Genome Biology | Volume 8 Issue 4

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	Volume 8 Issue 4
	Comment
	Comment It can't happen here - can it? Gregory A Petsko Genome Biology 2007, 8:105 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If scientific advice is to have any value, it must come from sources that are not under any obligation to any organisation, public or private. Most principal scientific organisations in Western countries have similar ideas about the importance of independence but the independence of American science is being eroded.
	Review
	Review Searching genomes for ribozymes and riboswitches Christian Hammann, Eric Westhof Genome Biology 2007, 8:210 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A discussion of experimental approaches and theoretical difficulties in the identification of ribozymes with novel catalytic functions.
	Minireview Maturation of the mammalian secretome Jeremy C Simpson, Alvaro Mateos, Rainer Pepperkok Genome Biology 2007, 8:211 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary What methodology will define the complete secretome?
	Report
	Meeting report New perspectives on an old disease: proteomics in cancer research Oriol Gallego, Anne-Claude Gavin Genome Biology 2007, 8:303 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the American Association for Cancer Research Conference 'Advances in Proteomics in Cancer Research', Amelia Island, USA, 27 February-2 March 2007.
	Meeting report Developing a systems-level understanding of gene expression Olivier Elemento Genome Biology 2007, 8:304 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the meeting 'Systems Biology: Global Regulation of Gene Expression' at the Cold Spring Harbor Laboratory, New York, USA, 28 March-1 April 2007.
	Research
	Research Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J Nielsen, Jakob H Havgaard, Carina Rosenkilde, Jun Wang, Heng Li, Ruiqiang Li, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Jun Yu, Jian Wang, Hans-Henrik Stærfeldt, Rasmus Wernersson, Lone B Madsen, Bo Thomsen, Henrik Hornshøj, Zhan Bujie, Xuegang Wang, Xuefei Wang, Lars Bolund, Søren Brunak, Huanming Yang, Christian Bendixen, Merete Fredholm et al. Genome Biology 2007, 8:R45 (2 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.
	Research A TATA binding protein regulatory network that governs transcription complex assembly Kathryn L Huisinga, B Franklin Pugh Genome Biology 2007, 8:R46 (2 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome is modeled and experimentally tested.
	Research Deafblindness in French Canadians from Quebec: a predominant founder mutation in the USH1C gene provides the first genetic link with the Acadian population Inga Ebermann, Irma Lopez, Maria Bitner-Glindzicz, Carolyn Brown, Robert Koenekoop, Hanno Bolz Genome Biology 2007, 8:R47 (3 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic characterisation of 15 French Canadian patients from different regions of the province of Quebec who were clinically diagnosed as USH1 reveals that carriers of the c.216G>A-allele haplotype belong to the early founders of both the Acadian and the Quebec population.
	Research A recessive genetic screen for host factors required for retroviral infection in a library of insertionally mutated Blm-deficient embryonic stem cells Wei Wang, Allan Bradley Genome Biology 2007, 8:R48 (3 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary <p>A recessive genetic screen of an insertionally mutated Blm-/- ES cell library identifies host factors required for retroviral infection, and confirms that mCat-1 is the ecotropic murine leukaemia virus receptor in ES cells.</p>
	Research Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression Shisong Ma, Hans J Bohnert Genome Biology 2007, 8:R49 (4 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The integration of stress-dependent, tissue- and cell-specific expression profiles and 5'-regulatory sequence motif analysis defines a common stress transcriptome, identifies major motifs for stress response, and places stress response in the context of tissue and cell lineages in the Arabidopsis root.
	Research Comparative analysis indicates regulatory neofunctionalization of yeast duplicates Itay Tirosh, Naama Barkai Genome Biology 2007, 8:R50 (5 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the expression profiles of S. cerevisiae duplicate pairs with that of their pre-duplication orthologs in C. albicans identified a class of genes that may present cases of regulatory neofunctionalization.
