Genome Biology | Volume 5 Issue 10

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	Volume 5 Issue 10
	Comment
	Comment Twilight of a hero Gregory A Petsko Genome Biology 2004, 5:116 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The hope for those afflicted with Parkinson’s is embryonic stem cell therapy, which depends on research that the Bush administration is doing its best to strangle.
	Review
	Minireview Hotspots of homologous recombination in the human genome: not all homologous sequences are equal James R Lupski Genome Biology 2004, 5:242 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies of homologous recombination hotspots show that they do not share common sequence motifs, but they do have other features in common.
	Minireview Global nucleosome distribution and the regulation of transcription in yeast Sevinc Ercan, Michael J Carrozza, Jerry L Workman Genome Biology 2004, 5:243 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies show that active regulatory regions of the yeast genome have a lower density of nucleosomes than other regions, and that there is an inverse correlation between nucleosome density and the transcription rate of a gene.
	Minireview Gene-dosage effects in Down syndrome and trisomic mouse models Katheleen Gardiner Genome Biology 2004, 5:244 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several groups have confirmed that the abnormalities found in Down syndrome (trisomy 21) result from increased expression of genes on chromosome 21 because of their higher gene dosage.
	Opinion Genomic and proteomic adaptations to growth at high temperature Donal A Hickey, Gregory AC Singer Genome Biology 2004, 5:117 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evidence is discussed for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes.
	Report
	Paper report Articles selected by Faculty of 1000: predicting worm 3' ends; mapping cohesins; pentatricopeptide review; environmental genomics of the rumen; new flatworm transposons Genome Biology 2004, 5:350 (7 September 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the prediction of worm 3' ends; the mapping of cohesins; a pentatricopeptide review; environmental genomics of the rumen; new flatworm transposons.
	Paper report Articles selected by Faculty of 1000: functional genomics of Bardet-Biedl syndrome; sumo proteomics; phosphopeptide arrays; plant phosphoproteomics; novel antibiotic resistance genes Genome Biology 2004, 5:351 (23 September 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the functional genomics of Bardet-Biedl syndrome; sumo proteomics; phosphopeptide arrays; plant phosphoproteomics; novel antibiotic resistance genes.
	Meeting report New pulses in plant research Thierry Huguet Genome Biology 2004, 5:348 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the second International Conference on Legume Genomics and Genetics, organized jointly with the fifth AEP European Conference on Grain Legumes "Legumes for the benefit of agriculture, nutrition and the environment: their genomics, their products and their improvement", Dijon, France, 7-11 June 2004.
	Meeting report Can we find the genes involved in complex traits? Mathew Pletcher, Tim Wiltshire Genome Biology 2004, 5:347 (22 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Complex Trait Consortium meeting, Bar Harbor, USA, 6-9 July 2004.
	Meeting report The lords of the genomes Mark Stapleton Genome Biology 2004, 5:349 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on The Biology of Genomes meeting, Cold Spring Harbor, USA, 12-16 May 2004.
