Genome Biology | Volume 4 Issue 10

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	Volume 4 Issue 10
	Comment
	Comment The usual suspects Gregory A Petsko Genome Biology 2003, 4:118 (22 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Any scientist will think twice before reporting any discrepancy or possible theft of biohazardous material to either his or her institution or to the government.
	Opinion New methods for finding disease-susceptibility genes: impact and potential Mark I McCarthy, Damian Smedley, Winston Hide Genome Biology 2003, 4:119 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Improved techniques for defining disease-gene location and evaluating the biological candidacy of regional transcripts will hasten disease-gene discovery.
	Review
	Protein family review KRAB-containing zinc-finger repressor proteins Raul Urrutia Genome Biology 2003, 4:231 (23 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The largest family of zinc-finger transcription factors comprises those containing the Krüppel-associated box (or KRAB domain). The KRAB domain behaves as a transcriptional repressor domain and the C₂H₂zinc-finger motifs bind DNA. Members of the family are involved in maintenance of the nucleolus, cell differentiation, cell proliferation, apoptosis, and neoplastic transformation.
	Minireview Probing the yeast proteome for RNA-processing factors Sander Granneman, Susan J Baserga Genome Biology 2003, 4:229 (22 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method has been developed to identify proteins required for the biogenesis of non-coding RNA in yeast, using a microarray to screen for aberrant patterns of RNA processing in mutant strains, and new proteins involved in the processing of ribosomal and non-coding RNAs have been found.
	Minireview Tackling an essential problem in functional proteomics of Saccharomyces cerevisiae Oscar M Aparicio Genome Biology 2003, 4:230 (24 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene inactivation is the cornerstone of functional genetic analysis, but the analysis of essential genes requires conditional inactivation of the gene product. A new study has adapted a simple method for creating conditional alleles to allow large-scale analysis of essential genes in Saccharomyces cerevisiae and has identified a role in DNA replication for a newly identified protein complex.
	Report
	Paper report Articles selected by Faculty of 1000: identifying antigens involved in autoimmune response; statistics in genomics; mouse full-length cDNA encylopedia; screen for Drosophila neural development genes; proteome of SARS-coronavirus Genome Biology 2003, 4:343 (8 September 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the identification of antigens involved in an autoimmune reseponse, the difference between false positive and false discovery rate, a mouse full-length cDNA encylopedia, analysis of bristle number in Drosophila mutants to identify neural development genes and an analysis of the proteome of SARS-coronavirus.
	Paper report Articles selected by Faculty of 1000: analysis of mouse chromosome 11; nuclear membrane protein identification; odor-guided behavior in Drosophila; ionomics in Arabidopsis; genomic comparison of two Prochlorococcus ecotypes Genome Biology 2003, 4:344 (17 September 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a genetic analysis of mouse chromosome 11, nuclear membrane protein identification, odor-guided behavior in Drosophila, profiling nutrient and trace elements in Arabidopsis and a genomic comparison of two Prochlorococcus ecotypes.
	Meeting report Unraveling nature's networks Lev Soinov, Misha Kapushesky Genome Biology 2003, 4:341 (16 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Unravelling Nature's Networks: from Microarray and Proteomic Analysis to Systems Biology', Sheffield, UK, 21-22 July 2003.
	Meeting report Mice and more Carol J Bult Genome Biology 2003, 4:340 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Mouse Initiatives V meeting 'Genomics of Complex Systems in Biomedical Research', The Jackson Laboratory, Bar Harbor, USA, 30 July-2 August 2003.
	Meeting report Decoding the epigenetic effects of chromatin Richard Festenstein, Luis Aragon Genome Biology 2003, 4:342 (23 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Alan Wolffe EMBO Workshop on 'Chromatin and Epigenetics', Heidelberg, Germany, 19-22 June 2003.