	Research Evolution of protein complexes by duplication of homomeric interactions Jose B Pereira-Leal, Emmanuel D Levy, Christel Kamp, Sarah A Teichmann Genome Biology 2007, 8:R51 (5 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of yeast protein complexes, complexes of known three-dimensional structure in the Protein Data Bank and clusters of pair-wise protein interactions in the networks of several organisms revealed that duplication of homomeric interactions often results in the formation of complexes of paralogous proteins.
	Research Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes Marco van het Hoog, Timothy J Rast, Mikhail Martchenko, Suzanne Grindle, Daniel Dignard, Hervé Hogues, Christine Cuomo, Matthew Berriman, Stewart Scherer, BB Magee, Malcolm Whiteway, Hiroji Chibana, André Nantel, PT Magee Genome Biology 2007, 8:R52 (9 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary For Assembly 20 of the Candida albicans genome, the sequence of each of the eight chromosomes was determined, revealing new insights into gene family creation and dispersion, subtelomere organization, and chromosome evolution.
	Research Comparative genomics using Fugu reveals insights into regulatory subfunctionalization Adam Woolfe, Greg Elgar Genome Biology 2007, 8:R53 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fish-mammal genomic alignments were used to compare over 800 conserved non-coding elements that associate with genes that have undergone fish-specific duplication and retention, revealing a pattern of element retention and loss between paralogs indicative of subfunctionalization.
	Research Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes Michael Doss, Johannes Winkler, Shuhua Chen, Rita Hippler-Altenburg, Isaia Sotiriadou, Marcel Halbach, Kurt Pfannkuche, Huamin Liang, Herbert Schulz, Oliver Hummel, Norbert Hübner, Ruth Rottscheidt, Jürgen Hescheler, Agapios Sachinidis Genome Biology 2007, 8:R56 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis reveals that the specific pattern of gene expression in cardiomyocytes derived from embryonic stem cells reflects the biological, physiological and functional processes occurring in mature cardiomyocytes.
	Research Ancient papillomavirus-host co-speciation in Felidae Annabel Rector, Philippe Lemey, Ruth Tachezy, Sara Mostmans, Shin-Je Ghim, Koenraad Van Doorslaer, Melody Roelke, Mitchell Bush, Richard J Montali, Janis Joslin, Robert D Burk, Alfred B Jenson, John P Sundberg, Beth Shapiro, Marc Van Ranst Genome Biology 2007, 8:R57 (12 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evolutionary rate of feline papillomaviruses is inferred from the phylogenetic analysis of their hosts, providing evidence for long-term virus-host co-speciation
	Research Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival Daniel L Miller, Chad L Myers, Brenden Rickards, Hilary A Coller, S Jane Flint Genome Biology 2007, 8:R58 (12 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The effects of the adenovirus Ad5 on basic host cell programs, such as cell-cycle regulation, were studied in a microarray analysis of human fibroblasts. About 2,000 genes were up- or down-regulated after Ad5 infection and Ad5 infection was shown to induce reversal of the quiescence program and recapitulation of the core serum response.
	Research The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss David J Miller, Georg Hemmrich, Eldon E Ball, David C Hayward, Konstantin Khalturin, Noriko Funayama, Kiyokazu Agata, Thomas CG Bosch Genome Biology 2007, 8:R59 (16 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of genomic resources available for cnidarians revealed that several key components of the vertebrate innate immune repertoire are present in representatives of the basal cnidarian class Anthozoa, but are missing in Hydra, a member of the class Hydrozoa, indicating ancient origins for many components of the innate immune system.
	Research On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation Byung-Hoon Kim, Xue Cai, Justin N Vaughn, Albrecht G von Arnim Genome Biology 2007, 8:R60 (17 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Reporter transgene assays and comparative polysome-microarray analysis reveal that the intact h subunit of Arabidopsis eIF3 contributes to efficient translation initiation on mRNA leader sequences harbouring multiple uORFs.