	Research news Olfactory research wins Nobel Stephen Pincock Genome Biology 2004, 5:spotlight-20041004-01 (4 October 2004) Abstract \| Full text \| Editor’s summary Prize in Physiology or Medicine awarded to Axel and Buck for research into the sense of smell
	Research news Lice tell mankind's story Nick Atkinson Genome Biology 2004, 5:spotlight-20041006-01 (6 October 2004) Abstract \| Full text \| Editor’s summary A study of head louse suggests that Homo erectus transmitted the parasite to Homo sapiens
	Research news Maurice Wilkins dies Stephen Pincock, Alison McCook Genome Biology 2004, 5:spotlight-20041007-01 (7 October 2004) Abstract \| Full text \| Editor’s summary Nobel Laureate who played a key role in the elucidation of the double helix was 88
	Research news Ubiquitin researchers win Nobel Stephen Pincock Genome Biology 2004, 5:spotlight-20041007-02 (7 October 2004) Abstract \| Full text \| Editor’s summary Ciechanover, Hershko, and Rose awarded for discovery of ubiquitin-mediated proteolysis
	Research news Novel riboswitch measures glycine Cathy Holding Genome Biology 2004, 5:spotlight-20041008-01 (8 October 2004) Abstract \| Full text \| Editor’s summary A study finds RNA self-regulation is as sophisticated and sensitive as protein regulation
	Research news Junk DNA controls embryos Cathy Holding Genome Biology 2004, 5:spotlight-20041012-01 (12 October 2004) Abstract \| Full text \| Editor’s summary Very early embryonic development may be controlled by random movements of repetitive elements
	Research news Lots of splicing regulators Charles Choi Genome Biology 2004, 5:spotlight-20041019-01 (19 October 2004) Abstract \| Full text \| Editor’s summary Researchers nearly triple the number of known alternative regulators in Drosophila
	Research news Refining the genome Cathy Holding Genome Biology 2004, 5:spotlight-20041022-01 (22 October 2004) Abstract \| Full text \| Editor’s summary Genome revised down to under 25,000 genes; failings of whole genome shotgun revealed
	Research news Bacteria fix DNA like mammals Charles Q Choi Genome Biology 2004, 5:spotlight-20041025-01 (25 October 2004) Abstract \| Full text \| Editor’s summary Double-strand DNA break repair pathways appear conserved, suggesting new ways to make libraries
	Research news Fish genes work in human cells Cathy Holding Genome Biology 2004, 5:spotlight-20041027-01 (27 October 2004) Abstract \| Full text \| Editor’s summary Understanding how mammal splicing enhancers differ from fish makes Fugu more useful
	Research news Platypus has 10 sex chromosomes Nick Atkinson Genome Biology 2004, 5:spotlight-20041029-01 (29 October 2004) Abstract \| Full text \| Editor’s summary Studies in PNAS and Nature find that sperm are either XXXXX (female) or YYYYY (male)
	Research news 'Dead' DNA feeds deep sea life Marta Paterlini Genome Biology 2004, 5:spotlight-20051006-02 (5 October 2005) Abstract \| Full text \| Editor’s summary Extracellular DNA plays a pivotal role in deep-sea ecosystems, researchers report in Science
	Research news Flu genome sequenced Ishani Ganguli Genome Biology 2004, 5:spotlight-20051006-01 (6 October 2005) Abstract \| Full text \| Editor’s summary Papers were published despite concerns the findings could aid bioterrorism
	Research news New control over worm rhythms Melissa Phillips Genome Biology 2004, 5:spotlight-20051011-01 (11 October 2005) Abstract \| Full text \| Editor’s summary Newly discovered gene controls swallowing, ovulation, and defecation
	Research news Sex detected in placozoans Charles Choi Genome Biology 2004, 5:spotlight-20051012-01 (12 October 2005) Abstract \| Full text \| Editor’s summary Simplest free-living animals could serve as models for understanding evolution of sex
	Research news Getting on top, genetically Ishani Ganguli Genome Biology 2004, 5:spotlight-20051019-01 (19 October 2005) Abstract \| Full text \| Editor’s summary Study shows rapid genetic response to social opportunity in cichlid fish
	Research news Non-coding DNA adapts Melissa Phillips Genome Biology 2004, 5:spotlight-20051026-01 (26 October 2005) Abstract \| Full text \| Editor’s summary Drosophila non-coding DNA exhibits both negative and positive selection
	Research
	Research Variation in alternative splicing across human tissues Gene Yeo, Dirk Holste, Gabriel Kreiman, Christopher B Burge Genome Biology 2004, 5:R74 (13 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the alternative splicing patterns of genomically aligned ESTs revealed that human brain, testis and liver have unusually high levels of alternative splicing and identified candidate cis-acting factors likely to play important roles in tissue-specific alternative splicing in human cells.
	Research Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species Michael W Rey, Preethi Ramaiya, Beth A Nelson, Shari D Brody-Karpin, Elizabeth J Zaretsky, Maria Tang, Alfredo de Leon, Henry Xiang, Veronica Gusti, Ib Groth Clausen, Peter B Olsen, Michael D Rasmussen, Jens T Andersen, Per L Jørgensen, Thomas S Larsen, Alexei Sorokin, Alexander Bolotin, Alla Lapidus, Nathalie Galleron, S Dusko Ehrlich, Randy M Berka Genome Biology 2004, 5:r77 (13 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The complete sequence of the Bacillus licheniformis ATCC 14580 genome was determined, revealing 4,208 predicted protein-coding genes, 7 rRNA operons and 72 tRNA genes.
