology 2001, 3:reviews1001-reviews1001.5 (14 December 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the human MASP-1/3 gene, which encodes two proteases of the lectin-triggered complement cascade, has revealed alternatively used serine-protease-encoding regions for the gene's two protein products. Phylogenetic studies indicate that one arose by retrotransposition early in vertebrate evolution, supporting the idea that the lectin branch of the complement cascade arose earlier than the 'classical' pathway.
	Minireview Functional genomics in the study of seed germination Jérôme Bove, Marc Jullien, Philippe Grappin Genome Biology 2001, 3:reviews1002-reviews1002.5 (21 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent proteomic analysis of germinating Arabidopsis thaliana seeds demonstrates the effectiveness of functional genomics for investigating the complexity of developmental regulatory networks, such as the development of the embryo into a young plant.
	Report
	Web report Monte Carlo cell simulations Chaitanya Athale Genome Biology 2001, 3:reports2001 (21 December 2001) Abstract \| Full text
	Web report Cell-simulations portal Chaitanya Athale Genome Biology 2001, 3:reports2002 (21 December 2001) Abstract \| Full text
	Web report Where to look for steroid receptor information Eliezer Kopf Genome Biology 2001, 3:reports2003 (21 December 2001) Abstract \| Full text
	Web report Tracking down pathways and molecular interactions Eliezer Kopf Genome Biology 2001, 3:reports2004 (21 December 2001) Abstract \| Full text
	Web report Unraveling worm biology in the post-genomic era Chang-Su Lim Genome Biology 2001, 3:reports2005 (21 December 2001) Abstract \| Full text \| Editor’s summary WormBase aims to provide scientists with easily accessible and timely information on the genetics and biology of the nematode Caenorhabditis elegans as well as on some closely related nematodes.
	Web report A novel approach to analyzing SNPs Chang-Su Lim Genome Biology 2001, 3:reports2006 (21 December 2001) Abstract \| Full text
	Web report Gateway to the worm community Chang-Su Lim Genome Biology 2001, 3:reports2007 (21 December 2001) Abstract \| Full text
	Paper report Puzzling out transcriptional networks on a genomic scale Reiner Veitia Genome Biology 2001, 3:reports0001 (18 December 2001) Abstract \| Full text \| Editor’s summary In silico searches of promoter sequence motifs, combined with analysis of microarray data, have revealed potential synergistic interactions within the yeast transcriptional regulatory network
	Paper report Transcriptional regulation of the cell cycle Agnieszka M Lichanska Genome Biology 2001, 3:reports0004 (18 December 2001) Abstract \| Full text
	Paper report AT targets for anti-tumor drugs Agnieszka M Lichanska Genome Biology 2001, 3:reports0002 (20 December 2001) Abstract \| Full text \| Editor’s summary Binding sites for the anti-tumor drug bizelesin in DNA are identified by in silico and in vitro analysis of AT-rich islands
	Paper report Enzyme active-site prediction Agnieszka M Lichanska Genome Biology 2001, 3:reports0003 (20 December 2001) Abstract \| Full text
	Paper report Signatures of tumor origin John C Rockett Genome Biology 2001, 3:reports0005 (20 December 2001) Abstract \| Full text
	Paper report A recipe for resurrection John C Rockett Genome Biology 2001, 3:reports0006 (20 December 2001) Abstract \| Full text
	Paper report Human TSIX - an evolutionary relic? Cathy Holding Genome Biology 2001, 3:reports0007 (20 December 2001) Abstract \| Full text \| Editor’s summary Analysis of the human TSIX transcript shows it to be a truncated and probably non-functional evolutionary relic
	Meeting report Post-genomic Pseudomonas Shawn Lewenza, Robert EW Hancock Genome Biology 2001, 3:reports4002-reports4002.2 (7 December 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the Pseudomonas 2001 Meeting, Brussels, Belgium, 17-21 September 2001.
	Meeting report SNPing variation from genomes David A Liberles Genome Biology 2001, 3:reports4001-reports4001.4 (12 December 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the fourth International Meeting on Single Nucleotide Polymorphisms and Complex Genome Analysis, Stockholm, Sweden, 10-13 October 2001.
	Meeting report The pleiotropic dividends of genomics Ann Schlesinger Genome Biology 2001, 3:reports4003-reports4003.2 (12 December 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the 19th Whitehead Institute Symposium, Cambridge, USA, 14-16 October 2001.
	Tutorial Tools and resources for identifying protein families, domains and motifs Nicola J Mulder, Rolf Apweiler Genome Biology 2001, 3:reviews2001-reviews2001.8 (19 December 2001) Abstract \| Full text \| PDF \| PubMed
	Deposited research article Characterization of the expression ratio noise structure in high-density oligonucleotide arrays Felix Naef, Coleen R Hacker, Nila Patil, Marcelo Magnasco Genome Biology 2001, 3:preprint0001-preprint0001.24 (7 December 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New scoring functions for expression ratios and associated quality measures provide a powerful method for assessing the significance of differential gene expression results from high-density oligonucleotide arrays, relative to the noise resulting from the enzymatic and hybridization steps.