	Research news Wellcome support for open access Stephen Pincock Genome Biology 2003, 4:spotlight-20031001-01 (1 October 2003) Abstract \| Full text \| Editor’s summary British charity wants a system of open and unrestricted access for research it funds
	Research news The human genome on a chip Andrew Scott Genome Biology 2003, 4:spotlight-20031003-01 (3 October 2003) Abstract \| Full text \| Editor’s summary The first single-chip microarray for the human genome will soon be joined by rivals
	Research news Protein database unveiled Charles Q Choi Genome Biology 2003, 4:spotlight-20031006-01 (6 October 2003) Abstract \| Full text \| Editor’s summary An international team hopes to set a standard for easily accessible protein data
	Research news Bacterial insecticides Cathy Holding Genome Biology 2003, 4:spotlight-20031006-02 (6 October 2003) Abstract \| Full text \| Editor’s summary The Photorhabdus genome yields novel compounds active against pathogen-bearing insects
	Research news France failing young scientists Jane Burgermeister Genome Biology 2003, 4:spotlight-20031008-01 (8 October 2003) Abstract \| Full text \| Editor’s summary Critics say moves to invigorate research have been undermined by the axing of permanent posts
	Research news Plant genomics gets a $100 million infusion Charles Q Choi Genome Biology 2003, 4:spotlight-20031010-01 (10 October 2003) Abstract \| Full text \| Editor’s summary New NSF-funded virtual centers are created to cultivate speedy collaboration
	Research news Metastatic teamwork Tudor Toma Genome Biology 2003, 4:spotlight-20031010-02 (10 October 2003) Abstract \| Full text \| Editor’s summary Ras mutations require additional cell polarity genetic alterations to promote metastatic progression
	Research news Parasitism derived Cathy Holding Genome Biology 2003, 4:spotlight-20031014-01 (14 October 2003) Abstract \| Full text \| Editor’s summary Genomic analysis of a parasitic archaeon suggests nonreductive evolution
	Research news Think big, think yeast David Secko Genome Biology 2003, 4:spotlight-20031016-01 (16 October 2003) Abstract \| Full text \| Editor’s summary Genome-wide protein tagging provides a global picture of protein levels and localization
	Research news Gene deserts bear fruit Cathy Holding Genome Biology 2003, 4:spotlight-20031017-01 (17 October 2003) Abstract \| Full text \| Editor’s summary Regulatory elements can be identified in noncoding genomic sequences
	Research news A twist on ribosomal protein function David Secko Genome Biology 2003, 4:spotlight-20031022-01 (22 October 2003) Abstract \| Full text \| Editor’s summary L13a exits the ribosome upon IFN-γ treatment to translationally silence specific mRNA
	Research news Six percent in 6 Cathy Holding Genome Biology 2003, 4:spotlight-20031023-01 (23 October 2003) Abstract \| Full text \| Editor’s summary An analysis and annotation of human chromosome 6, containing 6% of the human genome has now been published
	Research news Open access Europe Ned Stafford Genome Biology 2003, 4:spotlight-20031023-02 (23 October 2003) Abstract \| Full text \| Editor’s summary Leading centers say they'll encourage researchers to publish in open-access journals
	Research news Genetics and nongenetics of breast cancer Cathy Holding Genome Biology 2003, 4:spotlight-20031024-01 (24 October 2003) Abstract \| Full text \| Editor’s summary Exercise and nonobesity during adolescence delay breast cancer development in at-risk women
	Research news Researchers boycott Cell Press Alison McCook Genome Biology 2003, 4:spotlight-20031024-02 (24 October 2003) Abstract \| Full text \| Editor’s summary UCSF faculty say the publisher charges too much for electronic access to its material
	Research news National Medals for molecular biology Jack Lucentini Genome Biology 2003, 4:spotlight-20031027-01 (27 October 2003) Abstract \| Full text \| Editor’s summary Two US scientists receive highest presidential honor for groundbreaking work
	Research news Euro research area agreement Stephen Pincock Genome Biology 2003, 4:spotlight-20031027-02 (27 October 2003) Abstract \| Full text \| Editor’s summary Big science organizations sign joint statement with the European Commission
	Research news Urchin, meet starfish Cathy Holding Genome Biology 2003, 4:spotlight-20031028-01 (28 October 2003) Abstract \| Full text \| Editor’s summary Investigating interacting networks yields another tool for genome comparisons
	Research news Prion researcher awarded Ned Stafford Genome Biology 2003, 4:spotlight-20031030-01 (30 October 2003) Abstract \| Full text \| Editor’s summary Winning the €65,000 Koch award, Adriano Aguzzi says science is still the biggest thrill
	Research news Irish science funds on 'pause' Amanda Haverty Genome Biology 2003, 4:spotlight-20031031-01 (31 October 2003) Abstract \| Full text \| Editor’s summary Scientists urge government to lift the threat to research funding
	Research news Science slowed by fires Eugene Russo Genome Biology 2003, 4:spotlight-20031031-03 (31 October 2003) Abstract \| Full text \| Editor’s summary San Diego area researchers hampered by logistics, but few suffered severe losses
	Research
	Research The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism L Aravind, Lakshminarayan M Iyer, Vivek Anantharaman Genome Biology 2003, 4:R64 (8 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The Alba superfamily of chromosomal proteins appear to have originated as RNA-binding proteins and to have been recruited to chromosomes possibly only within the crenarchaeal lineage.