	Research A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network Anaïs Baudot, Bernard Jacq, Christine Brun Genome Biology 2004, 5:R76 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protein-protein interaction networks were used to analyze the functional evolution of duplicated genes in yeast. Pairs of paralogs can be grouped into 3 classes, which likely form part of a continuous scale of diversity.
	Research A comprehensive transcript index of the human genome generated using microarrays and computational approaches Eric E Schadt, Stephen W Edwards, Debraj GuhaThakurta, Dan Holder, Lisa Ying, Vladimir Svetnik, Amy Leonardson, Kyle W Hart, Archie Russell, Guoya Li, Guy Cavet, John Castle, Paul McDonagh, Zhengyan Kan, Ronghua Chen, Andrew Kasarskis, Mihai Margarint, Ramon M Caceres, Jason M Johnson, Christopher D Armour, Philip W Garrett-Engele, Nicholas F Tsinoremas, Daniel D Shoemaker Genome Biology 2004, 5:R73 (23 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts, providing the first experiment-driven annotation of the human genome.
	Research Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae Brooke D Peterson-Burch, Dan Nettleton, Daniel F Voytas Genome Biology 2004, 5:R78 (29 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The full complement of Arabidopsis LTR retroelements was identified and relative ages of full-length elements estimated showing that Pseudoviridae are much younger than Metaviridae. The distribution of retroelement insertions across the genome was shown to be non-uniform.
	Research Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome Vini Pereira Genome Biology 2004, 5:R79 (29 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of the distribution and age of LTR retrotransposons in the Arabidopsis genome revealed that Pseudoviridae insert randomly along the chromosome and have been recently active whereas Metaviridae were more active in the past and preferentially target heterochromatin.
	Research Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific Bahar Taneri, Ben Snyder, Alexey Novoradovsky, Terry Gaasterland Genome Biology 2004, 5:R75 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Splice variants of 461 transcription factor loci were analyzed using a new database of splice variants in the mouse transcriptome, MouSDB3, providing quantitative evidence that alternative splicing preferentially adds or deletes domains important to the DNA-binding function of the TFs.
	Method Bioconductor: open software development for computational biology and bioinformatics Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang Genome Biology 2004, 5:R80 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
	Method Genome-wide mutagenesis of Zea mays L. using RescueMu transposons John Fernandes, Qunfeng Dong, Bret Schneider, Darren J Morrow, Guo-Ling Nan, Volker Brendel, Virginia Walbot Genome Biology 2004, 5:R82 (23 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors describe a large-scale transposon-tagging study in maize using the RescueMu system. The study provides a large resource of tagged and sequenced maize alleles, as well as some insights into the biology of RescueMu.
	Method Development of a method for screening short-lived proteins using green fluorescent protein Xin Jiang, Philip Coffino, Xianqiang Li Genome Biology 2004, 5:R81 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying short-live proteins using a GFP-fusion cDNA library for monitoring degradation kinetics is described.
	Method A reverse genetic screen in Drosophila using a deletion-inducing mutagen Knud Nairz, Peder Zipperlen, Charles Dearolf, Konrad Basler, Ernst Hafen Genome Biology 2004, 5:R83 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new reverse-genetics mutagenesis method that uses the crosslinking drug hexamethylphosphoramide to introduce small deletions has been used to generate and screen pools of mutagenized Drosophila, identifying two mutants.
	Method A genome annotation-driven approach to cloning the human ORFeome John E Collins, Charmain L Wright, Carol A Edwards, Matthew P Davis, James A Grinham, Charlotte G Cole, Melanie E Goward, Begoña Aguado, Meera Mallya, Younes Mokrab, Elizabeth J Huckle, David M Beare, Ian Dunham Genome Biology 2004, 5:R84 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a new systematic approach to generating cDNA clones containing full-length open reading frames, clones representing 70% of genes on human chromosome 22 were obtained.