	Research news Miniature Genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020102-01 (2 January 2002) Abstract \| Full text \| Editor’s summary The short-lived chordate Oikopleura dioica has a small and compact genome.
	Research news Re-evaluating the yeast genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020103-01 (3 January 2002) Abstract \| Full text \| Editor’s summary An integrated bioinformatic and functional genomic strategy has been used to discover 137 new genes within the yeast genome.
	Research news Monkey map Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020104-01 (4 January 2002) Abstract \| Full text \| Editor’s summary Japanese researchers have constructed a human-chimpanzee comparative clone map.
	Research news Damage in worms Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020107-01 (7 January 2002) Abstract \| Full text \| Editor’s summary Combined functional genomics approaches help to identify novel genes involved in the DNA damage response pathway in nematodes.
	Research news Variation on the fourth Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020108-01 (8 January 2002) Abstract \| Full text \| Editor’s summary Researchers have discovered evidence for sequence variation and recombination on the fourth chromosome of Drosophila.
	Research news SMaRT correction Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020109-01 (9 January 2002) Abstract \| Full text \| Editor’s summary Gene therapists have developed a RNA-mediated technique for correcting gene defects that cause cystic fibrosis.
	Research news Systematic proteomics in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020110-01 (10 January 2002) Abstract \| Full text \| Editor’s summary Large-scale purification and mass spectrometry has been used to characterize hundreds of multiprotein complexes in yeast.
	Research news Plasmodium Py235 profiles Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020111-01 (11 January 2002) Abstract \| Full text \| Editor’s summary The malaria parasite expresses genes encoding different rhoptry proteins at specific stages of its life cycle.
	Research news Keeping an eye on gene expression Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020114-01 (14 January 2002) Abstract \| Full text \| Editor’s summary Gene profiling has identified sets of genes associated with different cell types within the human eye.
	Research news p53 mysteries Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020115-02 (15 January 2002) Abstract \| Full text \| Editor’s summary Researchers explore models for p53 function using chromatin immunoprecipitation methodology.
	Research news Finding the bug in the system Tudor Toma Genome Biology 2002, 3:spotlight-20020115-01 (15 January 2002) Abstract \| Full text \| Editor’s summary Computational subtraction uses the human genome to detect possible microbial causes for infectious diseases.
	Research news Analysing Xist Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020116-01 (16 January 2002) Abstract \| Full text \| Editor’s summary Different domains of the Xist RNA are involved in chromosomal localization and gene silencing during X inactivation.
	Research news Crenarchaeon sequence Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020117-01 (17 January 2002) Abstract \| Full text \| Editor’s summary The genome sequence of Pyrobaculum aerophilum gives clues about its unusual biology and its sulfur intolerance.
	Research news 'Flesh-eater' genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020118-01 (18 January 2002) Abstract \| Full text \| Editor’s summary Japanese researchers report the complete genome sequence of the gangrene-causing pathogen Clostridium perfringens.
	Research news In silico chromosome staining Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020121-01 (21 January 2002) Abstract \| Full text \| Editor’s summary A computation method can re-create the chromosomal banding patterns characteristic of Giemsa staining.
	Research news Hybrid vigor in rock pools Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020122-01 (22 January 2002) Abstract \| Full text \| Editor’s summary A study of Daphnia water flea populations in rock pools emphasises the importance of interbreeding and gene flow.
	Research news cis-regulatory modules Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020123-01 (23 January 2002) Abstract \| Full text \| Editor’s summary Clusters of transcription factor binding sites can predict developmentally regulated genes in Drosophila.
	Research news Smelly T-shirts Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020124-01 (24 January 2002) Abstract \| Full text \| Editor’s summary A woman may choose a mate who smells like her father.