	Research Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes M J Lehane, S Aksoy, W Gibson, A Kerhornou, M Berriman, J Hamilton, M B Soares, M F Bonaldo, S Lehane, N Hall Genome Biology 2003, 4:R63 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An expressed sequence tag (EST) project on the adult tsetse midgut, the major organ system for establishment and early development of trypanosomes has been undertaken. The most notable block of genes upregulated in response to trypanosome challenge are a series of Toll and Imd genes and a series of genes involved in oxidative stress responses.
	Research Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina Jindan Yu, Rafal Farjo, Sean P MacNee, Wolfgang Baehr, Dwight E Stambolian, Anand Swaroop Genome Biology 2003, 4:R65 (22 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The generation and analysis of 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries is reported that identifies a large number of potentially interesting genes for biological investigation.
	Research Time- and exercise-dependent gene regulation in human skeletal muscle Alexander C Zambon, Erin L McDearmon, Nathan Salomonis, Karen M Vranizan, Kirsten L Johansen, Deborah Adey, Joseph S Takahashi, Morris Schambelan, Bruce R Conklin Genome Biology 2003, 4:R61 (25 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary Skeletal muscle remodeling is a critical component of an organism's response to environmental changes. Exercise causes structural changes in muscle and can induce phase shifts in circadian rhythms, fluctuations in physiology and behavior with a period of around 24 hours that are maintained by a core clock mechanism. Both exercise-induced remodeling and circadian rhythms rely on the transcriptional regulation of key genes.
	Research Caste- and development-associated gene expression in a lower termite Michael E Scharf, Dancia Wu-Scharf, Barry R Pittendrigh, Gary W Bennett Genome Biology 2003, 4:R62 (26 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Social insects such as termites express dramatic polyphenism (the occurrence of multiple forms in a species on the basis of differential gene expression) both in association with caste differentiation and between castes after differentiation. We have used cDNA macroarrays to compare gene expression between polyphenic castes and intermediary developmental stages of the termite Reticulitermes flavipes.
	Method A high performance test of differential gene expression for oligonucleotide arrays William J Lemon, Sandya Liyanarachchi, Ming You Genome Biology 2003, 4:R67 (10 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method, Logit-t, for normalization of microarray data and for finding significantly differentially expressed genes has been described.
	Method Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing John Castle, Phil Garrett-Engele, Christopher D Armour, Sven J Duenwald, Patrick M Loerch, Michael R Meyer, Eric E Schadt, Roland Stoughton, Mark L Parrish, Daniel D Shoemaker, Jason M Johnson Genome Biology 2003, 4:R66 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions.
	Software An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets Karen I Zeller, Anil G Jegga, Bruce J Aronow, Kathryn A O'Donnell, Chi V Dang Genome Biology 2003, 4:R69 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A database of genes responsive to the c-Myc oncogenic transcription factor is described. The database Myc Target Gene prioritizes candidate target genes according to experimental evidence and clusters responsive genes into functional groups.
	Software Identifying biological themes within lists of genes with EASE Douglas A Hosack, Glynn Dennis, Brad T Sherman, H Lane, Richard A Lempicki Genome Biology 2003, 4:R70 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data.
	Software DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization Steven B Cannon, Alexander Kozik, Brian Chan, Richard Michelmore, Nevin D Young Genome Biology 2003, 4:R68 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity.