	Volume 5 Issue 10
	Comment
	Comment Twilight of a hero Gregory A Petsko Genome Biology 2004, 5:116 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The hope for those afflicted with Parkinson’s is embryonic stem cell therapy, which depends on research that the Bush administration is doing its best to strangle.
	Review
	Minireview Hotspots of homologous recombination in the human genome: not all homologous sequences are equal James R Lupski Genome Biology 2004, 5:242 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies of homologous recombination hotspots show that they do not share common sequence motifs, but they do have other features in common.
	Minireview Global nucleosome distribution and the regulation of transcription in yeast Sevinc Ercan, Michael J Carrozza, Jerry L Workman Genome Biology 2004, 5:243 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies show that active regulatory regions of the yeast genome have a lower density of nucleosomes than other regions, and that there is an inverse correlation between nucleosome density and the transcription rate of a gene.
	Minireview Gene-dosage effects in Down syndrome and trisomic mouse models Katheleen Gardiner Genome Biology 2004, 5:244 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Several groups have confirmed that the abnormalities found in Down syndrome (trisomy 21) result from increased expression of genes on chromosome 21 because of their higher gene dosage.
	Opinion Genomic and proteomic adaptations to growth at high temperature Donal A Hickey, Gregory AC Singer Genome Biology 2004, 5:117 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evidence is discussed for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes.
	Report
	Paper report Articles selected by Faculty of 1000: predicting worm 3' ends; mapping cohesins; pentatricopeptide review; environmental genomics of the rumen; new flatworm transposons Genome Biology 2004, 5:350 (7 September 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the prediction of worm 3' ends; the mapping of cohesins; a pentatricopeptide review; environmental genomics of the rumen; new flatworm transposons.
	Paper report Articles selected by Faculty of 1000: functional genomics of Bardet-Biedl syndrome; sumo proteomics; phosphopeptide arrays; plant phosphoproteomics; novel antibiotic resistance genes Genome Biology 2004, 5:351 (23 September 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the functional genomics of Bardet-Biedl syndrome; sumo proteomics; phosphopeptide arrays; plant phosphoproteomics; novel antibiotic resistance genes.
	Meeting report New pulses in plant research Thierry Huguet Genome Biology 2004, 5:348 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the second International Conference on Legume Genomics and Genetics, organized jointly with the fifth AEP European Conference on Grain Legumes "Legumes for the benefit of agriculture, nutrition and the environment: their genomics, their products and their improvement", Dijon, France, 7-11 June 2004.
	Meeting report Can we find the genes involved in complex traits? Mathew Pletcher, Tim Wiltshire Genome Biology 2004, 5:347 (22 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Complex Trait Consortium meeting, Bar Harbor, USA, 6-9 July 2004.
	Meeting report The lords of the genomes Mark Stapleton Genome Biology 2004, 5:349 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on The Biology of Genomes meeting, Cold Spring Harbor, USA, 12-16 May 2004.