	Research Evolutionary conservation of sequence and secondary structures in CRISPR repeats Victor Kunin, Rotem Sorek, Philip Hugenholtz Genome Biology 2007, 8:R61 (18 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The categorisation and structural analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sequences from 195 microbial genomes show that repeats from diverse organisms can be grouped based on sequence similarity, and that some groups have pronounced secondary structures with compensatory base changes.
	Research Deciphering the molecular machinery of stem cells: a look at the neoblast gene expression profile Leonardo Rossi, Alessandra Salvetti, Francesco M Marincola, Annalisa Lena, Paolo Deri, Linda Mannini, Renata Batistoni, Ena Wang, Vittorio Gremigni Genome Biology 2007, 8:R62 (20 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene-expression profiles of planarians in which all adult pluripotent stem cells (neoblasts) were eliminated and wild-type worms identified a putative neoblast-restricted gene set. This included many genes involved in chromatin modeling and RNA metabolism, suggesting that epigenetic modifications and post-transcriptional regulation are important for neoblast regulation.
	Research Global analyses of mRNA translational control during early Drosophila embryogenesis Xiaoli Qin, Soyeon Ahn, Terence P Speed, Gerald M Rubin Genome Biology 2007, 8:R63 (22 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The polysomal profiles of over 15,000 transcripts during the first ten hours after egg laying have been determined.
	Research Discovery of tissue-specific exons using comprehensive human exon microarrays Tyson A Clark, Anthony C Schweitzer, Tina X Chen, Michelle K Staples, Gang Lu, Hui Wang, Alan Williams, John E Blume Genome Biology 2007, 8:R64 (24 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comprehensive exon microarrays with a simple intra-gene normalization algorithm were used to detect human tissue-specific alternative splicing events, suggesting significant expression outside of known exons and well annotated genes and a high frequency of alternative splicing events.
	Research Gene expression patterns during adaptation of a helminth parasite to different environmental niches Emmitt R Jolly, Chen-Shan Chin, Steve Miller, Mahmoud M Bahgat, KC Lim, Joseph DeRisi, James H McKerrow Genome Biology 2007, 8:R65 (24 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a genomic microarray, gene expression at three different developmental stages of the schistosome parasite were analyzed, resulting in the identification of 1154 developmentally enriched transcripts.
	Research Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions Sergi Beltran, Mireia Angulo, Miguel Pignatelli, Florenci Serras, Montserrat Corominas Genome Biology 2007, 8:R67 (28 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the gene expression profiles of wing imaginal discs from ash2 and ash1 mutants shows that they are highly similar, supporting a model in which they act together to maintain stable states of transcription.
	Research A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map Michel Solignac, Florence Mougel, Dominique Vautrin, Monique Monnerot, Jean-Marie Cornuet Genome Biology 2007, 8:R66 (21 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The meiotic map of the honey bee is presented, including the main features that emerged from comparisons with the sequence-based physical map. The map is based on 2,008 markers and is about 40 M long, corresponding to a recombination rate of 22 cM/Mb.
	Method Statistical tools for synthesizing lists of differentially expressed features in related experiments Marta Blangiardo, Sylvia Richardson Genome Biology 2007, 8:R54 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach for finding a list of features that are commonly perturbed in two or more experiments, quantifying the evidence of dependence between the experiments by a ratio.
	Method A major zebrafish polymorphism resource for genetic mapping Kevin M Bradley, J Bradford Elmore, Joan P Breyer, Brian L Yaspan, Jason R Jessen, Ela W Knapik, Jeffrey R Smith Genome Biology 2007, 8:R55 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 645,088 candidate polymorphisms in zebrafish were identified and positioned on genetic and physical maps as a resource for positional cloning.
	Correspondence
	Correspondence Power-law-like distributions in biomedical publications and research funding Andrew I Su, John B Hogenesch Genome Biology 2007, 8:404 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A search of the literature reveals that researchers study relatively few genes out of the total human genome.