	Research news Antisense RNA Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020125-01 (25 January 2002) Abstract \| Full text \| Editor’s summary Short antisense RNA molecules can induce gene-silencing in worms.
	Research news Microsatellites in plant genomes Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020128-01 (28 January 2002) Abstract \| Full text \| Editor’s summary Analysis of several plant genomes reveals that microsatellites are associated with non-repetitive, transcribed genome sequences.
	Research news Mitochondrial mutations Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020129-01 (29 January 2002) Abstract \| Full text \| Editor’s summary Homoplasmic mutations in mitochondrial DNA cause severe respiratory chain defects.
	Research news Transgenic frogs Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020130-01 (30 January 2002) Abstract \| Full text \| Editor’s summary A binary transgenic system used often in flies has been successfully adapted to drive transgene expression in Xenopus.
	Research news Plant pathogen genome Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020131-01 (31 January 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of the plant pathogen Ralstonia solanacearum reveals clues about its pathogenicity.
	Research
	Research From genome to function: the Arabidopsis aquaporins Francoise Quigley, Joshua M Rosenberg, Yair Shachar-Hill, Hans J Bohnert Genome Biology 2001, 3:research0001-research0001.17 (7 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The aquaporins are membrane proteins that have been characterized as facilitators of water flux. The Arabidopsis genome contains 38 sequences with homology to aquaporin in four subfamilies. Using the A. thaliana genome sequence, aquaporin family structure and expression have been analyzed.
	Research The Spin/Ssty repeat: a new motif identified in proteins involved in vertebrate development from gamete to embryo Eike Staub, Detlev Mennerich, André Rosenthal Genome Biology 2001, 3:research0003-research0003.6 (7 December 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Spin/Ssty genes might be important in the transition from sperm cells and oocytes to the early embryo. The discovery of a new protein motif of around 50 amino acids in length, the Spin/Ssty repeat is reported. Each repeat resides in its own exon, supporting the view that Spin/Ssty repeats are independent functional units.
	Research Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins Donald Jones, Emily Crowe, Tracy A Stevens, E Peter M Candido Genome Biology 2001, 3:research0002-research0002.15 (12 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA interference experiments in Caenorhabditis elegans suggest functional overlap in many ubiquitin-conjugating enzymes (UBCs). Phylogenetic analysis of C. elegans, Drosophila, and human genes implies that the numbers of UBCs increases with developmental complexity.
	Research Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants Gary Xie, Christian Forst, Carol Bonner, Roy A Jensen Genome Biology 2001, 3:research0004-research0004.13 (14 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tryptophan synthase consists of two subunits, α and β. Two subgroups of β chain exist; the major group TrpEb_1 and the minor group, TrpEb_2. Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the α chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. at least six lineages of the Archaea are likely to use TrpEb_2 as the functional β chain.
	Research Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip^® arrays Eugene Chudin, Randal Walker, Alan Kosaka, Sue X Wu, Douglas Rabert, Thomas K Chang, Dirk E Kreder Genome Biology 2001, 3:research0005-research0005.10 (14 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Affymetrix microarrays have been shown to give a signal proportional to actual transcript concentration, to distinguish concentration levels within a factor of 2, and to detect transcript frequencies as low as 1 in 2,000,000. We assessed these representations through a series of 'spike-in' hybridizations involving four prokaryotic transcripts in the absence and presence of fixed eukaryotic background. A linear relationship between transcript abundance and signal was consistently observed between 1 pM and 10 pM transcripts. Landmark studies outlining an observed linear relationship between signal and transcript concentration may not extend to commercially available arrays under routine operating conditions.
	Research Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain Naoki Osada, Munetomo Hida, Jun Kusuda, Reiko Tanuma, Makoto Hirata, Momoki Hirai, Keiji Terao, Yutaka Suzuki, Sumio Sugano, Katsuyuki Hashimoto Genome Biology 2001, 3:research0006-research0006.5 (19 December 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Twenty-nine novel human genes were predicted with putative coding regions sharing an open reading frame with the cynomolgus monkey, and the expression of 21 pairs of genes was confirmed by reverse transcription-coupled polymerase chain reaction.

Explore Genome Biology

Articles

Volume 3 Issue 1

Comment

Review

Report

Research