	Volume 4 Issue 10
	Comment
	Comment The usual suspects Gregory A Petsko Genome Biology 2003, 4:118 (22 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Any scientist will think twice before reporting any discrepancy or possible theft of biohazardous material to either his or her institution or to the government.
	Opinion New methods for finding disease-susceptibility genes: impact and potential Mark I McCarthy, Damian Smedley, Winston Hide Genome Biology 2003, 4:119 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Improved techniques for defining disease-gene location and evaluating the biological candidacy of regional transcripts will hasten disease-gene discovery.
	Review
	Protein family review KRAB-containing zinc-finger repressor proteins Raul Urrutia Genome Biology 2003, 4:231 (23 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The largest family of zinc-finger transcription factors comprises those containing the Krüppel-associated box (or KRAB domain). The KRAB domain behaves as a transcriptional repressor domain and the C₂H₂zinc-finger motifs bind DNA. Members of the family are involved in maintenance of the nucleolus, cell differentiation, cell proliferation, apoptosis, and neoplastic transformation.
	Minireview Probing the yeast proteome for RNA-processing factors Sander Granneman, Susan J Baserga Genome Biology 2003, 4:229 (22 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method has been developed to identify proteins required for the biogenesis of non-coding RNA in yeast, using a microarray to screen for aberrant patterns of RNA processing in mutant strains, and new proteins involved in the processing of ribosomal and non-coding RNAs have been found.
	Minireview Tackling an essential problem in functional proteomics of Saccharomyces cerevisiae Oscar M Aparicio Genome Biology 2003, 4:230 (24 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gene inactivation is the cornerstone of functional genetic analysis, but the analysis of essential genes requires conditional inactivation of the gene product. A new study has adapted a simple method for creating conditional alleles to allow large-scale analysis of essential genes in Saccharomyces cerevisiae and has identified a role in DNA replication for a newly identified protein complex.
	Report
	Paper report Articles selected by Faculty of 1000: identifying antigens involved in autoimmune response; statistics in genomics; mouse full-length cDNA encylopedia; screen for Drosophila neural development genes; proteome of SARS-coronavirus Genome Biology 2003, 4:343 (8 September 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the identification of antigens involved in an autoimmune reseponse, the difference between false positive and false discovery rate, a mouse full-length cDNA encylopedia, analysis of bristle number in Drosophila mutants to identify neural development genes and an analysis of the proteome of SARS-coronavirus.
	Paper report Articles selected by Faculty of 1000: analysis of mouse chromosome 11; nuclear membrane protein identification; odor-guided behavior in Drosophila; ionomics in Arabidopsis; genomic comparison of two Prochlorococcus ecotypes Genome Biology 2003, 4:344 (17 September 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a genetic analysis of mouse chromosome 11, nuclear membrane protein identification, odor-guided behavior in Drosophila, profiling nutrient and trace elements in Arabidopsis and a genomic comparison of two Prochlorococcus ecotypes.
	Meeting report Unraveling nature's networks Lev Soinov, Misha Kapushesky Genome Biology 2003, 4:341 (16 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Unravelling Nature's Networks: from Microarray and Proteomic Analysis to Systems Biology', Sheffield, UK, 21-22 July 2003.
	Meeting report Mice and more Carol J Bult Genome Biology 2003, 4:340 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Mouse Initiatives V meeting 'Genomics of Complex Systems in Biomedical Research', The Jackson Laboratory, Bar Harbor, USA, 30 July-2 August 2003.
	Meeting report Decoding the epigenetic effects of chromatin Richard Festenstein, Luis Aragon Genome Biology 2003, 4:342 (23 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Alan Wolffe EMBO Workshop on 'Chromatin and Epigenetics', Heidelberg, Germany, 19-22 June 2003.