	Research news Olfactory research wins Nobel Stephen Pincock Genome Biology 2004, 5:spotlight-20041004-01 (4 October 2004) Abstract \| Full text \| Editor’s summary Prize in Physiology or Medicine awarded to Axel and Buck for research into the sense of smell
	Research news Lice tell mankind's story Nick Atkinson Genome Biology 2004, 5:spotlight-20041006-01 (6 October 2004) Abstract \| Full text \| Editor’s summary A study of head louse suggests that Homo erectus transmitted the parasite to Homo sapiens
	Research news Maurice Wilkins dies Stephen Pincock, Alison McCook Genome Biology 2004, 5:spotlight-20041007-01 (7 October 2004) Abstract \| Full text \| Editor’s summary Nobel Laureate who played a key role in the elucidation of the double helix was 88
	Research news Ubiquitin researchers win Nobel Stephen Pincock Genome Biology 2004, 5:spotlight-20041007-02 (7 October 2004) Abstract \| Full text \| Editor’s summary Ciechanover, Hershko, and Rose awarded for discovery of ubiquitin-mediated proteolysis
	Research news Novel riboswitch measures glycine Cathy Holding Genome Biology 2004, 5:spotlight-20041008-01 (8 October 2004) Abstract \| Full text \| Editor’s summary A study finds RNA self-regulation is as sophisticated and sensitive as protein regulation
	Research news Junk DNA controls embryos Cathy Holding Genome Biology 2004, 5:spotlight-20041012-01 (12 October 2004) Abstract \| Full text \| Editor’s summary Very early embryonic development may be controlled by random movements of repetitive elements
	Research news Lots of splicing regulators Charles Choi Genome Biology 2004, 5:spotlight-20041019-01 (19 October 2004) Abstract \| Full text \| Editor’s summary Researchers nearly triple the number of known alternative regulators in Drosophila
	Research news Refining the genome Cathy Holding Genome Biology 2004, 5:spotlight-20041022-01 (22 October 2004) Abstract \| Full text \| Editor’s summary Genome revised down to under 25,000 genes; failings of whole genome shotgun revealed
	Research news Bacteria fix DNA like mammals Charles Q Choi Genome Biology 2004, 5:spotlight-20041025-01 (25 October 2004) Abstract \| Full text \| Editor’s summary Double-strand DNA break repair pathways appear conserved, suggesting new ways to make libraries
	Research news Fish genes work in human cells Cathy Holding Genome Biology 2004, 5:spotlight-20041027-01 (27 October 2004) Abstract \| Full text \| Editor’s summary Understanding how mammal splicing enhancers differ from fish makes Fugu more useful
	Research news Platypus has 10 sex chromosomes Nick Atkinson Genome Biology 2004, 5:spotlight-20041029-01 (29 October 2004) Abstract \| Full text \| Editor’s summary Studies in PNAS and Nature find that sperm are either XXXXX (female) or YYYYY (male)
	Research news 'Dead' DNA feeds deep sea life Marta Paterlini Genome Biology 2004, 5:spotlight-20051006-02 (5 October 2005) Abstract \| Full text \| Editor’s summary Extracellular DNA plays a pivotal role in deep-sea ecosystems, researchers report in Science
	Research news Flu genome sequenced Ishani Ganguli Genome Biology 2004, 5:spotlight-20051006-01 (6 October 2005) Abstract \| Full text \| Editor’s summary Papers were published despite concerns the findings could aid bioterrorism
	Research news New control over worm rhythms Melissa Phillips Genome Biology 2004, 5:spotlight-20051011-01 (11 October 2005) Abstract \| Full text \| Editor’s summary Newly discovered gene controls swallowing, ovulation, and defecation
	Research news Sex detected in placozoans Charles Choi Genome Biology 2004, 5:spotlight-20051012-01 (12 October 2005) Abstract \| Full text \| Editor’s summary Simplest free-living animals could serve as models for understanding evolution of sex
	Research news Getting on top, genetically Ishani Ganguli Genome Biology 2004, 5:spotlight-20051019-01 (19 October 2005) Abstract \| Full text \| Editor’s summary Study shows rapid genetic response to social opportunity in cichlid fish
	Research news Non-coding DNA adapts Melissa Phillips Genome Biology 2004, 5:spotlight-20051026-01 (26 October 2005) Abstract \| Full text \| Editor’s summary Drosophila non-coding DNA exhibits both negative and positive selection
	Research
	Research Variation in alternative splicing across human tissues Gene Yeo, Dirk Holste, Gabriel Kreiman, Christopher B Burge Genome Biology 2004, 5:R74 (13 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the alternative splicing patterns of genomically aligned ESTs revealed that human brain, testis and liver have unusually high levels of alternative splicing and identified candidate cis-acting factors likely to play important roles in tissue-specific alternative splicing in human cells.
	Research Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species Michael W Rey, Preethi Ramaiya, Beth A Nelson, Shari D Brody-Karpin, Elizabeth J Zaretsky, Maria Tang, Alfredo de Leon, Henry Xiang, Veronica Gusti, Ib Groth Clausen, Peter B Olsen, Michael D Rasmussen, Jens T Andersen, Per L Jørgensen, Thomas S Larsen, Alexei Sorokin, Alexander Bolotin, Alla Lapidus, Nathalie Galleron, S Dusko Ehrlich, Randy M Berka Genome Biology 2004, 5:r77 (13 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The complete sequence of the Bacillus licheniformis ATCC 14580 genome was determined, revealing 4,208 predicted protein-coding genes, 7 rRNA operons and 72 tRNA genes.