	Volume 8 Issue 4
	Comment
	Comment It can't happen here - can it? Gregory A Petsko Genome Biology 2007, 8:105 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary If scientific advice is to have any value, it must come from sources that are not under any obligation to any organisation, public or private. Most principal scientific organisations in Western countries have similar ideas about the importance of independence but the independence of American science is being eroded.
	Review
	Review Searching genomes for ribozymes and riboswitches Christian Hammann, Eric Westhof Genome Biology 2007, 8:210 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A discussion of experimental approaches and theoretical difficulties in the identification of ribozymes with novel catalytic functions.
	Minireview Maturation of the mammalian secretome Jeremy C Simpson, Alvaro Mateos, Rainer Pepperkok Genome Biology 2007, 8:211 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary What methodology will define the complete secretome?
	Report
	Meeting report New perspectives on an old disease: proteomics in cancer research Oriol Gallego, Anne-Claude Gavin Genome Biology 2007, 8:303 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the American Association for Cancer Research Conference 'Advances in Proteomics in Cancer Research', Amelia Island, USA, 27 February-2 March 2007.
	Meeting report Developing a systems-level understanding of gene expression Olivier Elemento Genome Biology 2007, 8:304 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the meeting 'Systems Biology: Global Regulation of Gene Expression' at the Cold Spring Harbor Laboratory, New York, USA, 28 March-1 April 2007.
	Research
	Research Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J Gilchrist, Frank Panitz, Claus Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J Nielsen, Jakob H Havgaard, Carina Rosenkilde, Jun Wang, Heng Li, Ruiqiang Li, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Jun Yu, Jian Wang, Hans-Henrik Stærfeldt, Rasmus Wernersson, Lone B Madsen, Bo Thomsen, Henrik Hornshøj, Zhan Bujie, Xuegang Wang, Xuefei Wang, Lars Bolund, Søren Brunak, Huanming Yang, Christian Bendixen, Merete Fredholm et al. Genome Biology 2007, 8:R45 (2 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.
	Research A TATA binding protein regulatory network that governs transcription complex assembly Kathryn L Huisinga, B Franklin Pugh Genome Biology 2007, 8:R46 (2 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome is modeled and experimentally tested.
	Research Deafblindness in French Canadians from Quebec: a predominant founder mutation in the USH1C gene provides the first genetic link with the Acadian population Inga Ebermann, Irma Lopez, Maria Bitner-Glindzicz, Carolyn Brown, Robert Koenekoop, Hanno Bolz Genome Biology 2007, 8:R47 (3 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genetic characterisation of 15 French Canadian patients from different regions of the province of Quebec who were clinically diagnosed as USH1 reveals that carriers of the c.216G>A-allele haplotype belong to the early founders of both the Acadian and the Quebec population.
	Research A recessive genetic screen for host factors required for retroviral infection in a library of insertionally mutated Blm-deficient embryonic stem cells Wei Wang, Allan Bradley Genome Biology 2007, 8:R48 (3 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary <p>A recessive genetic screen of an insertionally mutated Blm-/- ES cell library identifies host factors required for retroviral infection, and confirms that mCat-1 is the ecotropic murine leukaemia virus receptor in ES cells.</p>
	Research Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression Shisong Ma, Hans J Bohnert Genome Biology 2007, 8:R49 (4 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The integration of stress-dependent, tissue- and cell-specific expression profiles and 5'-regulatory sequence motif analysis defines a common stress transcriptome, identifies major motifs for stress response, and places stress response in the context of tissue and cell lineages in the Arabidopsis root.
	Research Comparative analysis indicates regulatory neofunctionalization of yeast duplicates Itay Tirosh, Naama Barkai Genome Biology 2007, 8:R50 (5 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the expression profiles of S. cerevisiae duplicate pairs with that of their pre-duplication orthologs in C. albicans identified a class of genes that may present cases of regulatory neofunctionalization.