	Research news Wellcome support for open access Stephen Pincock Genome Biology 2003, 4:spotlight-20031001-01 (1 October 2003) Abstract \| Full text \| Editor’s summary British charity wants a system of open and unrestricted access for research it funds
	Research news The human genome on a chip Andrew Scott Genome Biology 2003, 4:spotlight-20031003-01 (3 October 2003) Abstract \| Full text \| Editor’s summary The first single-chip microarray for the human genome will soon be joined by rivals
	Research news Protein database unveiled Charles Q Choi Genome Biology 2003, 4:spotlight-20031006-01 (6 October 2003) Abstract \| Full text \| Editor’s summary An international team hopes to set a standard for easily accessible protein data
	Research news Bacterial insecticides Cathy Holding Genome Biology 2003, 4:spotlight-20031006-02 (6 October 2003) Abstract \| Full text \| Editor’s summary The Photorhabdus genome yields novel compounds active against pathogen-bearing insects
	Research news France failing young scientists Jane Burgermeister Genome Biology 2003, 4:spotlight-20031008-01 (8 October 2003) Abstract \| Full text \| Editor’s summary Critics say moves to invigorate research have been undermined by the axing of permanent posts
	Research news Plant genomics gets a $100 million infusion Charles Q Choi Genome Biology 2003, 4:spotlight-20031010-01 (10 October 2003) Abstract \| Full text \| Editor’s summary New NSF-funded virtual centers are created to cultivate speedy collaboration
	Research news Metastatic teamwork Tudor Toma Genome Biology 2003, 4:spotlight-20031010-02 (10 October 2003) Abstract \| Full text \| Editor’s summary Ras mutations require additional cell polarity genetic alterations to promote metastatic progression
	Research news Parasitism derived Cathy Holding Genome Biology 2003, 4:spotlight-20031014-01 (14 October 2003) Abstract \| Full text \| Editor’s summary Genomic analysis of a parasitic archaeon suggests nonreductive evolution
	Research news Think big, think yeast David Secko Genome Biology 2003, 4:spotlight-20031016-01 (16 October 2003) Abstract \| Full text \| Editor’s summary Genome-wide protein tagging provides a global picture of protein levels and localization
	Research news Gene deserts bear fruit Cathy Holding Genome Biology 2003, 4:spotlight-20031017-01 (17 October 2003) Abstract \| Full text \| Editor’s summary Regulatory elements can be identified in noncoding genomic sequences
	Research news A twist on ribosomal protein function David Secko Genome Biology 2003, 4:spotlight-20031022-01 (22 October 2003) Abstract \| Full text \| Editor’s summary L13a exits the ribosome upon IFN-γ treatment to translationally silence specific mRNA
	Research news Six percent in 6 Cathy Holding Genome Biology 2003, 4:spotlight-20031023-01 (23 October 2003) Abstract \| Full text \| Editor’s summary An analysis and annotation of human chromosome 6, containing 6% of the human genome has now been published
	Research news Open access Europe Ned Stafford Genome Biology 2003, 4:spotlight-20031023-02 (23 October 2003) Abstract \| Full text \| Editor’s summary Leading centers say they'll encourage researchers to publish in open-access journals
	Research news Genetics and nongenetics of breast cancer Cathy Holding Genome Biology 2003, 4:spotlight-20031024-01 (24 October 2003) Abstract \| Full text \| Editor’s summary Exercise and nonobesity during adolescence delay breast cancer development in at-risk women
	Research news Researchers boycott Cell Press Alison McCook Genome Biology 2003, 4:spotlight-20031024-02 (24 October 2003) Abstract \| Full text \| Editor’s summary UCSF faculty say the publisher charges too much for electronic access to its material
	Research news National Medals for molecular biology Jack Lucentini Genome Biology 2003, 4:spotlight-20031027-01 (27 October 2003) Abstract \| Full text \| Editor’s summary Two US scientists receive highest presidential honor for groundbreaking work
	Research news Euro research area agreement Stephen Pincock Genome Biology 2003, 4:spotlight-20031027-02 (27 October 2003) Abstract \| Full text \| Editor’s summary Big science organizations sign joint statement with the European Commission
	Research news Urchin, meet starfish Cathy Holding Genome Biology 2003, 4:spotlight-20031028-01 (28 October 2003) Abstract \| Full text \| Editor’s summary Investigating interacting networks yields another tool for genome comparisons
	Research news Prion researcher awarded Ned Stafford Genome Biology 2003, 4:spotlight-20031030-01 (30 October 2003) Abstract \| Full text \| Editor’s summary Winning the €65,000 Koch award, Adriano Aguzzi says science is still the biggest thrill
	Research news Irish science funds on 'pause' Amanda Haverty Genome Biology 2003, 4:spotlight-20031031-01 (31 October 2003) Abstract \| Full text \| Editor’s summary Scientists urge government to lift the threat to research funding
	Research news Science slowed by fires Eugene Russo Genome Biology 2003, 4:spotlight-20031031-03 (31 October 2003) Abstract \| Full text \| Editor’s summary San Diego area researchers hampered by logistics, but few suffered severe losses
	Research
	Research The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism L Aravind, Lakshminarayan M Iyer, Vivek Anantharaman Genome Biology 2003, 4:R64 (8 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The Alba superfamily of chromosomal proteins appear to have originated as RNA-binding proteins and to have been recruited to chromosomes possibly only within the crenarchaeal lineage.