	Research A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network Anaïs Baudot, Bernard Jacq, Christine Brun Genome Biology 2004, 5:R76 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Protein-protein interaction networks were used to analyze the functional evolution of duplicated genes in yeast. Pairs of paralogs can be grouped into 3 classes, which likely form part of a continuous scale of diversity.
	Research A comprehensive transcript index of the human genome generated using microarrays and computational approaches Eric E Schadt, Stephen W Edwards, Debraj GuhaThakurta, Dan Holder, Lisa Ying, Vladimir Svetnik, Amy Leonardson, Kyle W Hart, Archie Russell, Guoya Li, Guy Cavet, John Castle, Paul McDonagh, Zhengyan Kan, Ronghua Chen, Andrew Kasarskis, Mihai Margarint, Ramon M Caceres, Jason M Johnson, Christopher D Armour, Philip W Garrett-Engele, Nicholas F Tsinoremas, Daniel D Shoemaker Genome Biology 2004, 5:R73 (23 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts, providing the first experiment-driven annotation of the human genome.
	Research Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae Brooke D Peterson-Burch, Dan Nettleton, Daniel F Voytas Genome Biology 2004, 5:R78 (29 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The full complement of Arabidopsis LTR retroelements was identified and relative ages of full-length elements estimated showing that Pseudoviridae are much younger than Metaviridae. The distribution of retroelement insertions across the genome was shown to be non-uniform.
	Research Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome Vini Pereira Genome Biology 2004, 5:R79 (29 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of the distribution and age of LTR retrotransposons in the Arabidopsis genome revealed that Pseudoviridae insert randomly along the chromosome and have been recently active whereas Metaviridae were more active in the past and preferentially target heterochromatin.
	Research Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific Bahar Taneri, Ben Snyder, Alexey Novoradovsky, Terry Gaasterland Genome Biology 2004, 5:R75 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Splice variants of 461 transcription factor loci were analyzed using a new database of splice variants in the mouse transcriptome, MouSDB3, providing quantitative evidence that alternative splicing preferentially adds or deletes domains important to the DNA-binding function of the TFs.
	Method Bioconductor: open software development for computational biology and bioinformatics Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang Genome Biology 2004, 5:R80 (15 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
	Method Genome-wide mutagenesis of Zea mays L. using RescueMu transposons John Fernandes, Qunfeng Dong, Bret Schneider, Darren J Morrow, Guo-Ling Nan, Volker Brendel, Virginia Walbot Genome Biology 2004, 5:R82 (23 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors describe a large-scale transposon-tagging study in maize using the RescueMu system. The study provides a large resource of tagged and sequenced maize alleles, as well as some insights into the biology of RescueMu.
	Method Development of a method for screening short-lived proteins using green fluorescent protein Xin Jiang, Philip Coffino, Xianqiang Li Genome Biology 2004, 5:R81 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying short-live proteins using a GFP-fusion cDNA library for monitoring degradation kinetics is described.
	Method A reverse genetic screen in Drosophila using a deletion-inducing mutagen Knud Nairz, Peder Zipperlen, Charles Dearolf, Konrad Basler, Ernst Hafen Genome Biology 2004, 5:R83 (28 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new reverse-genetics mutagenesis method that uses the crosslinking drug hexamethylphosphoramide to introduce small deletions has been used to generate and screen pools of mutagenized Drosophila, identifying two mutants.
	Method A genome annotation-driven approach to cloning the human ORFeome John E Collins, Charmain L Wright, Carol A Edwards, Matthew P Davis, James A Grinham, Charlotte G Cole, Melanie E Goward, Begoña Aguado, Meera Mallya, Younes Mokrab, Elizabeth J Huckle, David M Beare, Ian Dunham Genome Biology 2004, 5:R84 (30 September 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a new systematic approach to generating cDNA clones containing full-length open reading frames, clones representing 70% of genes on human chromosome 22 were obtained.

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