	Research Evolution of protein complexes by duplication of homomeric interactions Jose B Pereira-Leal, Emmanuel D Levy, Christel Kamp, Sarah A Teichmann Genome Biology 2007, 8:R51 (5 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of yeast protein complexes, complexes of known three-dimensional structure in the Protein Data Bank and clusters of pair-wise protein interactions in the networks of several organisms revealed that duplication of homomeric interactions often results in the formation of complexes of paralogous proteins.
	Research Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes Marco van het Hoog, Timothy J Rast, Mikhail Martchenko, Suzanne Grindle, Daniel Dignard, Hervé Hogues, Christine Cuomo, Matthew Berriman, Stewart Scherer, BB Magee, Malcolm Whiteway, Hiroji Chibana, André Nantel, PT Magee Genome Biology 2007, 8:R52 (9 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary For Assembly 20 of the Candida albicans genome, the sequence of each of the eight chromosomes was determined, revealing new insights into gene family creation and dispersion, subtelomere organization, and chromosome evolution.
	Research Comparative genomics using Fugu reveals insights into regulatory subfunctionalization Adam Woolfe, Greg Elgar Genome Biology 2007, 8:R53 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fish-mammal genomic alignments were used to compare over 800 conserved non-coding elements that associate with genes that have undergone fish-specific duplication and retention, revealing a pattern of element retention and loss between paralogs indicative of subfunctionalization.
	Research Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes Michael Doss, Johannes Winkler, Shuhua Chen, Rita Hippler-Altenburg, Isaia Sotiriadou, Marcel Halbach, Kurt Pfannkuche, Huamin Liang, Herbert Schulz, Oliver Hummel, Norbert Hübner, Ruth Rottscheidt, Jürgen Hescheler, Agapios Sachinidis Genome Biology 2007, 8:R56 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray analysis reveals that the specific pattern of gene expression in cardiomyocytes derived from embryonic stem cells reflects the biological, physiological and functional processes occurring in mature cardiomyocytes.
	Research Ancient papillomavirus-host co-speciation in Felidae Annabel Rector, Philippe Lemey, Ruth Tachezy, Sara Mostmans, Shin-Je Ghim, Koenraad Van Doorslaer, Melody Roelke, Mitchell Bush, Richard J Montali, Janis Joslin, Robert D Burk, Alfred B Jenson, John P Sundberg, Beth Shapiro, Marc Van Ranst Genome Biology 2007, 8:R57 (12 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evolutionary rate of feline papillomaviruses is inferred from the phylogenetic analysis of their hosts, providing evidence for long-term virus-host co-speciation
	Research Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival Daniel L Miller, Chad L Myers, Brenden Rickards, Hilary A Coller, S Jane Flint Genome Biology 2007, 8:R58 (12 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The effects of the adenovirus Ad5 on basic host cell programs, such as cell-cycle regulation, were studied in a microarray analysis of human fibroblasts. About 2,000 genes were up- or down-regulated after Ad5 infection and Ad5 infection was shown to induce reversal of the quiescence program and recapitulation of the core serum response.
	Research The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss David J Miller, Georg Hemmrich, Eldon E Ball, David C Hayward, Konstantin Khalturin, Noriko Funayama, Kiyokazu Agata, Thomas CG Bosch Genome Biology 2007, 8:R59 (16 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of genomic resources available for cnidarians revealed that several key components of the vertebrate innate immune repertoire are present in representatives of the basal cnidarian class Anthozoa, but are missing in Hydra, a member of the class Hydrozoa, indicating ancient origins for many components of the innate immune system.
	Research On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation Byung-Hoon Kim, Xue Cai, Justin N Vaughn, Albrecht G von Arnim Genome Biology 2007, 8:R60 (17 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Reporter transgene assays and comparative polysome-microarray analysis reveal that the intact h subunit of Arabidopsis eIF3 contributes to efficient translation initiation on mRNA leader sequences harbouring multiple uORFs.