	Research Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes M J Lehane, S Aksoy, W Gibson, A Kerhornou, M Berriman, J Hamilton, M B Soares, M F Bonaldo, S Lehane, N Hall Genome Biology 2003, 4:R63 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An expressed sequence tag (EST) project on the adult tsetse midgut, the major organ system for establishment and early development of trypanosomes has been undertaken. The most notable block of genes upregulated in response to trypanosome challenge are a series of Toll and Imd genes and a series of genes involved in oxidative stress responses.
	Research Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina Jindan Yu, Rafal Farjo, Sean P MacNee, Wolfgang Baehr, Dwight E Stambolian, Anand Swaroop Genome Biology 2003, 4:R65 (22 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The generation and analysis of 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries is reported that identifies a large number of potentially interesting genes for biological investigation.
	Research Time- and exercise-dependent gene regulation in human skeletal muscle Alexander C Zambon, Erin L McDearmon, Nathan Salomonis, Karen M Vranizan, Kirsten L Johansen, Deborah Adey, Joseph S Takahashi, Morris Schambelan, Bruce R Conklin Genome Biology 2003, 4:R61 (25 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary Skeletal muscle remodeling is a critical component of an organism's response to environmental changes. Exercise causes structural changes in muscle and can induce phase shifts in circadian rhythms, fluctuations in physiology and behavior with a period of around 24 hours that are maintained by a core clock mechanism. Both exercise-induced remodeling and circadian rhythms rely on the transcriptional regulation of key genes.
	Research Caste- and development-associated gene expression in a lower termite Michael E Scharf, Dancia Wu-Scharf, Barry R Pittendrigh, Gary W Bennett Genome Biology 2003, 4:R62 (26 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Social insects such as termites express dramatic polyphenism (the occurrence of multiple forms in a species on the basis of differential gene expression) both in association with caste differentiation and between castes after differentiation. We have used cDNA macroarrays to compare gene expression between polyphenic castes and intermediary developmental stages of the termite Reticulitermes flavipes.
	Method A high performance test of differential gene expression for oligonucleotide arrays William J Lemon, Sandya Liyanarachchi, Ming You Genome Biology 2003, 4:R67 (10 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method, Logit-t, for normalization of microarray data and for finding significantly differentially expressed genes has been described.
	Method Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing John Castle, Phil Garrett-Engele, Christopher D Armour, Sven J Duenwald, Patrick M Loerch, Michael R Meyer, Eric E Schadt, Roland Stoughton, Mark L Parrish, Daniel D Shoemaker, Jason M Johnson Genome Biology 2003, 4:R66 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions.
	Software An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets Karen I Zeller, Anil G Jegga, Bruce J Aronow, Kathryn A O'Donnell, Chi V Dang Genome Biology 2003, 4:R69 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A database of genes responsive to the c-Myc oncogenic transcription factor is described. The database Myc Target Gene prioritizes candidate target genes according to experimental evidence and clusters responsive genes into functional groups.
	Software Identifying biological themes within lists of genes with EASE Douglas A Hosack, Glynn Dennis, Brad T Sherman, H Lane, Richard A Lempicki Genome Biology 2003, 4:R70 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data.
	Software DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization Steven B Cannon, Alexander Kozik, Brian Chan, Richard Michelmore, Nevin D Young Genome Biology 2003, 4:R68 (19 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity.

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Volume 4 Issue 10

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