	Research Evolutionary conservation of sequence and secondary structures in CRISPR repeats Victor Kunin, Rotem Sorek, Philip Hugenholtz Genome Biology 2007, 8:R61 (18 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The categorisation and structural analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sequences from 195 microbial genomes show that repeats from diverse organisms can be grouped based on sequence similarity, and that some groups have pronounced secondary structures with compensatory base changes.
	Research Deciphering the molecular machinery of stem cells: a look at the neoblast gene expression profile Leonardo Rossi, Alessandra Salvetti, Francesco M Marincola, Annalisa Lena, Paolo Deri, Linda Mannini, Renata Batistoni, Ena Wang, Vittorio Gremigni Genome Biology 2007, 8:R62 (20 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene-expression profiles of planarians in which all adult pluripotent stem cells (neoblasts) were eliminated and wild-type worms identified a putative neoblast-restricted gene set. This included many genes involved in chromatin modeling and RNA metabolism, suggesting that epigenetic modifications and post-transcriptional regulation are important for neoblast regulation.
	Research Global analyses of mRNA translational control during early Drosophila embryogenesis Xiaoli Qin, Soyeon Ahn, Terence P Speed, Gerald M Rubin Genome Biology 2007, 8:R63 (22 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The polysomal profiles of over 15,000 transcripts during the first ten hours after egg laying have been determined.
	Research Discovery of tissue-specific exons using comprehensive human exon microarrays Tyson A Clark, Anthony C Schweitzer, Tina X Chen, Michelle K Staples, Gang Lu, Hui Wang, Alan Williams, John E Blume Genome Biology 2007, 8:R64 (24 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comprehensive exon microarrays with a simple intra-gene normalization algorithm were used to detect human tissue-specific alternative splicing events, suggesting significant expression outside of known exons and well annotated genes and a high frequency of alternative splicing events.
	Research Gene expression patterns during adaptation of a helminth parasite to different environmental niches Emmitt R Jolly, Chen-Shan Chin, Steve Miller, Mahmoud M Bahgat, KC Lim, Joseph DeRisi, James H McKerrow Genome Biology 2007, 8:R65 (24 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a genomic microarray, gene expression at three different developmental stages of the schistosome parasite were analyzed, resulting in the identification of 1154 developmentally enriched transcripts.
	Research Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions Sergi Beltran, Mireia Angulo, Miguel Pignatelli, Florenci Serras, Montserrat Corominas Genome Biology 2007, 8:R67 (28 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the gene expression profiles of wing imaginal discs from ash2 and ash1 mutants shows that they are highly similar, supporting a model in which they act together to maintain stable states of transcription.
	Research A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map Michel Solignac, Florence Mougel, Dominique Vautrin, Monique Monnerot, Jean-Marie Cornuet Genome Biology 2007, 8:R66 (21 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The meiotic map of the honey bee is presented, including the main features that emerged from comparisons with the sequence-based physical map. The map is based on 2,008 markers and is about 40 M long, corresponding to a recombination rate of 22 cM/Mb.
	Method Statistical tools for synthesizing lists of differentially expressed features in related experiments Marta Blangiardo, Sylvia Richardson Genome Biology 2007, 8:R54 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel approach for finding a list of features that are commonly perturbed in two or more experiments, quantifying the evidence of dependence between the experiments by a ratio.
	Method A major zebrafish polymorphism resource for genetic mapping Kevin M Bradley, J Bradford Elmore, Joan P Breyer, Brian L Yaspan, Jason R Jessen, Ela W Knapik, Jeffrey R Smith Genome Biology 2007, 8:R55 (11 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 645,088 candidate polymorphisms in zebrafish were identified and positioned on genetic and physical maps as a resource for positional cloning.
	Correspondence
	Correspondence Power-law-like distributions in biomedical publications and research funding Andrew I Su, John B Hogenesch Genome Biology 2007, 8:404 (30 April 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A search of the literature reveals that researchers study relatively few genes out of the total human genome.

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Volume 8 Issue 4

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